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1.
Accomando, William Paul.
Epigenetic Biomarkers for the Detection and Quantification
of Human Leukocytes in Blood and Tissue.
Degree: PhD, Pathobiology, 2013, Brown University
URL: https://repository.library.brown.edu/studio/item/bdr:320602/
► Different types of human cells, defined by function and morphology, are typically detected and enumerated in complex mixtures using a variety of physical, optical and…
(more)
▼ Different types of human cells, defined by function
and morphology, are typically detected and enumerated in complex
mixtures using a variety of physical, optical and proteomic
characteristics. We hypothesize that epigenetic marks, such as
patterns of
DNA methylation, can also be used to distinguish
different types of human cells, since lineage commitment during
cellular differentiation is marked by mitotically heritable
epigenetic changes that reflect transcriptional programming of gene
expression. The human immune system plays a critical role in the
development of nearly every human disease, including cancers, and
the composition of leukocyte populations is known to reflect disease
states and toxicant exposures. Therefore, the ability to detect an
improper balance of immune cells is valuable in both clinical and
research settings. However, research aimed at further understanding
immune modulations is restricted by the limitations of
immunodiagnostic methods. Therefore, we developed
DNA-based
approaches that exploit the human methylome in order to detect and
quantify different types of human leukocytes in blood and tissue.
Thus we established novel epigenetic immunodiagnostic methods that
do not require intact cells and can therefore be applied to
virtually any sample. These include PCR-based assays (each
measuring a single type of immune cell) and an array-based method
allowing for the simultaneous assessment of the entire distribution
of white blood cells. The approaches were validated in several
ways, including direct comparison to conventional methods of
immunological assessment in human blood and tissue. In addition,
the approaches were employed to assess immune modulations in
population-based and hospital-based studies of human diseases,
including glioma and head and neck squamous cell
carcinoma.
Advisors/Committee Members: Kelsey, Karl (Director), Marsit, Carmen (Reader), Houseman, Eugene (Reader), Sharma, Surendra (Reader), Wiencke, John (Reader).
Subjects/Keywords: DNA methylation
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APA (6th Edition):
Accomando, W. P. (2013). Epigenetic Biomarkers for the Detection and Quantification
of Human Leukocytes in Blood and Tissue. (Doctoral Dissertation). Brown University. Retrieved from https://repository.library.brown.edu/studio/item/bdr:320602/
Chicago Manual of Style (16th Edition):
Accomando, William Paul. “Epigenetic Biomarkers for the Detection and Quantification
of Human Leukocytes in Blood and Tissue.” 2013. Doctoral Dissertation, Brown University. Accessed March 01, 2021.
https://repository.library.brown.edu/studio/item/bdr:320602/.
MLA Handbook (7th Edition):
Accomando, William Paul. “Epigenetic Biomarkers for the Detection and Quantification
of Human Leukocytes in Blood and Tissue.” 2013. Web. 01 Mar 2021.
Vancouver:
Accomando WP. Epigenetic Biomarkers for the Detection and Quantification
of Human Leukocytes in Blood and Tissue. [Internet] [Doctoral dissertation]. Brown University; 2013. [cited 2021 Mar 01].
Available from: https://repository.library.brown.edu/studio/item/bdr:320602/.
Council of Science Editors:
Accomando WP. Epigenetic Biomarkers for the Detection and Quantification
of Human Leukocytes in Blood and Tissue. [Doctoral Dissertation]. Brown University; 2013. Available from: https://repository.library.brown.edu/studio/item/bdr:320602/
2.
Smith, Ashley A.
Integration of Genetic and Epigenetic Alterations in the
Discovery of Molecular Drivers of Malignancy in Glioma.
Degree: PhD, Pathobiology, 2014, Brown University
URL: https://repository.library.brown.edu/studio/item/bdr:386178/
► Gliomas are a family of extremely aggressive brain cancers, which, despite current treatment options, have poor prognoses. There are distinct subtypes of gliomas, and accurately…
(more)
▼ Gliomas are a family of extremely aggressive brain
cancers, which, despite current treatment options, have poor
prognoses. There are distinct subtypes of gliomas, and accurately
identifying these is critical for diagnosis and management. Often,
the pathologic diagnosis of these subtypes is difficult, and
research is underway to discover novel biomarkers that aid in
accurate subtype identification and prognostication. This thesis
focuses on the joint analysis of
DNA methylation profiles with
somatic mutation and gene expression data in glioma, assessing the
nature of their association with each other and, subsequently, with
histology and disease outcome. The ultimate goal is to develop
potential prognostic biomarkers of the disease.