You searched for subject:(Messenger RNA).
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University of Hong Kong
1.
雷雲; Lui, Wan, Thomas.
An analysis of the functional significance of the
3'-untranslated region of CHOP/Gadd153 messenger RNA.
Degree: PhD, 2013, University of Hong Kong
URL: Lui,
W.
T.
[雷雲].
(2013).
An
analysis
of
the
functional
significance
of
the
3'-untranslated
region
of
CHOP/Gadd153
messenger
RNA.
(Thesis).
University
of
Hong
Kong,
Pokfulam,
Hong
Kong
SAR.
Retrieved
from
http://dx.doi.org/10.5353/th_b5089985 
;
http://dx.doi.org/10.5353/th_b5089985
;
http://hdl.handle.net/10722/192840
► CHOP, or Gadd153, is a 29 kDa protein that plays a pivotal role in the mediation of cellular stress-induced cell death. The expression of the…
(more)
▼ CHOP, or Gadd153, is a 29 kDa protein that plays a
pivotal role in the mediation of cellular stress-induced cell
death. The expression of the gene encoding CHOP/Gadd153 is
regulated at both the transcriptional and post-transcriptional
levels. Compared to transcription, the regulation of Chop gene
expression at the post-transcriptional level is much less
understood. In this study, the role played by the 3’-untranslated
region of CHOP mRNA (3UTRChop) in mediating mRNA stability was
examined. A reporter plasmid was constructed so that the mRNA
expressed has 3UTRChop as its 3’-untranslated region. Partial 5’
deletions, or deletion of short internal (~30 nucleotides)
sequences, or the deletion of a putative AU-rich element (ARE)
within 3UTRChop, all resulted in the elevation of the steady state
levels of mRNA and the encoded reporter protein, EGFP. Deletion of
the ARE or sequences remote from ARE resulted in the reduced rate
of mRNA degradation. Such data suggested that 3UTRChop is closely
related to mRNA stability.
The effect of cellular stress on the
functioning of 3UTRChop was studied by examining the change in mRNA
level in cells treated with arsenic trioxide (ATO). The presence of
arsenic stress stimulated a marked increase in the steady state
level of not only the reporter mRNA, but also control mRNAs that
did not have 3UTRChop as the 3’-untranslated region. A non-specific
effect of arsenic stress on mRNA levels was therefore suggested.
Consistent with the increase in the level of reporter mRNA, the
expression of EGFP protein was also increased. Arsenic stress and
partial deletion of 3UTRChop produce additive increase in mRNA
level and EGFP protein level implying that the mRNA destabilizing
function of 3UTRChop is unlikely to be stress-regulated.
The
contribution of 3UTRChop in mRNA translation was then examined
using reporter constructs that expressed EGFP mRNA having its
original 5’ and 3’-untranslated regions replaced with 5UTRChop and
3UTRChop respectively. In the presence of wild-type 3UTRChop, the
abolition of the translation repressor functions of 5UTRChop
produced only mild increase in EGFP expression. However, the
additional partial deletion of 3UTRChop resulted in massive
increase in EGFP expression. In the presence of wild-type 5UTRChop,
the partial deletion of 3UTRChop resulted in only a small increase
in EGFP expression. Such data demonstrated a complementary
relationship between 5UTRChop and 3UTRChop in the regulation of
Chop expression in unstressed cells. EGFP mRNA having 5UTRChop and
3UTRChop as the 5’ and 3’-untranslated region respectively
expressed significant EGFP protein only in the presence of ATO. The
expression of EGFP was not significantly affected with swopping of
3UTRChop with another 3UTR. 3UTRChop is therefore not essential for
the mediation of ATO-stimulated expression of EGFP.
The present
study demonstrated that full length 3UTRChop may have constitutive
mRNA destabilizing effect that is not alleviated by cellular
stress. The evaluation of the relative contributions of…
Advisors/Committee Members: Wong, NS.
Subjects/Keywords: Messenger RNA.
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APA (6th Edition):
雷雲; Lui, Wan, T. (2013). An analysis of the functional significance of the
3'-untranslated region of CHOP/Gadd153 messenger RNA. (Doctoral Dissertation). University of Hong Kong. Retrieved from Lui, W. T. [雷雲]. (2013). An analysis of the functional significance of the 3'-untranslated region of CHOP/Gadd153 messenger RNA. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5089985 ; http://dx.doi.org/10.5353/th_b5089985 ; http://hdl.handle.net/10722/192840
Chicago Manual of Style (16th Edition):
雷雲; Lui, Wan, Thomas. “An analysis of the functional significance of the
3'-untranslated region of CHOP/Gadd153 messenger RNA.” 2013. Doctoral Dissertation, University of Hong Kong. Accessed February 26, 2020.
Lui, W. T. [雷雲]. (2013). An analysis of the functional significance of the 3'-untranslated region of CHOP/Gadd153 messenger RNA. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5089985 ; http://dx.doi.org/10.5353/th_b5089985 ; http://hdl.handle.net/10722/192840.
MLA Handbook (7th Edition):
雷雲; Lui, Wan, Thomas. “An analysis of the functional significance of the
3'-untranslated region of CHOP/Gadd153 messenger RNA.” 2013. Web. 26 Feb 2020.
Vancouver:
雷雲; Lui, Wan T. An analysis of the functional significance of the
3'-untranslated region of CHOP/Gadd153 messenger RNA. [Internet] [Doctoral dissertation]. University of Hong Kong; 2013. [cited 2020 Feb 26].
Available from: Lui, W. T. [雷雲]. (2013). An analysis of the functional significance of the 3'-untranslated region of CHOP/Gadd153 messenger RNA. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5089985 ; http://dx.doi.org/10.5353/th_b5089985 ; http://hdl.handle.net/10722/192840.
Council of Science Editors:
雷雲; Lui, Wan T. An analysis of the functional significance of the
3'-untranslated region of CHOP/Gadd153 messenger RNA. [Doctoral Dissertation]. University of Hong Kong; 2013. Available from: Lui, W. T. [雷雲]. (2013). An analysis of the functional significance of the 3'-untranslated region of CHOP/Gadd153 messenger RNA. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5089985 ; http://dx.doi.org/10.5353/th_b5089985 ; http://hdl.handle.net/10722/192840
University of Hong Kong
2.
黃寶如; Wong, Po-yu.
The 3'-untranslated region of CHOP mRNA encodes
information that determines the expression level of the CHOP
gene.
Degree: M. Phil., 2015, University of Hong Kong
URL: Wong,
P.
[黃寶如].
(2015).
The
3'-untranslated
region
of
CHOP
mRNA
encodes
information
that
determines
the
expression
level
of
the
CHOP
gene.
(Thesis).
University
of
Hong
Kong,
Pokfulam,
Hong
Kong
SAR.
Retrieved
from
http://dx.doi.org/10.5353/th_b5719479
;
http://hdl.handle.net/10722/223569
► CHOP is a stress-inducible protein that acts as a transcription co-regulatory factor for genes that are involved in cellular responses to stress. Previous studies demonstrated…
(more)
▼ CHOP is a stress-inducible protein that acts as a
transcription co-regulatory factor for genes that are involved in
cellular responses to stress. Previous studies demonstrated that
the activation of promoter activity of the CHOP gene is a major
mechanism underlying the increase in the mRNA level of the CHOP
gene in stressed cells. It is however not certain if the cellular
mRNA degradation mechanism for CHOP mRNA might also be
stress-sensitive so that together with stress-stimulated
transcription a highly precise control of CHOP mRNA level can be
achieved. To examine such a possibility, a series of
CHOP-expressing plasmids were constructed and used to express the
full length CHOP mRNA with or without deletion mutations in its
3’untranslated region in cultured cells. Realtime PCR quantitation
demonstrated that the level of the expressed full length CHOP mRNA
was the same in unstressed and stressed cells. Deletion mutations
of the 3UTR of CHOP mRNA resulted in changes of CHOP-mRNA levels
relative to the wild type mRNA but otherwise such changes were not
affected by cellular stress. To ascertain if deletion mutations of
the 3’UTR of CHOP mRNA alone were sufficient to cause changes in
mRNA levels without requiring the participation of the rest of the
CHOP mRNA sequence, another series of expression plasmids were
constructed that will express EGFP mRNA having its original 3’UTR
replaced with either the 3’UTR of CHOP mRNA, or 3’UTR of CHOP mRNA
with deletions mutations the same as those of the pCHOP series of
plasmids. Analysis of real-time PCR data obtained for the
quantitation of mRNA levels expressed from the E3 series of
plasmids showed the same changes of the expressed mRNA levels
caused by the deletion mutations in the 3’UTR. The changes in mRNA
levels were again independent of cellular stress. To examine if the
change in mRNA levels would result in proportionate changes of
translation, the abundance of the reporter protein (GFP) expressed
from plasmids of the E3-series was quantitated directly by Western
blot and indirectly by measurement of FITC fluorescence by FACS
analysis. The decrease in mRNA expression due to the deletion of
the first 30 ribonucleotides in the 3’UTR CHOP is always met with
more of less proportionate decrease in the reporter protein
expressed from this mutant mRNA. However, the change in mRNA level
expressed from other pCHOP and E3 deletion mutants may not always
cause a corresponding change in level of translational product.
Results of this study suggest that unlike transcriptional synthesis
of CHOP mRNA that is tightly stress-regulated, the degradation
mechanism of CHOP mRNA is stress-insensitive and it may only be
passively involved in preventing excessive synthesis of the CHOP
mRNA. The degradation of the CHOP is closely related to the
nucleotide sequence of its 3’UTR. Additional function of the
nucleotide sequence of the 3’UTR of CHOP mRNA is also suggested by
results of the present study.
published_or_final_version
Biomedical Sciences
Master
Master of Philosophy
Subjects/Keywords: Messenger RNA; Cytogenetics
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
黃寶如; Wong, P. (2015). The 3'-untranslated region of CHOP mRNA encodes
information that determines the expression level of the CHOP
gene. (Masters Thesis). University of Hong Kong. Retrieved from Wong, P. [黃寶如]. (2015). The 3'-untranslated region of CHOP mRNA encodes information that determines the expression level of the CHOP gene. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5719479 ; http://hdl.handle.net/10722/223569
Chicago Manual of Style (16th Edition):
黃寶如; Wong, Po-yu. “The 3'-untranslated region of CHOP mRNA encodes
information that determines the expression level of the CHOP
gene.” 2015. Masters Thesis, University of Hong Kong. Accessed February 26, 2020.
Wong, P. [黃寶如]. (2015). The 3'-untranslated region of CHOP mRNA encodes information that determines the expression level of the CHOP gene. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5719479 ; http://hdl.handle.net/10722/223569.
MLA Handbook (7th Edition):
黃寶如; Wong, Po-yu. “The 3'-untranslated region of CHOP mRNA encodes
information that determines the expression level of the CHOP
gene.” 2015. Web. 26 Feb 2020.
Vancouver:
黃寶如; Wong P. The 3'-untranslated region of CHOP mRNA encodes
information that determines the expression level of the CHOP
gene. [Internet] [Masters thesis]. University of Hong Kong; 2015. [cited 2020 Feb 26].
Available from: Wong, P. [黃寶如]. (2015). The 3'-untranslated region of CHOP mRNA encodes information that determines the expression level of the CHOP gene. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5719479 ; http://hdl.handle.net/10722/223569.
Council of Science Editors:
黃寶如; Wong P. The 3'-untranslated region of CHOP mRNA encodes
information that determines the expression level of the CHOP
gene. [Masters Thesis]. University of Hong Kong; 2015. Available from: Wong, P. [黃寶如]. (2015). The 3'-untranslated region of CHOP mRNA encodes information that determines the expression level of the CHOP gene. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5719479 ; http://hdl.handle.net/10722/223569
University of Hong Kong
3.
Chan, Yin-tung, Crystal.
Demonstration of specific physical interaction between
CHOP mRNA and intracellular proteins.
Degree: M. Phil., 2011, University of Hong Kong
URL: Chan,
Y.
C.
[陳燕彤].
(2011).
Demonstration
of
specific
physical
interaction
between
CHOP
mRNA
and
intracellular
proteins.
(Thesis).
University
of
Hong
Kong,
Pokfulam,
Hong
Kong
SAR.
Retrieved
from
http://dx.doi.org/10.5353/th_b4716936
;
http://dx.doi.org/10.5353/th_b4716936
;
http://hdl.handle.net/10722/174332
► The ability of a cell to respond precisely to environmental stress depends on the expression of a large number of genes in a finely coordinated…
(more)
▼ The ability of a cell to respond precisely to
environmental stress depends on the expression of a large number of
genes in a finely coordinated manner. One of such genes is CHOP
that encodes the CCAAT/Enhancer-Binding Protein Homologous Protein.
CHOP is usually expressed to mediate apoptosis under the condition
of excessive stress. The expression of CHOP therefore has to be
stringently regulated as its expression will determine the fate of
a cell under stress. The expression of many genes is regulated at
the posttranscriptional level through the metabolism of their mRNA,
such as maturation, transport, storage, and degradation of mRNA.
Many metabolic processes of mRNA are known to be mediated by
RNA-binding proteins that specifically interact with the mRNA.
RNA-binding proteins that interact with the CHOP mRNA have until
present not been identified. The aim of this study is to
investigate what proteins may bind specifically to CHOP mRNA. The
study will enable further understanding regarding how the
expression of CHOP is regulated in cellular stress response.
Proteins extracted from HeLa cells were incubated with a 335bp
[3H]-labelled CHOP RNA probe that spans over a part of the coding
region and the 3’UTR of CHOP mRNA. Sucrose density gradient
ultracentrifugation revealed that after incubation with proteins
extracted from HeLa cells, the sedimentation rate of the [3H]-CHOP
RNA probe was significantly higher than that of the free [3H]-RNA
probe. The formation of heavy molecular complexes involving the
[3H]-CHOP RNA probe was therefore suggested. However, no increase
in sedimentation rate of the [3H]-CHOP RNA probe was observed in
the presence of an excess of unlabelled CHOP RNA probe. Similar
observations were made when the experiments were performed using
proteins isolated from cells treated with As2O3. Two putative
sequence elements, the Adenylate-Uridylate-Rich Element (ARE) and
the Putative Regulatory Element (PRE) located respectively in the
3’UTR and coding region of the CHOP mRNA were then examined for
their involvement in RNA-protein interaction. The deletion of ARE
and/or PRE, from the [3H]-CHOP RNA probe had little effect on the
binding of the RNA probe to the HeLa cell proteins. Consistently,
unlabelled CHOP RNA probes with the same deletions were only
slightly weaker in competing with the intact [3H]-CHOP RNA probe to
bind to HeLa cell proteins. Human Antigen R (HuR) was identified by
Western blot analysis to be present in the proteins that were
obtained by pull-down assays using biotinylated CHOP RNA as a
probe. The deletion of ARE and/or PRE resulted in a slight
reduction of HuR obtained by pull down assays. This study provides
the first evidence that physical binding interaction occurs between
intracellular RNA-binding proteins and CHOP mRNA. More importantly,
one such protein is HuR. Data suggest that HuR binding to the CHOP
mRNA is mediated by sequences in the CHOP mRNA other than ARE and
PRE.
published_or_final_version
Biochemistry
Master
Master of Philosophy
Advisors/Committee Members: Wong, NS.
Subjects/Keywords: Messenger RNA.; RNA-protein interactions.
Record Details
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Record Details
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Chan, Yin-tung, C. (2011). Demonstration of specific physical interaction between
CHOP mRNA and intracellular proteins. (Masters Thesis). University of Hong Kong. Retrieved from Chan, Y. C. [陳燕彤]. (2011). Demonstration of specific physical interaction between CHOP mRNA and intracellular proteins. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b4716936 ; http://dx.doi.org/10.5353/th_b4716936 ; http://hdl.handle.net/10722/174332
Chicago Manual of Style (16th Edition):
Chan, Yin-tung, Crystal. “Demonstration of specific physical interaction between
CHOP mRNA and intracellular proteins.” 2011. Masters Thesis, University of Hong Kong. Accessed February 26, 2020.
Chan, Y. C. [陳燕彤]. (2011). Demonstration of specific physical interaction between CHOP mRNA and intracellular proteins. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b4716936 ; http://dx.doi.org/10.5353/th_b4716936 ; http://hdl.handle.net/10722/174332.
MLA Handbook (7th Edition):
Chan, Yin-tung, Crystal. “Demonstration of specific physical interaction between
CHOP mRNA and intracellular proteins.” 2011. Web. 26 Feb 2020.
Vancouver:
Chan, Yin-tung C. Demonstration of specific physical interaction between
CHOP mRNA and intracellular proteins. [Internet] [Masters thesis]. University of Hong Kong; 2011. [cited 2020 Feb 26].
Available from: Chan, Y. C. [陳燕彤]. (2011). Demonstration of specific physical interaction between CHOP mRNA and intracellular proteins. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b4716936 ; http://dx.doi.org/10.5353/th_b4716936 ; http://hdl.handle.net/10722/174332.
Council of Science Editors:
Chan, Yin-tung C. Demonstration of specific physical interaction between
CHOP mRNA and intracellular proteins. [Masters Thesis]. University of Hong Kong; 2011. Available from: Chan, Y. C. [陳燕彤]. (2011). Demonstration of specific physical interaction between CHOP mRNA and intracellular proteins. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b4716936 ; http://dx.doi.org/10.5353/th_b4716936 ; http://hdl.handle.net/10722/174332
University of Hong Kong
4.
江家耀; Kong, Ka-yiu.
Characterization of the roles of yeast nuclear exosome
cofactor TRAMP complex in pre-mRNA splicing.
Degree: PhD, 2013, University of Hong Kong
URL: Kong,
K.
[江家耀].
(2013).
Characterization
of
the
roles
of
yeast
nuclear
exosome
cofactor
TRAMP
complex
in
pre-mRNA
splicing.
(Thesis).
University
of
Hong
Kong,
Pokfulam,
Hong
Kong
SAR.
Retrieved
from
http://dx.doi.org/10.5353/th_b5108671
;
http://dx.doi.org/10.5353/th_b5108671
;
http://hdl.handle.net/10722/193522
► In budding yeast, the Trf4/5p-Air1/2p-Mtr4p polyadenylation (TRAMP) complex recognizes unwanted RNA transcripts in the nucleus and then targets them to the nuclear exosome for rapid…
(more)
▼ In budding yeast, the Trf4/5p-Air1/2p-Mtr4p
polyadenylation (TRAMP) complex recognizes unwanted RNA transcripts
in the nucleus and then targets them to the nuclear exosome for
rapid degradation, constituting an important pathway of nuclear RNA
quality control. Each pre-mRNA splicing event unavoidably generates
a RNA side-product that should be recognized by TRAMP and then
removed by the nuclear exosome to prevent the potentially harmful
sequestration of splicing factors and/or ribonucleotides. While
successful pre-mRNA splicing inevitably produces a spliced-out
intron, errors in pre-mRNA splicing lead to the emergence of either
an abnormal splicing intermediate, or a splicing-incompetent
pre-mRNA that cannot be properly spliced. However, it remains
unclear how and when these RNA side-products of pre-mRNA splicing
are recognized by TRAMP. In this study, chromatin
immunoprecipitation (ChIP) was applied to demonstrate that both
TRAMP and the nuclear exosome component Rrp6p are
cotranscriptionally recruited to nascent RNA transcripts,
particularly to intronic sequences, indicating that splicing
side-products are recognized by TRAMP and committed to subsequent
nuclear-exosome-mediated degradation in a cotranscriptional manner.
Deletion of TRF4, of both AIR1 and AIR2, or of RRP6, resulted in
accumulation of unspliced pre-mRNAs. Surprisingly, while such
pre-mRNAs accumulated in rrp6 cells owing to defects in pre-mRNA
degradation, the same phenotype in trf4 and air1air2 cells
involved splicing defects, demonstrating that only TRAMP, but not
the nuclear exosome, contributes to optimal pre-mRNA splicing.
Consistent with a direct stimulatory role for TRAMP in pre-mRNA
splicing, negative genetic interactions and physical interactions
between Trf4p and several splicing factors were observed, and that
Trf4p was further shown to be required for optimal recruitment of
the splicing factor Msl5p. The direct facilitation of pre-mRNA
splicing by TRAMP may act as a fail-safe mechanism to ensure the
cotranscriptional recruitment of TRAMP to nascent intron-containing
transcripts before or during pre-mRNA splicing, such that the
subsequently generated spliced-out introns, abnormal splicing
intermediates, or splicing-incompetent pre-mRNAs can be recognized
immediately by TRAMP, and then targeted to the nuclear exosome for
prompt degradation before their potentially harmful accumulation.
Since most TRAMP and nuclear exosome components found in budding
yeast also contain functional human homologs, this work provides
important insights into how splicing side-products are rapidly
degraded by the nuclear RNA quality control system in human cells,
which have a much higher frequency of introns within their genome,
and certainly require a much more efficient pathway for the removal
of an increased amount of splicing side-products due to the greater
number of splicing events.
published_or_final_version
Biochemistry
Doctoral
Doctor of Philosophy
Advisors/Committee Members: Jin, D, Yao, KM.
Subjects/Keywords: Messenger RNA; Yeast - Molecular aspects
Record Details
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Share »
Record Details
Similar Records
Cite
« Share
❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
江家耀; Kong, K. (2013). Characterization of the roles of yeast nuclear exosome
cofactor TRAMP complex in pre-mRNA splicing. (Doctoral Dissertation). University of Hong Kong. Retrieved from Kong, K. [江家耀]. (2013). Characterization of the roles of yeast nuclear exosome cofactor TRAMP complex in pre-mRNA splicing. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5108671 ; http://dx.doi.org/10.5353/th_b5108671 ; http://hdl.handle.net/10722/193522
Chicago Manual of Style (16th Edition):
江家耀; Kong, Ka-yiu. “Characterization of the roles of yeast nuclear exosome
cofactor TRAMP complex in pre-mRNA splicing.” 2013. Doctoral Dissertation, University of Hong Kong. Accessed February 26, 2020.
Kong, K. [江家耀]. (2013). Characterization of the roles of yeast nuclear exosome cofactor TRAMP complex in pre-mRNA splicing. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5108671 ; http://dx.doi.org/10.5353/th_b5108671 ; http://hdl.handle.net/10722/193522.
MLA Handbook (7th Edition):
江家耀; Kong, Ka-yiu. “Characterization of the roles of yeast nuclear exosome
cofactor TRAMP complex in pre-mRNA splicing.” 2013. Web. 26 Feb 2020.
Vancouver:
江家耀; Kong K. Characterization of the roles of yeast nuclear exosome
cofactor TRAMP complex in pre-mRNA splicing. [Internet] [Doctoral dissertation]. University of Hong Kong; 2013. [cited 2020 Feb 26].
Available from: Kong, K. [江家耀]. (2013). Characterization of the roles of yeast nuclear exosome cofactor TRAMP complex in pre-mRNA splicing. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5108671 ; http://dx.doi.org/10.5353/th_b5108671 ; http://hdl.handle.net/10722/193522.
Council of Science Editors:
江家耀; Kong K. Characterization of the roles of yeast nuclear exosome
cofactor TRAMP complex in pre-mRNA splicing. [Doctoral Dissertation]. University of Hong Kong; 2013. Available from: Kong, K. [江家耀]. (2013). Characterization of the roles of yeast nuclear exosome cofactor TRAMP complex in pre-mRNA splicing. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5108671 ; http://dx.doi.org/10.5353/th_b5108671 ; http://hdl.handle.net/10722/193522
The Ohio State University
5.
Hage, Rosemary.
Identification and characterization of YNL187, a novel
factor that promotes stable association of the U1 SNRNP with the
5’SS during pre-messenger RNA splicing.
Degree: PhD, Molecular Genetics, 2007, The Ohio State University
URL: http://rave.ohiolink.edu/etdc/view?acc_num=osu1193268127
► This dissertation describes the identification of a novel splicing factor, Ynl187p, and characterization of its role in precursor-messenger RNA splicing in the budding yeast, Saccharomyces…
(more)
▼ This dissertation describes the identification of a
novel splicing factor, Ynl187p, and characterization of its role in
precursor-
messenger RNA splicing in the budding yeast,
Saccharomyces cerevisiae. The discovery that loss of function
mutations in YNL187w can bypass the requirement for Prp28p, an
otherwise essential DExH/D-box protein and splicing factor,
suggests that Ynl187p is a potential target of Prp28p. Because
Prp28p is required for dislodging the U1 snRNP from the intron 5'
splice site during pre-mRNA splicing, its targets are predicted to
promote stable U1 snRNP/5' ss association during 5' ss recognition
and commitment complex formation. I show here that Ynl187p is
synthetic-lethal with loss of function mutations in a specific
subset of factors that stabilize the U1/5' ss interaction, most of
which also bypass Prp28p. Deletion of Ynl187p is sufficient to
overcome hyperstabilization of the U1 snRNA/5' ss interaction,
indicating that it makes a significant contribution to U1/5' ss
stability. Cross-linking studies revealed that contacts between
specific proteins and the pre-mRNA are diminished in the absence of
Ynl187p and that commitment complexes are unstable. Ynl187p
localizes primarily to the nucleus and interacts directly with all
five major spliceosomal snRNAs, demonstrating that it interacts
with the spliceosome, but is not a snRNP-specific component. Taken
together, these findings indicate an important role for Ynl187p in
5' ss recognition and in promoting proper assembly of the first
commitment complex in splicing.
Advisors/Committee Members: Chang, Tien-Hsien (Advisor).
Subjects/Keywords: pre-messenger RNA splicing
Record Details
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APA (6th Edition):
Hage, R. (2007). Identification and characterization of YNL187, a novel
factor that promotes stable association of the U1 SNRNP with the
5’SS during pre-messenger RNA splicing. (Doctoral Dissertation). The Ohio State University. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=osu1193268127
Chicago Manual of Style (16th Edition):
Hage, Rosemary. “Identification and characterization of YNL187, a novel
factor that promotes stable association of the U1 SNRNP with the
5’SS during pre-messenger RNA splicing.” 2007. Doctoral Dissertation, The Ohio State University. Accessed February 26, 2020.
http://rave.ohiolink.edu/etdc/view?acc_num=osu1193268127.
MLA Handbook (7th Edition):
Hage, Rosemary. “Identification and characterization of YNL187, a novel
factor that promotes stable association of the U1 SNRNP with the
5’SS during pre-messenger RNA splicing.” 2007. Web. 26 Feb 2020.
Vancouver:
Hage R. Identification and characterization of YNL187, a novel
factor that promotes stable association of the U1 SNRNP with the
5’SS during pre-messenger RNA splicing. [Internet] [Doctoral dissertation]. The Ohio State University; 2007. [cited 2020 Feb 26].
Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1193268127.
Council of Science Editors:
Hage R. Identification and characterization of YNL187, a novel
factor that promotes stable association of the U1 SNRNP with the
5’SS during pre-messenger RNA splicing. [Doctoral Dissertation]. The Ohio State University; 2007. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1193268127
Rutgers University
6.
Zhou, Mi, 1987-.
Role of DcpS in mammalian RNA regulation and human diseases.
Degree: PhD, Cell and Developmental Biology, 2015, Rutgers University
URL: https://rucore.libraries.rutgers.edu/rutgers-lib/48745/
► In eukaryotic cells, mRNA degradation plays an important role in the control of gene expression and is therefore highly regulated. The scavenger decapping enzyme DcpS…
(more)
▼ In eukaryotic cells, mRNA degradation plays an important role in the control of gene expression and is therefore highly regulated. The scavenger decapping enzyme DcpS is a multifunctional protein that plays a critical role in mRNA degradation. We first sought to identify DcpS target genes in mammalian cells using a cell permeable DcpS inhibitor compound, RG3039, which was initially developed for therapeutic treatment of Spinal Muscular Atrophy (SMA). Microarray analysis following DcpS decapping inhibition by RG3039 revealed the steady state levels of 222 RNAs were altered. Of a subset selected for validation by qRT-PCR, two non-coding transcripts dependent on DcpS decapping activity, were identified and referred to as DcpS Responsive Noncoding Transcript (DRNT) 1 and 2 respectively. Only the increase in DRNT1 transcript was accompanied with an increase of its RNA stability and this increase was dependent on both DcpS and Xrn1. Our data indicate that DcpS is a transcript-restricted modulator of RNA stability in mammalian cells and the RG3039 quinazoline compound is pleotropic, influence gene expression in both an apparent DcpS dependent and independent manner. A surprising development was uncovered in a collaborative study where two distinct mutations in the DcpS gene (c.636+1G>A, DcpSIns15 and c.947C>T, DcpST316M) were identified as the underlying cause of autosomal recessive intellectual disability within a consanguineous family. Both of the mutations were confirmed to disrupt DcpS decapping activity in vitro and/or in vivo, indicating that the decapping activity of DcpS is critical for normal neurological development. Consistent with a role for DcpS in neuronal cells, our studies with the DcpSIns15 variant uncovered a link between this variant DcpS and Spinal Muscular Atrophy (SMA). Exogenous expression of DcpSIns15 in SMA patient fibroblast cells increased SMN2 mRNA and corresponding SMN protein levels. Our findings suggest that strategies to shift wild type DcpS splicing patterns to partially yield the variant DcpS Ins15 splicing pattern may be beneficial for SMA therapeutics.
Advisors/Committee Members: Kiledjian, Megerditch (chair), Covey, Lori (internal member), Gunderson, Samuel (internal member), Copeland, Paul (outside member).
Subjects/Keywords: Messenger RNA; Gene expression
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APA (6th Edition):
Zhou, Mi, 1. (2015). Role of DcpS in mammalian RNA regulation and human diseases. (Doctoral Dissertation). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/48745/
Chicago Manual of Style (16th Edition):
Zhou, Mi, 1987-. “Role of DcpS in mammalian RNA regulation and human diseases.” 2015. Doctoral Dissertation, Rutgers University. Accessed February 26, 2020.
https://rucore.libraries.rutgers.edu/rutgers-lib/48745/.
MLA Handbook (7th Edition):
Zhou, Mi, 1987-. “Role of DcpS in mammalian RNA regulation and human diseases.” 2015. Web. 26 Feb 2020.
Vancouver:
Zhou, Mi 1. Role of DcpS in mammalian RNA regulation and human diseases. [Internet] [Doctoral dissertation]. Rutgers University; 2015. [cited 2020 Feb 26].
Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/48745/.
Council of Science Editors:
Zhou, Mi 1. Role of DcpS in mammalian RNA regulation and human diseases. [Doctoral Dissertation]. Rutgers University; 2015. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/48745/
University of Missouri – Columbia
7.
Shebl, Bassem.
The influence of mRNA secondary structures on ribosome conformational dynamics.
Degree: 2016, University of Missouri – Columbia
URL: http://hdl.handle.net/10355/62520
► [ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] Synthesizing proteins in the cell is a critical aspect of life. Protein synthesis is a…
(more)
▼ [ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] Synthesizing proteins in the cell is a critical aspect of life. Protein synthesis is a complicated process and involve highly functional machines at a molecular level. The ribosome is the molecular machine that translate coded sequences of nucleic acids into functional proteins. Understanding how ribosomes function is key to understanding protein synthesis / translation. We focus our work on ribosomes from bacterial cells. This allows us to study much simpler systems and extrapolate our knowledge to higher levels. One key challenge in the field is to be able to isolate a high quantity of good and active ribosomes out of the cell to study it in a controlled environment. Classically known methods involve extensive resources, high technical expertise, and a week of preparation. We developed a one-step protocol to purify ribosomes that are more active than the ones purified from classical methods. This developed technique saves time and money and results in much higher amounts of product. This approach also makes the technique approachable to a wider community of scientists and researchers. The same methodology could be applied towards purifying other molecular machines in the cells. Using these ribosomes, we wanted to investigate how the ribosomes function in cells when faced with specific signals. These signals are utilized by the cells to control protein synthesis. However, in dome diseased cells and for some viruses, normal protein synthesis is overridden by the invaders to produce faulty proteins that could result in a wide range of diseases such as Alzheimer and others. In this study, we investigated how the ribosome functions in the presence of such signals and how close do they need to be to the ribosome to affect protein synthesis. This allows us to design drugs to mimic or inhibit such changes thus fixing faulty protein production or sometimes induce it to inhibit protein synthesis in bacterial cells and as such designing and producing novel drugs.
Advisors/Committee Members: Cornish, Peter (advisor).
Subjects/Keywords: Proteins – Synthesis; Messenger RNA; Ribosomes
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APA (6th Edition):
Shebl, B. (2016). The influence of mRNA secondary structures on ribosome conformational dynamics. (Thesis). University of Missouri – Columbia. Retrieved from http://hdl.handle.net/10355/62520
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Shebl, Bassem. “The influence of mRNA secondary structures on ribosome conformational dynamics.” 2016. Thesis, University of Missouri – Columbia. Accessed February 26, 2020.
http://hdl.handle.net/10355/62520.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Shebl, Bassem. “The influence of mRNA secondary structures on ribosome conformational dynamics.” 2016. Web. 26 Feb 2020.
Vancouver:
Shebl B. The influence of mRNA secondary structures on ribosome conformational dynamics. [Internet] [Thesis]. University of Missouri – Columbia; 2016. [cited 2020 Feb 26].
Available from: http://hdl.handle.net/10355/62520.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Shebl B. The influence of mRNA secondary structures on ribosome conformational dynamics. [Thesis]. University of Missouri – Columbia; 2016. Available from: http://hdl.handle.net/10355/62520
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Lethbridge
8.
University of Lethbridge. Faculty of Arts and Science.
Elucidating the role of eukaryotic initiation factor 5B (eIF5B) in non-canonical translation initiation
.
Degree: 2019, University of Lethbridge
URL: http://hdl.handle.net/10133/5666
► Cap-dependent translation drives the global synthesis of proteins. Under stress conditions global protein production is attenuated, yet the translation of ATF4 is upregulated through uORF-…
(more)
▼ Cap-dependent translation drives the global synthesis of proteins. Under stress conditions global protein production is attenuated, yet the translation of ATF4 is upregulated through uORF- mediated translation initiation. eIF5B has been shown to deliver initiator-tRNA during non-canonical translation initiation. As such, we defined the role of eIF5B in the non-canonical translation of ATF4, and p27. Through polysome profiling and luciferase reporter assays, we confirmed that eIF5B facilitates uORF2-mediated repression of ATF4 translation. We determined that eIF5B has transcriptome-wide effects on signaling pathways, verifying activation of the JNK arm of the MAPK pathway and upregulation of dyskerin. I investigated the role eIF5B has in regulation of p27, and suggest that the mechanism is IRES-dependent. This study furthers the understanding into mechanisms of alternative translation initiation, which is critical to gene expression regulation.
Subjects/Keywords: Messenger RNA;
Proteins – Synthesis;
Ribosomes
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Export
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APA (6th Edition):
Science, U. o. L. F. o. A. a. (2019). Elucidating the role of eukaryotic initiation factor 5B (eIF5B) in non-canonical translation initiation
. (Thesis). University of Lethbridge. Retrieved from http://hdl.handle.net/10133/5666
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Science, University of Lethbridge. Faculty of Arts and. “Elucidating the role of eukaryotic initiation factor 5B (eIF5B) in non-canonical translation initiation
.” 2019. Thesis, University of Lethbridge. Accessed February 26, 2020.
http://hdl.handle.net/10133/5666.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Science, University of Lethbridge. Faculty of Arts and. “Elucidating the role of eukaryotic initiation factor 5B (eIF5B) in non-canonical translation initiation
.” 2019. Web. 26 Feb 2020.
Vancouver:
Science UoLFoAa. Elucidating the role of eukaryotic initiation factor 5B (eIF5B) in non-canonical translation initiation
. [Internet] [Thesis]. University of Lethbridge; 2019. [cited 2020 Feb 26].
Available from: http://hdl.handle.net/10133/5666.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Science UoLFoAa. Elucidating the role of eukaryotic initiation factor 5B (eIF5B) in non-canonical translation initiation
. [Thesis]. University of Lethbridge; 2019. Available from: http://hdl.handle.net/10133/5666
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Minnesota
9.
Nair, Asha.
A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs.
Degree: PhD, Biomedical Informatics and Computational Biology, 2018, University of Minnesota
URL: http://hdl.handle.net/11299/199034
► High-throughput Next Generation RNA sequencing (RNA-Seq) technology is affluent with information about the transcriptome, which includes both protein-coding and multiple non-coding regions. In a diseased…
(more)
▼ High-throughput Next Generation RNA sequencing (RNA-Seq) technology is affluent with information about the transcriptome, which includes both protein-coding and multiple non-coding regions. In a diseased state, complex interactions between these regions can go awry. Identification of such interactions is critical to translate the underlying biology of the transcriptome, especially for lethal diseases such as cancer. The field of bioinformatics is currently deficient in workflows that can analyze both coding and non-coding regions together efficiently, to identify disease-specific interactions. In this dissertation, I developed three coherent bioinformatics solutions that aim to address these shortcomings in RNA-Seq. First, a comprehensive workflow called MAPR-Seq was developed to analyze and report various features of protein-coding messenger RNAs. Second, a workflow for non-coding circular RNAs, called Circ-Seq, was developed to identify, quantify and annotate expressed circular RNAs. Third, an integration workflow called ReMIx was developed to identify microRNA response elements (MREs) and integrate them with the different types of RNAs (messenger RNAs, circular RNAs, and microRNAs). Collectively, the three workflows were applied to the largest cohort of breast cancer samples (n=885) from The Cancer Genome Atlas (TCGA). Based on the results obtained from these workflows, I present several key findings that are pertinent to breast cancer. I show that circular RNAs may be a marker for tumor proliferation in estrogen response positive (ER+) breast cancer subtype. I also show how triple negative (TN) breast cancer subtype-specific MRE signatures of messenger RNA – microRNA interactions can be obtained using RNA-Seq data, which has not been explored to date and thus, is a novel undertaking. In the end, my results highlight candidate messenger RNAs, circular RNAs and microRNAs that are found to be associated with MAPK and PI3K/AKT signaling cascades in TN breast cancer subtype. In general, the developed bioinformatics solutions can also be applied to RNA-Seq data of other cancer subtypes and diseases to identify unique messenger RNA – microRNA – circular RNA candidates that could be promising diagnostic targets towards improving treatment options for complex diseases.
Subjects/Keywords: circular RNA; integration; messenger RNA; micro RNA; MRE; RNA-Seq
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APA ·
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MLA ·
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Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Nair, A. (2018). A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs. (Doctoral Dissertation). University of Minnesota. Retrieved from http://hdl.handle.net/11299/199034
Chicago Manual of Style (16th Edition):
Nair, Asha. “A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs.” 2018. Doctoral Dissertation, University of Minnesota. Accessed February 26, 2020.
http://hdl.handle.net/11299/199034.
MLA Handbook (7th Edition):
Nair, Asha. “A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs.” 2018. Web. 26 Feb 2020.
Vancouver:
Nair A. A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs. [Internet] [Doctoral dissertation]. University of Minnesota; 2018. [cited 2020 Feb 26].
Available from: http://hdl.handle.net/11299/199034.
Council of Science Editors:
Nair A. A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs. [Doctoral Dissertation]. University of Minnesota; 2018. Available from: http://hdl.handle.net/11299/199034
University of Utah
10.
Ball, Jennifer R.
RNA recognition by the nucleoporin Nup153;.
Degree: PhD, Oncological Sciences;, 2004, University of Utah
URL: http://content.lib.utah.edu/cdm/singleitem/collection/etd1/id/11/rec/1150
► Trafficking events across the nuclear envelope (NE) require specific interactions between cargo-receptor complexes and proteins of the nuclear pore complex (NPC). Although great strides have…
(more)
▼ Trafficking events across the nuclear envelope (NE) require specific interactions between cargo-receptor complexes and proteins of the nuclear pore complex (NPC). Although great strides have been made to elucidate protein and RNA transport pathways, many aspects of nuclear transport, particularly how cargo interacts with components of the NPC, remain undefined. In order to better understand the interactions that drive RNA export, I have focused on further defining the association between RNA cargo and the nucleoporin Nup153, a central regulator of nuclear transport. Overexpression of a C-terminal fragment of Nup153 in somatic cells inhibited poly(A)+ RNA export suggesting that Nup153 contributes to mRNA export. Further, perturbation of Nup153 function in Xenopus oocytes demonstrated Nup153 is important for mRNA, U snRNA and 5S rRNA export. Moreover, an RNA binding domain was mapped within the N-terminus of Nup 153 and was shown to bind RNA directly. The property of RNA association is conserved in Drosophila, Xenopus and human, underscoring the importance of this domain in higher eukaryotes. Although it is clear that Nup153 function is important for RNA export, exactly how this nuclear pore protein contributes to RNA export is unknown. One way to elucidate how Nup153 interfaces with RNA in the cell is to dissect the interactions mediated by this nucleoporin. Towards this end, the goal of this dissertation is to define the molecular targets of Nup153 in order to better understand the mechanisms by which Nup153, and the pore itself, functions. Initially, I found that the RNA binding domain (RBD) of Nup153 associates with cellular RNA and further characterization of this domain revealed that Nup153 preferentially associates with single-stranded RNA in a manner that distinctly mirrors properties that relay the identity of mRNA to the nuclear export machinery. I have also defined minimal length and base composition requirements for RNA association with Nup153. In collaboration with others, I have correlated Nup153-RNA association with functional RNA export in vivo. These collaborative studies indicate that direct contact between mRNA and Nup153 may occur cooperatively with protein contacts and that this interface between Nup153, mRNA and protein is critical to mRNA export and potentially concurrent mRNP remodeling and quality control.
Subjects/Keywords: Physiology; RNA Messenger
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APA ·
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Export
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APA (6th Edition):
Ball, J. R. (2004). RNA recognition by the nucleoporin Nup153;. (Doctoral Dissertation). University of Utah. Retrieved from http://content.lib.utah.edu/cdm/singleitem/collection/etd1/id/11/rec/1150
Chicago Manual of Style (16th Edition):
Ball, Jennifer R. “RNA recognition by the nucleoporin Nup153;.” 2004. Doctoral Dissertation, University of Utah. Accessed February 26, 2020.
http://content.lib.utah.edu/cdm/singleitem/collection/etd1/id/11/rec/1150.
MLA Handbook (7th Edition):
Ball, Jennifer R. “RNA recognition by the nucleoporin Nup153;.” 2004. Web. 26 Feb 2020.
Vancouver:
Ball JR. RNA recognition by the nucleoporin Nup153;. [Internet] [Doctoral dissertation]. University of Utah; 2004. [cited 2020 Feb 26].
Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd1/id/11/rec/1150.
Council of Science Editors:
Ball JR. RNA recognition by the nucleoporin Nup153;. [Doctoral Dissertation]. University of Utah; 2004. Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd1/id/11/rec/1150
11.
Roalofs, Scott F.
Gene activity analysis of Saccharomyces cerevisiae metallo-aminopeptidase gene deletion strains using DNA microarrays and verification with quantitative RT-PCR.
Degree: MS(M.S.), Applied Natural Science, 2018, Colorado State University – Pueblo
URL: http://hdl.handle.net/10217/187682
► Metallo-Aminopeptidase gene family 1 (M1AP) encode enzymes that cleave 1-3 amino acids from the N-terminus of a peptide. Previous studies involving M1AP inhibitors indicate that…
(more)
▼ Metallo-Aminopeptidase gene family 1 (M1AP) encode enzymes that cleave 1-3 amino acids from the N-terminus of a peptide. Previous studies involving M1AP inhibitors indicate that M1APs may be involved in the cell cycle and have been used in the treatment of cancers. In previous studies from this lab, yeast strains disrupted in the above enzymes show a G2/M phase delay. To investigate the effects of M1APs in the cell cycle, Saccharomyces cerevisiae strains were developed with gene mutations in the open reading frames YHR047c (AAP1'), and YKL157w (APE2). To understand the global changes to gene regulation due to M1AP mutations, a genome wide analysis of mRNA accumulation using microarrays was attempted using total RNA isolated from log phase wild type and mutant cells. cDNA probes were developed and used for competitive hybridization on microarrays. Our data showed that mRNA abundances in cell signaling and spindle/bud formation were affected. These results are consistent with a role of the aminopeptidases in the G2/M phase of the cell cycle. Differentially expressed mRNA abundances identified by microarrays were randomly verified by quantitative reverse-transcribed PCR (qRT-PCR). The identification of cell cycle genes in M1AP mutants may provide insights into the molecular events leading to the G2/M phase delay and further understanding of the cell cycle.
Subjects/Keywords: Saccharomyces cerevisiae; Aminopeptidases; DNA microarrays; Messenger RNA
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APA ·
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APA (6th Edition):
Roalofs, S. F. (2018). Gene activity analysis of Saccharomyces cerevisiae metallo-aminopeptidase gene deletion strains using DNA microarrays and verification with quantitative RT-PCR. (Masters Thesis). Colorado State University – Pueblo. Retrieved from http://hdl.handle.net/10217/187682
Chicago Manual of Style (16th Edition):
Roalofs, Scott F. “Gene activity analysis of Saccharomyces cerevisiae metallo-aminopeptidase gene deletion strains using DNA microarrays and verification with quantitative RT-PCR.” 2018. Masters Thesis, Colorado State University – Pueblo. Accessed February 26, 2020.
http://hdl.handle.net/10217/187682.
MLA Handbook (7th Edition):
Roalofs, Scott F. “Gene activity analysis of Saccharomyces cerevisiae metallo-aminopeptidase gene deletion strains using DNA microarrays and verification with quantitative RT-PCR.” 2018. Web. 26 Feb 2020.
Vancouver:
Roalofs SF. Gene activity analysis of Saccharomyces cerevisiae metallo-aminopeptidase gene deletion strains using DNA microarrays and verification with quantitative RT-PCR. [Internet] [Masters thesis]. Colorado State University – Pueblo; 2018. [cited 2020 Feb 26].
Available from: http://hdl.handle.net/10217/187682.
Council of Science Editors:
Roalofs SF. Gene activity analysis of Saccharomyces cerevisiae metallo-aminopeptidase gene deletion strains using DNA microarrays and verification with quantitative RT-PCR. [Masters Thesis]. Colorado State University – Pueblo; 2018. Available from: http://hdl.handle.net/10217/187682
University of Oxford
12.
Hardy, Jessica.
Human cleavage factor I (CFIm) and its role in alternative polyadenylation of pre-mRNA.
Degree: PhD, 2017, University of Oxford
URL: http://ora.ox.ac.uk/objects/uuid:a3ba5d10-b3fa-4ab7-9709-a0d642e21543
;
https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.740914
► For many human protein-coding genes, alternative cleavage and polyadenylation (APA) of pre-mRNA generates distinct 3' untranslated regions (3'UTRs) with differing regulatory potential. Widespread 3'UTR shortening…
(more)
▼ For many human protein-coding genes, alternative cleavage and polyadenylation (APA) of pre-mRNA generates distinct 3' untranslated regions (3'UTRs) with differing regulatory potential. Widespread 3'UTR shortening via APA occurs in proliferative cell states, including cancer, where it can lead to oncogene overexpression. There has therefore been significant interest in identifying factors which influence poly(A) site choice in different physiological states. The multi-subunit human cleavage factor I complex (CFIm), a core component of the mammalian pre-mRNA cleavage machinery, has been identified as a potential master regulator of APA, as its depletion leads to widespread 3'UTR shortening. However, mechanistic understanding of how CFIm influences poly(A) site selection, and how its activity is regulated, is lacking. In this work, gene editing was used to generate cell lines with substantial, permanent depletion of the 25 kDa or 68 kDa subunits of CFIm (CFIm25 and CFIm68), which exhibited the expected 3'UTR shortening for representative transcripts. Reversal of this 3'UTR shortening by CFIm25 or CFIm68 re-expression provided the basis for a complementation assay, which allowed various aspects of CFIm25 and CFIm68 function to be investigated in vivo. The capacity of CFIm25 to recognise UGUA RNA sequences was shown to make an important contribution to poly(A) site selection transcriptome-wide, and a novel function for the C-terminal arginine/serine-rich (RS domain) of CFIm68 in poly(A) site selection was identified. The potential contribution of CFIm post-translational modification (PTM) to APA regulation was also explored. Novel acetylation sites on CFIm25 and CFIm68 were identified, as well as extensive serine phosphorylation in the CFIm68 RS domain. Complementation analysis revealed that phosphomimetic mutations in this RS domain inhibited distal poly(A) site selection, suggesting a potential role for CFIm68 phosphorylation in APA regulation. Taken together, the findings presented here provide insights into several important determinants of CFIm function, and the complementation assay developed provides a useful tool for future investigations.
Subjects/Keywords: Messenger RNA; mRNA; alternative polyadenylation; cleavage factor
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APA ·
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MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Hardy, J. (2017). Human cleavage factor I (CFIm) and its role in alternative polyadenylation of pre-mRNA. (Doctoral Dissertation). University of Oxford. Retrieved from http://ora.ox.ac.uk/objects/uuid:a3ba5d10-b3fa-4ab7-9709-a0d642e21543 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.740914
Chicago Manual of Style (16th Edition):
Hardy, Jessica. “Human cleavage factor I (CFIm) and its role in alternative polyadenylation of pre-mRNA.” 2017. Doctoral Dissertation, University of Oxford. Accessed February 26, 2020.
http://ora.ox.ac.uk/objects/uuid:a3ba5d10-b3fa-4ab7-9709-a0d642e21543 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.740914.
MLA Handbook (7th Edition):
Hardy, Jessica. “Human cleavage factor I (CFIm) and its role in alternative polyadenylation of pre-mRNA.” 2017. Web. 26 Feb 2020.
Vancouver:
Hardy J. Human cleavage factor I (CFIm) and its role in alternative polyadenylation of pre-mRNA. [Internet] [Doctoral dissertation]. University of Oxford; 2017. [cited 2020 Feb 26].
Available from: http://ora.ox.ac.uk/objects/uuid:a3ba5d10-b3fa-4ab7-9709-a0d642e21543 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.740914.
Council of Science Editors:
Hardy J. Human cleavage factor I (CFIm) and its role in alternative polyadenylation of pre-mRNA. [Doctoral Dissertation]. University of Oxford; 2017. Available from: http://ora.ox.ac.uk/objects/uuid:a3ba5d10-b3fa-4ab7-9709-a0d642e21543 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.740914
Columbia University
13.
Martinez, Jose Carlos.
Regulation of Neuronal mRNA Localization by Exclusion.
Degree: 2018, Columbia University
URL: https://doi.org/10.7916/D8F49125
► Intra-axonal protein synthesis is important for the proper wiring of the nervous system and can have restorative or pathogenic effects in response to nerve injury…
(more)
▼ Intra-axonal protein synthesis is important for the proper wiring of the nervous system and can have restorative or pathogenic effects in response to nerve injury and neurodegenerative stimuli. The set of axonally translated transcripts, the axonal translatome, is regulated through the control of mRNA localization, stability, and translation. Targeting the axonal translatome could result in the development of novel therapies for the treatment of neurological disorders. Yet, there are gaps in our understanding of the selective mechanism regulating the specific localization of mRNAs into axons. Currently, axonal localization of transcripts is understood to be controlled by the presence of sequence elements that direct axonal transport. In an attempt to identify novel localization motifs, I found that a well-known motif corresponding to the Pumilio Binding Element (PBE) is significantly depleted in axonally enriched mRNAs. Moreover, I found this element to be highly informative of axonal mRNA localization and translation across different neuronal types and developmental stages suggesting that it is a highly conserved regulatory motif. I found Pum2 neuronal expression and subcellular localization to be highly consistent with the way the PBE predicts mRNA regulation. I then demonstrated that interfering with Pum2 function results in increased axonal localization of PBE containing mRNAs. Finally, Pum2 downregulation was associated with gross defects in axonal outgrowth, branching, and regeneration. Altogether, this data suggests that Pum2 regulates axonal mRNA localization through an exclusion mechanism that is important during neuronal development.
Subjects/Keywords: Neurosciences; Cytology; Messenger RNA; Nervous system
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APA (6th Edition):
Martinez, J. C. (2018). Regulation of Neuronal mRNA Localization by Exclusion. (Doctoral Dissertation). Columbia University. Retrieved from https://doi.org/10.7916/D8F49125
Chicago Manual of Style (16th Edition):
Martinez, Jose Carlos. “Regulation of Neuronal mRNA Localization by Exclusion.” 2018. Doctoral Dissertation, Columbia University. Accessed February 26, 2020.
https://doi.org/10.7916/D8F49125.
MLA Handbook (7th Edition):
Martinez, Jose Carlos. “Regulation of Neuronal mRNA Localization by Exclusion.” 2018. Web. 26 Feb 2020.
Vancouver:
Martinez JC. Regulation of Neuronal mRNA Localization by Exclusion. [Internet] [Doctoral dissertation]. Columbia University; 2018. [cited 2020 Feb 26].
Available from: https://doi.org/10.7916/D8F49125.
Council of Science Editors:
Martinez JC. Regulation of Neuronal mRNA Localization by Exclusion. [Doctoral Dissertation]. Columbia University; 2018. Available from: https://doi.org/10.7916/D8F49125
University of Texas Southwestern Medical Center
14.
Tsai, Pei-Ling.
The Role of NS1-BP in Influenza Virus Replication.
Degree: 2012, University of Texas Southwestern Medical Center
URL: http://hdl.handle.net/2152.5/1100
► Influenza A viruses are negative-sense, segmented RNA viruses which cause about 500,000 deaths worldwide per year. Genomic studies have shown that the non-structural protein (NS1)…
(more)
▼ Influenza A viruses are negative-sense, segmented
RNA viruses which cause about 500,000 deaths worldwide per year. Genomic studies have shown that the non-structural protein (NS1) of influenza A virus is a major virulence factor that is essential for pathogenesis. NS1 is a multifunctional protein localized in the nucleus and in the cytoplasm. In the cytoplasm, NS1 inhibits host signaling pathways that result in down-regulation of interferon expression and innate immune response. In the nucleus, NS1 represses host gene expression. I have shown that NS1 binds an mRNA complex containing NXF1/TAP, NXT/p15, Rae1, and E1B-AP5, which are key components of the mRNA export machinery. By targeting this complex, NS1 blocks host mRNA export, and cells become highly permissive to viral replication. Another intranuclear pool of NS1 was found to interact with a host protein termed NS1-BP, which has been suggested to play a role in pre-mRNA splicing. However, the functions and mechanisms of NS1-BP involved in influenza life cycle remain to be elucidated. To investigate the function of NS1-BP, I first identified its binding partners by immunoprecipitation followed by mass spectrometry. I found interactions of NS1-BP with viral polymerase complex and host
RNA polymerase II indicating that NS1-BP has a role in regulating viral
RNA transcription and replication. I further showed that low levels of NS1-BP led to a decrease in viral polymerase activity resulting in inhibition of virus replication. Thus, I identified NS1-BP as a novel pro-viral factor required for proper replication of influenza virus. Since NS1 is a key contributor to the virulence of influenza viruses, discovering the function of NS1 interacting partners has major implications for antiviral therapy.
Advisors/Committee Members: Fontoura, Beatriz.
Subjects/Keywords: Nuclear Pore; Influenza A Virus; RNA, Messenger
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APA (6th Edition):
Tsai, P. (2012). The Role of NS1-BP in Influenza Virus Replication. (Thesis). University of Texas Southwestern Medical Center. Retrieved from http://hdl.handle.net/2152.5/1100
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Tsai, Pei-Ling. “The Role of NS1-BP in Influenza Virus Replication.” 2012. Thesis, University of Texas Southwestern Medical Center. Accessed February 26, 2020.
http://hdl.handle.net/2152.5/1100.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Tsai, Pei-Ling. “The Role of NS1-BP in Influenza Virus Replication.” 2012. Web. 26 Feb 2020.
Vancouver:
Tsai P. The Role of NS1-BP in Influenza Virus Replication. [Internet] [Thesis]. University of Texas Southwestern Medical Center; 2012. [cited 2020 Feb 26].
Available from: http://hdl.handle.net/2152.5/1100.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Tsai P. The Role of NS1-BP in Influenza Virus Replication. [Thesis]. University of Texas Southwestern Medical Center; 2012. Available from: http://hdl.handle.net/2152.5/1100
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Texas Southwestern Medical Center
15.
Tuckerman, Jason Robert.
Heme-Based Oxygen Sensors of Commensal, Symbiotic, and Pathogenic Bacteria.
Degree: 2012, University of Texas Southwestern Medical Center
URL: http://hdl.handle.net/2152.5/1115
► Direct oxygen sensors are proteins that serve as "on-off switches" to cause reversible and adaptive changes in the activities of other proteins or genes, with…
(more)
▼ Direct oxygen sensors are proteins that serve as "on-off switches" to cause reversible and adaptive changes in the activities of other proteins or genes, with great specificity in response to fluctuations in oxygen concentration. The heme-based oxygen sensors are a large class of direct oxygen sensors that feature direct binding of oxygen to a sensory heme-containing domain. This heme-binding region couples to a regulatory domain within the same polypeptide. The types of functionalities controlled by these oxygen-specific switches are diverse, and include the regulation of protein activities, gene expression, and second
messenger elaboration. A primary focus of this work was the biochemical characterization of a pair of heme-based oxygen sensors involved in the control of the bacterial second
messenger cyclic diguanylic acid (c-di-GMP) in Escherichia coli. We discovered that these enzymes, designated DosC and DosP, serve as a diguanylate cyclase and c-di-GMP phosphodiesterase pair that associate with components of the E. coli
RNA degradosome in vivo. Importantly, one member of these degradosomes, PNPase, is a direct, high-affinity target of c-di-GMP. These findings imply that specialized oxygen-sensing degradosomes exist in E. coli. In these oxygen-sensing degradosomes cellular oxygen levels regulate PNPase processing of specific
RNA transcripts via c-di-GMP.
A secondary focus of this work was the characterization of a novel two-component system in M. tuberculosis involved in the non-replicating persistent phase of this bacterium in a typical TB infection. Here, the activities of two heme-containing histidine kinases, DosT and DevS, were discovered to be inhibited specifically by oxygen. As DosT and DevS are the primary regulators of the dormancy survival regulator (DosR/DevR) transcription factor, these results contributed a molecular explanation for the numerous observations linking oxygen and DevR to the dormancy phenotype of M. tuberculosis seen both in vitro and in vivo.
Advisors/Committee Members: Gilles-Gonzalez, Marie-Alda.
Subjects/Keywords: Cyclic GMP; RNA; Second Messenger Systems
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APA (6th Edition):
Tuckerman, J. R. (2012). Heme-Based Oxygen Sensors of Commensal, Symbiotic, and Pathogenic Bacteria. (Thesis). University of Texas Southwestern Medical Center. Retrieved from http://hdl.handle.net/2152.5/1115
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Tuckerman, Jason Robert. “Heme-Based Oxygen Sensors of Commensal, Symbiotic, and Pathogenic Bacteria.” 2012. Thesis, University of Texas Southwestern Medical Center. Accessed February 26, 2020.
http://hdl.handle.net/2152.5/1115.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Tuckerman, Jason Robert. “Heme-Based Oxygen Sensors of Commensal, Symbiotic, and Pathogenic Bacteria.” 2012. Web. 26 Feb 2020.
Vancouver:
Tuckerman JR. Heme-Based Oxygen Sensors of Commensal, Symbiotic, and Pathogenic Bacteria. [Internet] [Thesis]. University of Texas Southwestern Medical Center; 2012. [cited 2020 Feb 26].
Available from: http://hdl.handle.net/2152.5/1115.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Tuckerman JR. Heme-Based Oxygen Sensors of Commensal, Symbiotic, and Pathogenic Bacteria. [Thesis]. University of Texas Southwestern Medical Center; 2012. Available from: http://hdl.handle.net/2152.5/1115
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
New Jersey Institute of Technology
16.
Nambiar, Ram Mohan.
PolyA DB3: a database cataloging polyadenation sites(pas) across different species and their conservation.
Degree: MSin Bioinformatics - (M.S.), Computer Science, 2018, New Jersey Institute of Technology
URL: https://digitalcommons.njit.edu/theses/1636
► Polyadenation is an important process occurring in the messenger RNA that involves cleavage of 3 end nascent mRNAs and addition of poly(A) tails. For…
(more)
▼ Polyadenation is an important process occurring in the
messenger RNA that involves cleavage of 3 end nascent mRNAs and addition of poly(A) tails. For this thesis,I present PolyA DB3 ,a database cataloging cleavage and polyadenylation sites (PASs) in several genomes specifically for human,mouse,rat and chicken. This database is based on deep sequencing data. PASs are mapped by the 3’ region extraction and deep sequencing (3’READS) method, ensuring unequivocal PAS identification. Large volume of data based on diverse biological samples is used to increase PAS coverage and provide PAS usage information. Strand-specific
RNA-seq data were used to extend annotated 3’ ends of genes to obtain more thorough annotations of alternative polyadenylation (APA) sites. The database also has information regarding conservation of PAS between these species. Similar analysis has also been done on the PASs identified from frog samples and the identification of conservation of the PASs.
Advisors/Committee Members: Tian, Bin, Roshan, Usman W., Wei, Zhi.
Subjects/Keywords: Polyadenation; Messenger RNA; Bioinformatics; Computer Sciences
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APA (6th Edition):
Nambiar, R. M. (2018). PolyA DB3: a database cataloging polyadenation sites(pas) across different species and their conservation. (Thesis). New Jersey Institute of Technology. Retrieved from https://digitalcommons.njit.edu/theses/1636
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Nambiar, Ram Mohan. “PolyA DB3: a database cataloging polyadenation sites(pas) across different species and their conservation.” 2018. Thesis, New Jersey Institute of Technology. Accessed February 26, 2020.
https://digitalcommons.njit.edu/theses/1636.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Nambiar, Ram Mohan. “PolyA DB3: a database cataloging polyadenation sites(pas) across different species and their conservation.” 2018. Web. 26 Feb 2020.
Vancouver:
Nambiar RM. PolyA DB3: a database cataloging polyadenation sites(pas) across different species and their conservation. [Internet] [Thesis]. New Jersey Institute of Technology; 2018. [cited 2020 Feb 26].
Available from: https://digitalcommons.njit.edu/theses/1636.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Nambiar RM. PolyA DB3: a database cataloging polyadenation sites(pas) across different species and their conservation. [Thesis]. New Jersey Institute of Technology; 2018. Available from: https://digitalcommons.njit.edu/theses/1636
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Rutgers University
17.
Li, You.
Regulation of mammalian mRNA decapping.
Degree: PhD, Cell and Developmental Biology, 2011, Rutgers University
URL: http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000061329
► The modulation of mRNA degradation plays a critical role for regulation of gene expression. A major mRNA decay pathway in mammals proceeding from the 5'…
(more)
▼ The modulation of mRNA degradation plays a critical role for regulation of gene expression. A major mRNA decay pathway in mammals proceeding from the 5' to 3' end is initiated with shortening of 3' poly (A) tail, followed by the cleavage of the 5' cap structure (decapping) and degradation of the mRNA body by the Xrn1 exoribonuclease. Dcp2 is a well characterized mRNA decapping enzyme. It is an RNA binding protein that must bind the RNA in order to recognize the cap for hydrolysis. We identified mRNAs bound by human Dcp2 by coimmunoprecipitation and microarray analysis. Further biochemical assays identified a sequence element of 60 nucleotides at the 5´ terminus of the mRNA encoding Rrp41 as a specific Dcp2 substrate which could specifically bind Dcp2 protein and enhance Dcp2 decapping. Mutational analysis of this element revealed a stable stem-loop structure (termed DBDE) contained in the first 33 nucleotides is critical for Dcp2 decapping stimulation. A bioinformatic search was carried out to identify a subset of mRNAs that have a comparable stem-loop structure at the 5′ end as potential Dcp2 substrates. We identified a second cytoplasmic mRNA decapping enzyme Nudt16 in mammalian cells and established stable MEF cells that contained reduced level of Dcp2 and/or Nudt16 protein. Using these MEF cells, we demonstrated the distinct roles for Dcp2 and Nudt16 in nonsense mediated mRNA decay (NMD), ARE-mediated decay and miRNA mediated gene silencing. Our results indicated that NMD preferentially utilizes Dcp2 rather than Nudt16; Dcp2 and Nudt16 are redundant in miRNA mediated silencing; and Dcp2 and Nudt16 are differentially utilized for ARE-mRNA decay. At last, we demonstrated that anti-viral immune response was regulated by Dcp2 in mouse embryonic fibroblast. In MEF cells lacking Dcp2 protein, interferon-mediated anti-viral response was significantly elevated. We identified IRF7, a crucial transcription factor in anti-viral immunity, as the direct target of Dcp2. Knockdown of Dcp2 led to stabilization of IRF7 mRNA and increased IRF7 protein level. Therefore, Dcp2 functions as a negative regulator of interferon-mediated anti-viral immunity. Interestingly, Dcp2 expression is also induced in virus infection, suggesting a negative feedback loop in the anti-viral immune response.
Advisors/Committee Members: Li, You (author), Kiledjian, Megerditch (chair), Covey, Lori (internal member), Gunderson, Samuel (internal member), Xie, Ping (internal member), Copeland, Paul (outside member).
Subjects/Keywords: Messenger RNA; Gene expression; Genetic regulation
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APA (6th Edition):
Li, Y. (2011). Regulation of mammalian mRNA decapping. (Doctoral Dissertation). Rutgers University. Retrieved from http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000061329
Chicago Manual of Style (16th Edition):
Li, You. “Regulation of mammalian mRNA decapping.” 2011. Doctoral Dissertation, Rutgers University. Accessed February 26, 2020.
http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000061329.
MLA Handbook (7th Edition):
Li, You. “Regulation of mammalian mRNA decapping.” 2011. Web. 26 Feb 2020.
Vancouver:
Li Y. Regulation of mammalian mRNA decapping. [Internet] [Doctoral dissertation]. Rutgers University; 2011. [cited 2020 Feb 26].
Available from: http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000061329.
Council of Science Editors:
Li Y. Regulation of mammalian mRNA decapping. [Doctoral Dissertation]. Rutgers University; 2011. Available from: http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000061329
Hong Kong University of Science and Technology
18.
Lam, Sheung Wai LIFS.
Elucidating the role of Pabpn1 in mRNA alternative polyadenylation during satellite cell activation.
Degree: 2016, Hong Kong University of Science and Technology
URL: http://repository.ust.hk/ir/Record/1783.1-100400
;
https://doi.org/10.14711/thesis-b1626258
;
http://repository.ust.hk/ir/bitstream/1783.1-100400/1/th_redirect.html
► Satellite cells are muscle stem cells that are primarily quiescent in resting muscle. Upon injury, satellite cells will activate, proliferate, and differentiate to repair the…
(more)
▼ Satellite cells are muscle stem cells that are primarily quiescent in resting muscle. Upon injury, satellite cells will activate, proliferate, and differentiate to repair the damaged muscle. The quiescent state is a tightly regulated process. Dysregulation of the quiescent state will result in a depletion of the stem cell pool and impairment of muscle regeneration. Previously, our group has identified that the microRNA (miRNA) pathway is essential for the maintanence of satellite cell quiescence. As binding sites of miRNAs are on the 3’ UTR of mRNAs, the susceptibility of mRNA to miRNA regulation would depend on lengths of 3’ UTRs. Therefore, we hypothesized that alternative polyadenylation plays an important post-transcriptional regulation to maintain satellite cell quiescence. Alternative polyadenylation involves a number of proteins. In particular, poly(A) binding protein nuclear 1 (PABPN1) has been implicated as an important regulator of polyadenylation site selection. To better understand the role of PABPN1 in mRNA alternative polyadenylation, the expression level of PABPN1 in vivo in uninjured, regenerating and regenerated muscle was characterized. In addition, the expression level of PABPN1 during satellite cell activation on satellite cells associated muscle fibers ex vivo and during differentiation in primary myoblasts in vitro was investigated. We found that PABPN1 was highly expressed in regenerating muscle and activated satellite cells. Knockdown experiments were also performed on single fibers to investigate the effect of PABPN1 on satellite cell number and proliferation. The result of this project will shed lights on how alternative polyadenylation regulates muscle stem cell function.
Subjects/Keywords: Satellite cells
; Messenger RNA
; Gene expression
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APA (6th Edition):
Lam, S. W. L. (2016). Elucidating the role of Pabpn1 in mRNA alternative polyadenylation during satellite cell activation. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-100400 ; https://doi.org/10.14711/thesis-b1626258 ; http://repository.ust.hk/ir/bitstream/1783.1-100400/1/th_redirect.html
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Lam, Sheung Wai LIFS. “Elucidating the role of Pabpn1 in mRNA alternative polyadenylation during satellite cell activation.” 2016. Thesis, Hong Kong University of Science and Technology. Accessed February 26, 2020.
http://repository.ust.hk/ir/Record/1783.1-100400 ; https://doi.org/10.14711/thesis-b1626258 ; http://repository.ust.hk/ir/bitstream/1783.1-100400/1/th_redirect.html.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Lam, Sheung Wai LIFS. “Elucidating the role of Pabpn1 in mRNA alternative polyadenylation during satellite cell activation.” 2016. Web. 26 Feb 2020.
Vancouver:
Lam SWL. Elucidating the role of Pabpn1 in mRNA alternative polyadenylation during satellite cell activation. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2016. [cited 2020 Feb 26].
Available from: http://repository.ust.hk/ir/Record/1783.1-100400 ; https://doi.org/10.14711/thesis-b1626258 ; http://repository.ust.hk/ir/bitstream/1783.1-100400/1/th_redirect.html.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Lam SWL. Elucidating the role of Pabpn1 in mRNA alternative polyadenylation during satellite cell activation. [Thesis]. Hong Kong University of Science and Technology; 2016. Available from: http://repository.ust.hk/ir/Record/1783.1-100400 ; https://doi.org/10.14711/thesis-b1626258 ; http://repository.ust.hk/ir/bitstream/1783.1-100400/1/th_redirect.html
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Hong Kong University of Science and Technology
19.
Wong, Julie Hiu Tung.
Defining the role of ncbp-1 and ncbp-2 to regulate sensory ray identity in C. elegans.
Degree: 2012, Hong Kong University of Science and Technology
URL: http://repository.ust.hk/ir/Record/1783.1-7527
;
https://doi.org/10.14711/thesis-b1176678
;
http://repository.ust.hk/ir/bitstream/1783.1-7527/1/th_redirect.html
► Gene modulations in eukaryotes are very important for guiding the differentiation of cell types that are specialized to serve a particular function. Pre-messenger ribonucleic acid…
(more)
▼ Gene modulations in eukaryotes are very important for guiding the differentiation of cell types that are specialized to serve a particular function. Pre-messenger ribonucleic acid (mRNA)-splicing and microRNA processing, coupled with non-sense mediated decay are common strategies adopted to control gene expression. Cap-binding complexes, which have subunits ncbp-1 and ncbp-2, are implicated to be required in all of these events in plants to humans, which suggest that they play a conserved role in the determination of cell fate. Indeed, ncbp-1 and ncbp-2 have been found to determine the fate and identities of ray cells in Caenorhabditis elegans. I have demonstrated that by reducing the levels of either ncbp-1 or ncbp-2, this transforms the identity of ray 6 to that of ray 4, which results in rays 6-4 fusion. It has been confirmed that NCBP-1 and NCBP-2 co-localize at ray precursor cells and able to physically interact with each other via translational reporters and yeast-2-hybrid assays respectively. Therefore, it is suggested that they work together for ray patterning. In addition, ncbp-1/ncbp-2 is demonstrated to regulate ray identities by repressing Dbl/Sma signaling, rather than having a direct influence on the components of the pathway. ncbp-1/ncbp-2 is suggested to influence at the mRNA level, as it binds to the mRNA of dbl-1. This interaction is likely to be at the rays, and not at the ventral nerve cord. The findings of this study confirm the roles of ncbp-1 and ncbp-2 in cell fate determination, and inspire us on their possible mechanisms and targets.
Subjects/Keywords: Caenorhabditis elegans – Genetics
; Messenger RNA
; Protein binding
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APA (6th Edition):
Wong, J. H. T. (2012). Defining the role of ncbp-1 and ncbp-2 to regulate sensory ray identity in C. elegans. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-7527 ; https://doi.org/10.14711/thesis-b1176678 ; http://repository.ust.hk/ir/bitstream/1783.1-7527/1/th_redirect.html
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Wong, Julie Hiu Tung. “Defining the role of ncbp-1 and ncbp-2 to regulate sensory ray identity in C. elegans.” 2012. Thesis, Hong Kong University of Science and Technology. Accessed February 26, 2020.
http://repository.ust.hk/ir/Record/1783.1-7527 ; https://doi.org/10.14711/thesis-b1176678 ; http://repository.ust.hk/ir/bitstream/1783.1-7527/1/th_redirect.html.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Wong, Julie Hiu Tung. “Defining the role of ncbp-1 and ncbp-2 to regulate sensory ray identity in C. elegans.” 2012. Web. 26 Feb 2020.
Vancouver:
Wong JHT. Defining the role of ncbp-1 and ncbp-2 to regulate sensory ray identity in C. elegans. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2012. [cited 2020 Feb 26].
Available from: http://repository.ust.hk/ir/Record/1783.1-7527 ; https://doi.org/10.14711/thesis-b1176678 ; http://repository.ust.hk/ir/bitstream/1783.1-7527/1/th_redirect.html.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Wong JHT. Defining the role of ncbp-1 and ncbp-2 to regulate sensory ray identity in C. elegans. [Thesis]. Hong Kong University of Science and Technology; 2012. Available from: http://repository.ust.hk/ir/Record/1783.1-7527 ; https://doi.org/10.14711/thesis-b1176678 ; http://repository.ust.hk/ir/bitstream/1783.1-7527/1/th_redirect.html
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Columbia University
20.
Tan, Dazhi.
Molecular Basis for the Recognition of the Regulatory Stem-loop Structures in Eukaryotic Messenger RNAs.
Degree: 2014, Columbia University
URL: https://doi.org/10.7916/D8FN14B4
► Apart from carrying genetic information, RNAs also act as effectors of cellular processes through folding into intricate secondary and tertiary structures. The ubiquitous RNA structures…
(more)
▼ Apart from carrying genetic information, RNAs also act as effectors of cellular processes through folding into intricate secondary and tertiary structures. The ubiquitous RNA structures in eukaryotic mRNAs, in collaboration with specific RNA-binding proteins, control many aspects of the post-transcriptional regulation of gene expression. However, the molecular bases for the recognition of these mRNA structures by their protein partners remain poorly understood due to the lack of structural information.
This dissertation presents our structural studies on two protein-RNA complexes that both include regulatory mRNA stem-loop structures. We first describe the crystal structure of a ternary complex including the highly conserved human histone mRNA stem-loop (SL), the stem-loop binding protein (SLBP) and the 3′ to 5′ exonuclease 3′hExo. This structure identifies a single sequence-specific interaction between the SL and SLBP, and the mostly shape-dependent RNA-recognition mode by both proteins. In addition to explaining the large body of biochemical and biophysical data on this complex accumulated over the last two decades, we also for the first time elucidate the induced-fit mechanism underlying the cooperativity between SLBP and 3′hExo. We next shift our focus to a class of less conserved mRNA stem-loop structures named constitutive decay elements (CDE). The RNA-binding ROQ domain of Roquin recognizes the various CDEs and mediates the decay of CDE-containing mRNAs, which predominantly encode proteins responsible for inflammation and autoimmunity. Structural and biochemical studies of the ROQ domain in complex with two different CDE RNAs unexpectedly reveal two distinct RNA binding sites on this protein, one recognizing CDE stem-loops and the other binding to double-stranded RNAs. The stuctures are also in agreement with the versatility of Roquin and have opened up new avenues to investigating its functions in modulating the stability of target mRNAs.
Subjects/Keywords: Messenger RNA; RNA-protein interactions; Eukaryotic cells; Biology; Biochemistry; Molecular biology
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APA (6th Edition):
Tan, D. (2014). Molecular Basis for the Recognition of the Regulatory Stem-loop Structures in Eukaryotic Messenger RNAs. (Doctoral Dissertation). Columbia University. Retrieved from https://doi.org/10.7916/D8FN14B4
Chicago Manual of Style (16th Edition):
Tan, Dazhi. “Molecular Basis for the Recognition of the Regulatory Stem-loop Structures in Eukaryotic Messenger RNAs.” 2014. Doctoral Dissertation, Columbia University. Accessed February 26, 2020.
https://doi.org/10.7916/D8FN14B4.
MLA Handbook (7th Edition):
Tan, Dazhi. “Molecular Basis for the Recognition of the Regulatory Stem-loop Structures in Eukaryotic Messenger RNAs.” 2014. Web. 26 Feb 2020.
Vancouver:
Tan D. Molecular Basis for the Recognition of the Regulatory Stem-loop Structures in Eukaryotic Messenger RNAs. [Internet] [Doctoral dissertation]. Columbia University; 2014. [cited 2020 Feb 26].
Available from: https://doi.org/10.7916/D8FN14B4.
Council of Science Editors:
Tan D. Molecular Basis for the Recognition of the Regulatory Stem-loop Structures in Eukaryotic Messenger RNAs. [Doctoral Dissertation]. Columbia University; 2014. Available from: https://doi.org/10.7916/D8FN14B4
Columbia University
21.
Jurado, Ashley Rae.
Structural Studies of the Fungal pre-mRNA 3'-end Processing Machinery.
Degree: 2015, Columbia University
URL: https://doi.org/10.7916/D8W094VC
► During mRNA synthesis, pre-mRNAs must be cleaved and polyadenylated at their 3'-end to be fully mature, before being exported from the nucleus. In yeast, there…
(more)
▼ During mRNA synthesis, pre-mRNAs must be cleaved and polyadenylated at their 3'-end to be fully mature, before being exported from the nucleus. In yeast, there is a large protein machinery comprised of dozens of proteins that work together to perform these two reactions. Some of these proteins are capable of recognizing and binding key sequence elements in the pre-mRNA, effectively directing where in the transcript the cleavage and polyadenylation occur. In this thesis, recently reported structural findings related to the pre-mRNA 3'-end processing machinery are summarized. Within this machinery, the Cleavage Factor IA (CF-IA) complex is comprised of the Rna14, Rna15, and Pcf11 and Clp1 proteins. Results reported here include the crystal structure of the Rna14-Rna15 complex, which indicates that the Rna14 protein forms a dimer that has inherent conformational variability. The Rna15 protein binds to the C-terminal domain of Rna14, and is connected to the Rna14 HAT domain by a flexible linker, which may indicate that Rna15 functions somewhat independently of the Rna14 HAT domain. The complete CF-IA complex is explored in detail, including protein-protein interactions within the complex and the stoichiometric ratios of CF-IA components. Unlike previous reports, results indicate that CF-IA may form a dimer with a 2:2:2:2 stoichiometry of Rna14:Rna15:Clp1:Pcf11. Also reported are projects unrelated to CF-IA, including the crystal structure of the biotin-dependent alpha(6)beta(6) geranyl-CoA carboxylase (GCC) holoenzyme. Comparison of GCC to the closely related 3-methylcrotonyl CoA carboxylase (MCC) holoenzyme reveals a conserved domain swap in the carboxyltransferase (CT) domains of both enzymes. This domain swap is not present in the related biotin-dependent carboxylases propionyl-CoA carboxylase (PCC) and acetyl-CoA carboxylase (ACC), which may indicate a distinct lineage for biotin-dependent carboxylases that target the γ-carbon. In addition, comparison of the two structures also reveals a conserved Phe191 in MCC that is absent in GCC. Phe191 blocks a key substrate-binding pocket and explains the differences in substrate-specificities between MCC and GCC. The role of Phe191 is tested by site-directed mutagenesis to a Glycine to open the pocket in MCC and by mutating a structurally equivalent Glycine to Phe to close the pocket in GCC. These mutations can convert MCC to a GCC and vice versa.
Subjects/Keywords: Proteins; RNA splicing; Scission (Chemistry); Messenger RNA; Molecular biology; Biology; Biochemistry
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APA (6th Edition):
Jurado, A. R. (2015). Structural Studies of the Fungal pre-mRNA 3'-end Processing Machinery. (Doctoral Dissertation). Columbia University. Retrieved from https://doi.org/10.7916/D8W094VC
Chicago Manual of Style (16th Edition):
Jurado, Ashley Rae. “Structural Studies of the Fungal pre-mRNA 3'-end Processing Machinery.” 2015. Doctoral Dissertation, Columbia University. Accessed February 26, 2020.
https://doi.org/10.7916/D8W094VC.
MLA Handbook (7th Edition):
Jurado, Ashley Rae. “Structural Studies of the Fungal pre-mRNA 3'-end Processing Machinery.” 2015. Web. 26 Feb 2020.
Vancouver:
Jurado AR. Structural Studies of the Fungal pre-mRNA 3'-end Processing Machinery. [Internet] [Doctoral dissertation]. Columbia University; 2015. [cited 2020 Feb 26].
Available from: https://doi.org/10.7916/D8W094VC.
Council of Science Editors:
Jurado AR. Structural Studies of the Fungal pre-mRNA 3'-end Processing Machinery. [Doctoral Dissertation]. Columbia University; 2015. Available from: https://doi.org/10.7916/D8W094VC
Columbia University
22.
Bailey, Nevette Adia.
Dynamics of Translation Elongation in an mRNA Context with a High Frameshifting Propensity.
Degree: 2019, Columbia University
URL: https://doi.org/10.7916/d8-qsnc-d250
► Ribosomes are universally conserved macromolecular machines found within all living cells that catalyze protein synthesis, one of nature’s most fundamental processes. Ribosomes synthesize proteins, which…
(more)
▼ Ribosomes are universally conserved macromolecular machines found within all living cells that catalyze protein synthesis, one of nature’s most fundamental processes. Ribosomes synthesize proteins, which are polymeric chains of amino acids, by incorporating the amino acids one at a time via aminoacylated-transfer RNAs (aa-tRNAs), based on translation of the sequence of triplet- nucleotide codons presented by the messenger RNA (mRNA) template that is a direct readout of genomic DNA. Recent biochemical, structural, dynamic, and computational studies have uncovered large-scale conformational changes of the ribosome, its tRNA substrates, and the additional protein translation factors that play important roles in regulating protein synthesis, especially during the elongation phase of translation when the bulk of each protein is synthesized. How the ribosome, its translation elongation factors, tRNAs, and mRNA physically coordinate and regulate the movements of the tRNAs carrying amino acids into, through, and out of the ribosome remains one of the more fundamental questions in the mechanistic studies of protein synthesis. A complete understanding of the conformational dynamics of ribosomal complexes will improve our knowledge of how translation is regulated, including how ribosome-targeting antibiotics regulate translation elongation, and will provide crucial information for designing next-generation antibiotics. In this thesis I have investigated the conformational dynamics of the ribosome during the elongation phase of protein synthesis at the single-molecule level using single-molecule fluorescence resonance energy transfer (smFRET) microscopy experiments. Specifically, I have studied ribosomal dynamics during the elongation phase of translation in the presence of a tRNAPro in the context of an mRNA that has the propensity to shift out of the reading frame. My studies have revealed information about the mechanistic and regulatory functions of the posttranscriptional modifications of tRNAPro in a context in which the ribosomal complex has the propensity to undergo non-programmed +1-frameshifting, in which the tRNA-mRNA base pairing shifts one base toward the 3’ end of the mRNA, and if unchecked, leads to the synthesis of a polypeptide with a completely different sequence of amino acids. My data suggests that in this context, the mechanism underlying non-programmed +1-frameshifting involves the tRNA shifting out of frame prior to the tRNA being accommodated in the P site, i.e. either while the tRNA is in the A site, or more likely, during translocation of the tRNA from the A site to the P site, and not while the tRNA is already occupying the P site, as previously proposed.
Subjects/Keywords: Biophysics; Ribosomes; Proteins – Synthesis; Genetic translation; Messenger RNA; Transfer RNA
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APA (6th Edition):
Bailey, N. A. (2019). Dynamics of Translation Elongation in an mRNA Context with a High Frameshifting Propensity. (Doctoral Dissertation). Columbia University. Retrieved from https://doi.org/10.7916/d8-qsnc-d250
Chicago Manual of Style (16th Edition):
Bailey, Nevette Adia. “Dynamics of Translation Elongation in an mRNA Context with a High Frameshifting Propensity.” 2019. Doctoral Dissertation, Columbia University. Accessed February 26, 2020.
https://doi.org/10.7916/d8-qsnc-d250.
MLA Handbook (7th Edition):
Bailey, Nevette Adia. “Dynamics of Translation Elongation in an mRNA Context with a High Frameshifting Propensity.” 2019. Web. 26 Feb 2020.
Vancouver:
Bailey NA. Dynamics of Translation Elongation in an mRNA Context with a High Frameshifting Propensity. [Internet] [Doctoral dissertation]. Columbia University; 2019. [cited 2020 Feb 26].
Available from: https://doi.org/10.7916/d8-qsnc-d250.
Council of Science Editors:
Bailey NA. Dynamics of Translation Elongation in an mRNA Context with a High Frameshifting Propensity. [Doctoral Dissertation]. Columbia University; 2019. Available from: https://doi.org/10.7916/d8-qsnc-d250
University of Texas Southwestern Medical Center
23.
Irnov.
Regulatory RNAs at the Heart of Sugar Metabolism: New Mechanisms and Novel Discoveries.
Degree: 2011, University of Texas Southwestern Medical Center
URL: http://hdl.handle.net/2152.5/854
► Bacteria are adept at using a variety of posttranscriptional strategies to regulate gene expression. Specifically, various RNA-mediated genetic control elements have been discovered in the…
(more)
▼ Bacteria are adept at using a variety of posttranscriptional strategies to regulate gene expression. Specifically, various
RNA-mediated genetic control elements have been discovered in the past decade through a combination of genetics, bioinformatics, and transcriptomic approaches. Together, these
RNA elements control the expression of many genes involved in diverse cellular processes such as energy metabolism, stress response, biofilm formation, and pathogenesis. In the Gram-positive bacterium Bacillus subtilis, several
RNA elements have been shown to be required for the precise coordination of genes involved in various sugar utilization pathways. These genetic switches typically regulate gene expression by modulating the formation of a transcription termination element in a ligand-dependent manner. Interestingly, two unique elements, the glmS ribozyme and the eps-associated
RNA (EAR), are missing the signature elements required for control of transcription termination or translation initiation. The latter mechanism is more commonly found in Gram-negative bacteria. Our objective is to study the mechanisms by which these two RNAs control gene expression. Additionally, we would like to identify other regulatory RNAs that are important for sugar metabolism in Bacillus subtilis.
Both the glmS ribozyme and EAR are positioned at the center of the sugar metabolism pathways in B. subtilis. The glmS
RNA is a glucosamine-6-phosphate responsive element that regulates the expression of the GlmS enzyme, which directs sugar precursors from glycolysis into the cell wall biosynthesis pathway. The EAR element resides within the 16-kb eps operon that is required for biofilm exopolysaccharide production. Our data demonstrates that both RNAs employ novel mechanisms: the glmS ribozyme utilizes a ligand-specific RNase-mediated degradation event, while EAR uses a processive antitermination mechanism for complete synthesis of the long operon. Furthermore, by using high-throughput sequencing approach we have successfully identified many new regulatory
RNA candidates, including various long 5`-UTR, toxin-antitoxin systems, prophage-encoded RNAs, and several developmentally regulated small RNAs. Their functions are still under investigation.
Collectively, our studies provide important insights into the different aspects of bacterial physiology, including
RNA decay pathways, transcription of long operons and cellular differentiation. We argue that posttranscriptional regulation is of greater importance to Bacillus subtilis (and probably all bacteria) than previously realized.
Advisors/Committee Members: Winkler, Wade C..
Subjects/Keywords: Bacterial Proteins; RNA, Bacterial; RNA, Messenger; Genetic Transcription
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APA (6th Edition):
Irnov. (2011). Regulatory RNAs at the Heart of Sugar Metabolism: New Mechanisms and Novel Discoveries. (Thesis). University of Texas Southwestern Medical Center. Retrieved from http://hdl.handle.net/2152.5/854
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Irnov. “Regulatory RNAs at the Heart of Sugar Metabolism: New Mechanisms and Novel Discoveries.” 2011. Thesis, University of Texas Southwestern Medical Center. Accessed February 26, 2020.
http://hdl.handle.net/2152.5/854.
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Irnov. “Regulatory RNAs at the Heart of Sugar Metabolism: New Mechanisms and Novel Discoveries.” 2011. Web. 26 Feb 2020.
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Vancouver:
Irnov. Regulatory RNAs at the Heart of Sugar Metabolism: New Mechanisms and Novel Discoveries. [Internet] [Thesis]. University of Texas Southwestern Medical Center; 2011. [cited 2020 Feb 26].
Available from: http://hdl.handle.net/2152.5/854.
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Irnov. Regulatory RNAs at the Heart of Sugar Metabolism: New Mechanisms and Novel Discoveries. [Thesis]. University of Texas Southwestern Medical Center; 2011. Available from: http://hdl.handle.net/2152.5/854
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Not specified: Masters Thesis or Doctoral Dissertation
University of Texas Southwestern Medical Center
24.
Lee, Chien-Der.
Switching the Fate of mRNAs for Mitochondrial Biogenesis.
Degree: 2017, University of Texas Southwestern Medical Center
URL: http://hdl.handle.net/2152.5/7085
► Note: The general metadata – e.g., title, author, abstract, subject headings, etc. – is publicly available, but access to the submitted files is restricted to…
(more)
▼ Note: The general metadata – e.g., title, author, abstract, subject headings, etc. – is publicly available, but access to the submitted files is restricted to UT Southwestern campus access only.
mRNAs encoding mitochondrial biogenesis proteins are co-regulated in a manner closely linked to metabolism. In yeast growing in glucose, mitochondrial biogenesis is repressed, but must be induced upon glucose depletion to enable energy production using alternative carbon sources such as ethanol or acetate through mitochondrial respiration. Yeast cells growing in glucose constitutively transcribe nuclear-encoded mitochondrial ribosomal mRNAs at a basal level. However, instead of sharing a common upstream activating sequence for transcription, those mRNAs all harbor a common sequence motif within their 3'UTRs. Puf3p, an RNA-binding protein, can directly bind to this class of mRNA transcripts to promote degradation in glucose medium. However, the function of Puf3p upon glucose depletion is not clear.
In the first part of this study, I show how Puf3p responds to glucose availability to switch the fate of its bound transcripts that encode proteins required for mitochondrial biogenesis. This regulation allows cell to quickly respond to glucose depletion by switching the degradation fate of those mRNAs to translation. Thus, yeast can activate pre-existing mRNA without relying on de novo transcription for mitochondrial biogenesis. I then show Puf3p is subjected to phosphorylation downstream of a glucose sensing pathway. Puf3p is hypophosphorylated in glucose medium; however, upon glucose depletion, Puf3p becomes heavily phosphorylated within its N-terminal region of low complexity, associates with polysomes, and promotes translation of its target mRNAs.
In the second part of this study, I show that phosphorylation of Puf3p is required for translational activation of its bound mRNAs. Strikingly, a Puf3p mutant that prevents its phosphorylation no longer promotes mRNA translation but also becomes trapped in intracellular foci in an mRNA-dependent manner. These findings suggest how the inability to properly resolve Puf3p-containing RNA-protein granules via a phosphorylation-based mechanism might be toxic to a cell. The toxicity might be due to sequestration of translational factors in the Puf3p RNA protein granule in a manner reminiscent of neurodegenerative disease-related protein aggregation.
Advisors/Committee Members: Liu, Yi, Tu, Benjamin, McKnight, Steven L., Conrad, Nicholas.
Subjects/Keywords: Glucose; RNA, Messenger; RNA-Binding Proteins; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
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APA (6th Edition):
Lee, C. (2017). Switching the Fate of mRNAs for Mitochondrial Biogenesis. (Thesis). University of Texas Southwestern Medical Center. Retrieved from http://hdl.handle.net/2152.5/7085
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Lee, Chien-Der. “Switching the Fate of mRNAs for Mitochondrial Biogenesis.” 2017. Thesis, University of Texas Southwestern Medical Center. Accessed February 26, 2020.
http://hdl.handle.net/2152.5/7085.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Lee, Chien-Der. “Switching the Fate of mRNAs for Mitochondrial Biogenesis.” 2017. Web. 26 Feb 2020.
Vancouver:
Lee C. Switching the Fate of mRNAs for Mitochondrial Biogenesis. [Internet] [Thesis]. University of Texas Southwestern Medical Center; 2017. [cited 2020 Feb 26].
Available from: http://hdl.handle.net/2152.5/7085.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Lee C. Switching the Fate of mRNAs for Mitochondrial Biogenesis. [Thesis]. University of Texas Southwestern Medical Center; 2017. Available from: http://hdl.handle.net/2152.5/7085
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Western Australia
25.
Down, Christin Florence.
Examination of the role of the Hu proteins, HuR and HuD, in prostate cancer cells.
Degree: PhD, 2007, University of Western Australia
URL: http://repository.uwa.edu.au:80/R/?func=dbin-jump-full&object_id=9328&local_base=GEN01-INS01
► [Truncated abstract] Prostate cancer is a significant cause of morbidity and mortality in the male population, and despite its high prevalence, there have been few…
(more)
▼ [Truncated abstract] Prostate cancer is a significant cause of morbidity and mortality in the male population, and despite its high prevalence, there have been few advances in prostate cancer management during the past 20 years. The primary treatment for prostate cancer centres around inhibition of androgen signalling, halting tumour growth through down-regulation of important proliferative genes under control of the androgen receptor (AR). Frequently, prostate cancer progresses to an androgen-independent state that is resistant to AR-targeting therapies and is characterised by persistent AR expression and re-expression of ARregulated genes. Understanding the regulation of AR in prostate cancer is therefore of paramount importance for the development of new treatments to control advanced disease. The AR is regulated post-transcriptionally at the level of mRNA stability, and a UC-rich cis-element ("ARUC") within the 3' untranslated region (3'UTR) of the AR mRNA has been identified, which is bound by an mRNA-stabilising protein, HuR. HuR is a member of a family of four related mRNA-binding proteins that includes HuD, which is typically expressed in neuronal tissue. In this thesis, HuD expression was examined immunohistochemically in a cohort of 12 prostate specimens and was detected at low levels in benign prostatic hyperplasia (BPH), with up-regulated expression in prostate cancers, in particular in high-grade tumours. HuD mRNA expression was also confirmed in the LNCaP prostate cancer cell line using reverse-transcription (RT)-PCR. Like HuR, HuD binds U-rich mRNA and RNA electrophoretic mobility shift assays (REMSA's) confirmed HuD binding to the UC-rich ARUC motif in the AR mRNA 3'UTR, an association that could be disrupted by introduction of point mutations into the ARUC motif. ... To determine mRNA targets of HuR which may be important in prostate cancer proliferation or progression, an oligonucleotide micro-array analysis was performed on 22Rv1 cells that had been treated with siRNA directed against HuR. This identified a number of growth-associated signalling pathways in which multiple genes were down-regulated, including the mitogen-activated protein kinase (MAPK), focal adhesion, vascular endothelial growth factor (VEGF) and Wingless type/MMTV integration (Wnt) signalling pathways, as well as ubiquitin-mediated proteolysis. Further qPCR and IP-RT-PCR analysis of a subset of the regulated genes that contained 3'UTR HuR consensus binding sites confirmed mRNA down-regulation following HuR siRNA treatment and in vivo interaction with HuR of the CREBBP, PCAF, ELK1 and PAK2 transcripts. In summary, results presented in this thesis have identified aberrant upregulation of expression of the RNA-binding protein HuD in prostate cancer, which may contribute to the maintenance of AR expression via binding and stabilisation of the AR mRNA. HuR has been identified as an important protein for the control of AR gene expression and prostate cancer cell proliferation. Furthermore, HuR regulates expression of a range of key…
Subjects/Keywords: Androgen; Messenger RNA; Prostate; Protein binding; RNA editing; Prostate cancer; Androgen receptor; Hu; RNA stability
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APA ·
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APA (6th Edition):
Down, C. F. (2007). Examination of the role of the Hu proteins, HuR and HuD, in prostate cancer cells. (Doctoral Dissertation). University of Western Australia. Retrieved from http://repository.uwa.edu.au:80/R/?func=dbin-jump-full&object_id=9328&local_base=GEN01-INS01
Chicago Manual of Style (16th Edition):
Down, Christin Florence. “Examination of the role of the Hu proteins, HuR and HuD, in prostate cancer cells.” 2007. Doctoral Dissertation, University of Western Australia. Accessed February 26, 2020.
http://repository.uwa.edu.au:80/R/?func=dbin-jump-full&object_id=9328&local_base=GEN01-INS01.
MLA Handbook (7th Edition):
Down, Christin Florence. “Examination of the role of the Hu proteins, HuR and HuD, in prostate cancer cells.” 2007. Web. 26 Feb 2020.
Vancouver:
Down CF. Examination of the role of the Hu proteins, HuR and HuD, in prostate cancer cells. [Internet] [Doctoral dissertation]. University of Western Australia; 2007. [cited 2020 Feb 26].
Available from: http://repository.uwa.edu.au:80/R/?func=dbin-jump-full&object_id=9328&local_base=GEN01-INS01.
Council of Science Editors:
Down CF. Examination of the role of the Hu proteins, HuR and HuD, in prostate cancer cells. [Doctoral Dissertation]. University of Western Australia; 2007. Available from: http://repository.uwa.edu.au:80/R/?func=dbin-jump-full&object_id=9328&local_base=GEN01-INS01
University of Florida
26.
Dajac, Joshua.
DNA Micelles for Intracellular mRNA Imaging.
Degree: 2013, University of Florida
URL: http://ufdc.ufl.edu/AA00057039
► The in vivo imaging of endogenous mRNA transcripts can reveal abnormal patterns of gene expression characteristic of various diseases. Previous methods suffered from the need…
(more)
▼ The in vivo imaging of endogenous mRNA transcripts can reveal abnormal patterns of gene expression characteristic of various diseases. Previous methods suffered from the need to modify endogenous mRNA, which may affect normal gene activity, inefficient probe delivery, and low intracellular stability. We studied a novel design for mRNA imaging known as a molecular beacon micelle flare (MBMF) to overcome these limitations. MBMFs were self-assembled from diacyllipid-molecular beacon conjugates (L-MBs), producing a significant burst of fluorescence enhancement upon target binding. With several advantages including easy probe synthesis, efficient cellular uptake, improved enzymatic stability, enhanced binding affinity, high sensitivity, and excellent selectivity, MBMFs are great candidates for intracellular monitoring and disease diagnosis. ( en )
Subjects/Keywords: Beacons; Complementary DNA; Fluorescence; Imaging; Messenger RNA; Micelles; Nucleic acid probes; Oligonucleotide probes; Signals; Solvents; DNA; Messenger RNA; Micelles
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APA (6th Edition):
Dajac, J. (2013). DNA Micelles for Intracellular mRNA Imaging. (Thesis). University of Florida. Retrieved from http://ufdc.ufl.edu/AA00057039
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Dajac, Joshua. “DNA Micelles for Intracellular mRNA Imaging.” 2013. Thesis, University of Florida. Accessed February 26, 2020.
http://ufdc.ufl.edu/AA00057039.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Dajac, Joshua. “DNA Micelles for Intracellular mRNA Imaging.” 2013. Web. 26 Feb 2020.
Vancouver:
Dajac J. DNA Micelles for Intracellular mRNA Imaging. [Internet] [Thesis]. University of Florida; 2013. [cited 2020 Feb 26].
Available from: http://ufdc.ufl.edu/AA00057039.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Dajac J. DNA Micelles for Intracellular mRNA Imaging. [Thesis]. University of Florida; 2013. Available from: http://ufdc.ufl.edu/AA00057039
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
27.
Zervakis, Konstantinos.
Μελέτη έκφρασης και προγνωστικής αξίας της Poly (ADP-ribose) Polymerase 1 mRNA στα μυελοδυσπλαστικά σύνδρομα.
Degree: 2019, National and Kapodistrian University of Athens; Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών (ΕΚΠΑ)
URL: http://hdl.handle.net/10442/hedi/45792
► Poly (ADP-ribose) polymerase 1 (PARP-1) has a central role in the repair of DNA breaks and is a promising treatment target in malignancy. We measured…
(more)
▼ Poly (ADP-ribose) polymerase 1 (PARP-1) has a central role in the repair of DNA breaks and is a promising treatment target in malignancy. We measured PARP1 mRNA levels by a SYBR-green-based PCR in the bone marrow of 74 patients with myelodysplastic syndrome (MDS) and correlated them to their demographic, hematologic and prognostic characteristics. The median PARP1 mRNA levels were correlated to the type of MDS (2008/2016 WHO classication, P = 0.005) and to the IPSS score (P = 0.002). A correlation was also found with the IPSS-R score (P = 0.011) and the cytogenetic risk (P = 0.008). In all cases, higher PARP1 levels were correlated with a higher risk category. Moreover, we found a signicant survival disadvantage for patients with high PARP1 levels (median survival of 37.4 months versus ‘not reached’ for low PARP1 levels, P = 0.0001, and a 5-year survival rate of 29.8 versus 88.9%, respectively). PARP1 mRNA levels were found to be the stronger predictor of survival in multivariate analysis. These correlations have never been reported in the past and may render PARP1 a prognostic factor to be incorporated in the current prognostic systems for MDS, also laying the basis for clinical trials evaluating PARP1 inhibitors in higher-risk MDS.
Η πολυμεράση της πολυ (ADP-ριβόζης) 1 (PARP-1) αποτελεί βασικό μέλος οικογένειας πυρηνικών ενζύμων που συμμετέχουν στην επιδιόρθωση του DNA και ήδη είναι θεραπευτικός στόχος σε συμπαγείς όγκους. Στην παρούσα μελέτη ποσοτικοποιήθηκαν τα επίπεδα έκφρασης του mRNA της PARP1 με ποσοτική PCR (qpcr) και τη μέθοδο SYBR στον μυελό των οστών 74 ασθενών με διάγνωση μυελοδυσπλαστικού συνδρόμου (MDS). Τα επίπεδα έκφρασης του mRNA της PARP1 αποτυπώθηκαν με τη μορφή του λόγου των μεταγράφων parp1/actin και συσχετίστηκαν με τα δημογραφικά, αιματολογικά και προγνωστικά χαρακτηριστικά των ασθενών. Τα αποτελέσματα εκφράστηκαν ως διάμεσος ± απόκλιση λάθους (median± SEM). Τα επίπεδα έκφρασης του mRNA της PARP1 συσχετίστηκαν στη συνέχεια με τον τύπο MDS (ταξινόμηση WHO 2008/2016, p = 0.005) και με το IPSS score (p = 0.002). Επίσης, διαπιστώθηκε συσχέτιση με το IPSS-R (p = 0,011) και την προγνωστική σημασία των κυτταρογενετικών ευρημάτων (p = 0,008). Σε όλες τις περιπτώσεις, υψηλότερα επίπεδα PARP1 συσχετίστηκαν με υψηλότερη κατηγορία κινδύνου. Επιπλέον, διαπιστώθηκε ένα στατιστικά σημαντικό μειονέκτημα επιβίωσης για τους ασθενείς με υψηλά επίπεδα PARP1 ( η διάμεση επιβίωση ασθενών ήταν 37,4 μήνες, ενώ η διάμεση επιβίωση ασθενών με χαμηλά επίπεδα PARP1 δεν επιτεύχθηκε, p = 0,0001). Η επιβίωση στα 5 χρόνια ήταν 29,8% έναντι 88,9% αντίστοιχα. Τα επίπεδα mRNA της PARP1 βρέθηκαν να είναι ο ισχυρότερος προγνωστικός παράγοντας της επιβίωσης σε ανάλυση πολλαπλών μεταβλητών. Αυτές οι συσχετίσεις δεν έχουν αναφερθεί ποτέ στο παρελθόν και μπορεί να καταστήσουν την PARP1 έναν προγνωστικό παράγοντα που μπορεί να ενσωματωθεί στα τρέχοντα προγνωστικά συστήματα για το MDS, θέτοντας επίσης τη βάση για τις κλινικές δοκιμές που αξιολογούν τους αναστολείς PARP1 σε MDS υψηλού κινδύνου.
Subjects/Keywords: Μυελοδυσπλαστικά σύνδρομα (MDS); Poly (ADP-Ribose) Polymerase-1; RNA, messenger; Poly (ADP-Ribose) Polymerase-1; Myelodysplastic syndromes; RNA, messenger
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APA (6th Edition):
Zervakis, K. (2019). Μελέτη έκφρασης και προγνωστικής αξίας της Poly (ADP-ribose) Polymerase 1 mRNA στα μυελοδυσπλαστικά σύνδρομα. (Thesis). National and Kapodistrian University of Athens; Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών (ΕΚΠΑ). Retrieved from http://hdl.handle.net/10442/hedi/45792
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Zervakis, Konstantinos. “Μελέτη έκφρασης και προγνωστικής αξίας της Poly (ADP-ribose) Polymerase 1 mRNA στα μυελοδυσπλαστικά σύνδρομα.” 2019. Thesis, National and Kapodistrian University of Athens; Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών (ΕΚΠΑ). Accessed February 26, 2020.
http://hdl.handle.net/10442/hedi/45792.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Zervakis, Konstantinos. “Μελέτη έκφρασης και προγνωστικής αξίας της Poly (ADP-ribose) Polymerase 1 mRNA στα μυελοδυσπλαστικά σύνδρομα.” 2019. Web. 26 Feb 2020.
Vancouver:
Zervakis K. Μελέτη έκφρασης και προγνωστικής αξίας της Poly (ADP-ribose) Polymerase 1 mRNA στα μυελοδυσπλαστικά σύνδρομα. [Internet] [Thesis]. National and Kapodistrian University of Athens; Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών (ΕΚΠΑ); 2019. [cited 2020 Feb 26].
Available from: http://hdl.handle.net/10442/hedi/45792.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Zervakis K. Μελέτη έκφρασης και προγνωστικής αξίας της Poly (ADP-ribose) Polymerase 1 mRNA στα μυελοδυσπλαστικά σύνδρομα. [Thesis]. National and Kapodistrian University of Athens; Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών (ΕΚΠΑ); 2019. Available from: http://hdl.handle.net/10442/hedi/45792
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Florida
28.
Yao, Bing.
GW182 Silences microRNA Targets by Divergent Functional Domains and Regulates microRNA Stability.
Degree: PhD, Medical Sciences - Molecular Cell Biology (IDP), 2012, University of Florida
URL: http://ufdc.ufl.edu/UFE0044363
► MicroRNA (miRNA) is a relatively new class of shortendogenous non-coding RNA. MiRNA can pair to the 3’ untranslated region ofmRNA. This interaction inactivates protein translation…
(more)
▼ MicroRNA (miRNA) is a relatively new class of shortendogenous non-coding
RNA. MiRNA can pair to the 3’ untranslated region ofmRNA. This interaction inactivates protein translation from the mRNA, andeventually triggers mRNA decay. All important cellular processes are known tobe regulated in part by miRNA. Aberrant expression of miRNA often associateswith a variety of diseases including cancer. The goal of my dissertationresearch is to understand the miRNA silencing mechanism, identify andcharacterize key protein players in this process, and elucidate how the maturemiRNA level is regulated. These discoveries will expand our knowledge inunderstanding this key post-transcriptional gene regulation pathway and offerthe possibility in developing miRNA-mediated therapeutic approaches. GW182 is an 182kDaprotein with multiple glycine/tryptophan repeats (GW or WG) playing a centralrole in miRNA-mediated gene silencing. GW182 interacts with its functionalpartner Argonaute proteins (AGO) via multiple domains to exert its silencingactivity. Using tethering functional assays, we identified two non-overlappingGW182 silencing domains, namely , induced primarily translationalrepression rather than mRNA decay. GW orWG repeats on these two domains were critical for silencing activity. Thesedata implicated a dynamic and diversified role of GW182 in miRNA-mediated gene silencingconveyed by its silencing domains and further established GW182 as acentral player in silencing gene expression. Furthermore, we identified a newrole of GW182 in regulating miRNA stability aside from its silencing function.Depletion of GW182 reduced mature miRNA level in different time points andcaused impaired miRNA export through secretory vesicles termed exosomes. A3’-5’ exoribonuclease complex was identified to be responsible for the miRNAdegradation. These findings revealed a novel role of GW182 in regulating mature miRNA stability by binding to Argonaute proteins This work alsop supported of the importance of GW182 in miRNA-mediated silencing homeostasis. ( en )
Advisors/Committee Members: Chan, Edward K (committee chair), Zhou, Lei (committee member), Terada, Naohiro (committee member), Swanson, Maurice S (committee member), Kilberg, Michael S (committee member).
Subjects/Keywords: Exosomes; Journalism; Messenger RNA; MicroRNAs; Proteins; Repression; RNA; RNA stability; Small interfering RNA; Transfection; argonaute – gw182 – microrna
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APA ·
Chicago ·
MLA ·
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CSE |
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to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Yao, B. (2012). GW182 Silences microRNA Targets by Divergent Functional Domains and Regulates microRNA Stability. (Doctoral Dissertation). University of Florida. Retrieved from http://ufdc.ufl.edu/UFE0044363
Chicago Manual of Style (16th Edition):
Yao, Bing. “GW182 Silences microRNA Targets by Divergent Functional Domains and Regulates microRNA Stability.” 2012. Doctoral Dissertation, University of Florida. Accessed February 26, 2020.
http://ufdc.ufl.edu/UFE0044363.
MLA Handbook (7th Edition):
Yao, Bing. “GW182 Silences microRNA Targets by Divergent Functional Domains and Regulates microRNA Stability.” 2012. Web. 26 Feb 2020.
Vancouver:
Yao B. GW182 Silences microRNA Targets by Divergent Functional Domains and Regulates microRNA Stability. [Internet] [Doctoral dissertation]. University of Florida; 2012. [cited 2020 Feb 26].
Available from: http://ufdc.ufl.edu/UFE0044363.
Council of Science Editors:
Yao B. GW182 Silences microRNA Targets by Divergent Functional Domains and Regulates microRNA Stability. [Doctoral Dissertation]. University of Florida; 2012. Available from: http://ufdc.ufl.edu/UFE0044363
University of Florida
29.
Madzima, Thelma.
Blue-Light Regulation of Light-Harvesting Chlorophyll A/B Binding Transcript Stability.
Degree: PhD, Plant Molecular and Cellular Biology, 2009, University of Florida
URL: http://ufdc.ufl.edu/UFE0023731
► During early plant development environmental signals direct rapid changes in gene expression to establish growth patterns that conform to the immediate surroundings. Changes in gene…
(more)
▼ During early plant development environmental signals direct rapid changes in gene expression to establish growth patterns that conform to the immediate surroundings. Changes in gene expression affect morphology; physiology and biochemistry to best optimize the plant's ability to grow as an autotroph. One way to regulate gene expression is at the transcript level.
RNA degradation regulates accumulation of Light-harvesting chlorophyll a/b binding (Lhcb; formerly cab) transcripts. This has been demonstrated in etiolated seedlings, where Lhcb transcript levels increase in response to a short, single low fluence pulse of blue light (10
4 ?mol m
-2), but decrease following a pulse of blue-high-fluence light (10
5 ?mol m
-2). The decrease in steady-state accumulation is due to transcript destabilization. The 65 base 5'-UTR is necessary and sufficient to confer BHF-mediated destabilization and this response requires the phototropin1 (phot1) photoreceptor and the NPH3 scaffolding protein. In this study, the blue-light mediated regulation of Lhcb transcript stability is examined in the model plant Arabidopsis thaliana. A series of experiments were performed progressing from the phot1 photoreceptor to new proteins participating in transcript destabilization and coalescing in showing the effect of this system in transcript maintenance during diurnal cycles. The study implements phot1 LOV domain mutants to identify the role of the individual chromophore binding domains in the BHF-mediated destabilization process. To identify potential regulatory proteins, a yeast-three-hybrid screen was performed using the Lhcb 5'-UTR as an interaction target. Several bona fide interactors were obtained. One of these proteins is a novel F-box protein designated as KFR1 for Kelch domain, F-box
RNA-associated protein. Genetic tests using T-DNA insertion mutants and pharmacological tests using a proteasome inhibitor (MG132) indicate that Kfr1 is required for BHF-induced Lhcb transcript destabilization. To study this destabilization effect in an important biological process outside of de-etiolation, the decay kinetics of Lhcb transcripts under diurnal conditions is studied, and shows a discrete effect of the phot1-KFR1 system on transcript stability. This study advances previous understanding of the blue-light mediated regulation of transcript stability significantly and identifies new components that mediate this response. It addresses the relationship between signal input and changes in physiology to better our understanding in the mechanisms that direct light-regulation of transcript stability. ( en )
Advisors/Committee Members: Folta, Kevin M. (committee chair), Klee, Harry J. (committee member), Settles, Andrew M. (committee member), De Crecy-Lagard, Valerie (committee member).
Subjects/Keywords: Chloroplasts; Fluence; Messenger RNA; Plasmids; Proteins; Receptors; RNA; Seedlings; Untranslated regions; Yeasts
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
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APA (6th Edition):
Madzima, T. (2009). Blue-Light Regulation of Light-Harvesting Chlorophyll A/B Binding Transcript Stability. (Doctoral Dissertation). University of Florida. Retrieved from http://ufdc.ufl.edu/UFE0023731
Chicago Manual of Style (16th Edition):
Madzima, Thelma. “Blue-Light Regulation of Light-Harvesting Chlorophyll A/B Binding Transcript Stability.” 2009. Doctoral Dissertation, University of Florida. Accessed February 26, 2020.
http://ufdc.ufl.edu/UFE0023731.
MLA Handbook (7th Edition):
Madzima, Thelma. “Blue-Light Regulation of Light-Harvesting Chlorophyll A/B Binding Transcript Stability.” 2009. Web. 26 Feb 2020.
Vancouver:
Madzima T. Blue-Light Regulation of Light-Harvesting Chlorophyll A/B Binding Transcript Stability. [Internet] [Doctoral dissertation]. University of Florida; 2009. [cited 2020 Feb 26].
Available from: http://ufdc.ufl.edu/UFE0023731.
Council of Science Editors:
Madzima T. Blue-Light Regulation of Light-Harvesting Chlorophyll A/B Binding Transcript Stability. [Doctoral Dissertation]. University of Florida; 2009. Available from: http://ufdc.ufl.edu/UFE0023731
University of Florida
30.
Wang,Hui.
Molecular Engineering of Catalytic Nucleic Acid Probes for Bioanalytical and Biomedical Applications.
Degree: PhD, Chemistry, 2011, University of Florida
URL: http://ufdc.ufl.edu/UFE0043277
► Over the past few decades, the role of nucleic acids including deoxyribonucleic acids and ribonucleic acids in purely biological systems has been defined, and these…
(more)
▼ Over the past few decades, the role of nucleic acids including deoxyribonucleic acids and ribonucleic acids in purely biological systems has been defined, and these versatile compounds have also been integrated into nanoscience. The overall goal of this doctoral research is dedicated to engineering these biomolecular components with the objective of building novel molecular tools and devices for biological studies, biomedical research and therapeutic applications.
Advisors/Committee Members: Tan, Weihong (committee chair), Merz, Kenneth Malcolm (committee member), Fanucci, Gail E (committee member), Powell, David H (committee member), Liu, Chen (committee member).
Subjects/Keywords: DNA; Enzymes; Fluorescence; Lead; Messenger RNA; Micelles; Nucleic acids; RNA; Sensors; Signals
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Record Details
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
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APA (6th Edition):
Wang,Hui. (2011). Molecular Engineering of Catalytic Nucleic Acid Probes for Bioanalytical and Biomedical Applications. (Doctoral Dissertation). University of Florida. Retrieved from http://ufdc.ufl.edu/UFE0043277
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Chicago Manual of Style (16th Edition):
Wang,Hui. “Molecular Engineering of Catalytic Nucleic Acid Probes for Bioanalytical and Biomedical Applications.” 2011. Doctoral Dissertation, University of Florida. Accessed February 26, 2020.
http://ufdc.ufl.edu/UFE0043277.
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
MLA Handbook (7th Edition):
Wang,Hui. “Molecular Engineering of Catalytic Nucleic Acid Probes for Bioanalytical and Biomedical Applications.” 2011. Web. 26 Feb 2020.
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Vancouver:
Wang,Hui. Molecular Engineering of Catalytic Nucleic Acid Probes for Bioanalytical and Biomedical Applications. [Internet] [Doctoral dissertation]. University of Florida; 2011. [cited 2020 Feb 26].
Available from: http://ufdc.ufl.edu/UFE0043277.
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Council of Science Editors:
Wang,Hui. Molecular Engineering of Catalytic Nucleic Acid Probes for Bioanalytical and Biomedical Applications. [Doctoral Dissertation]. University of Florida; 2011. Available from: http://ufdc.ufl.edu/UFE0043277
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
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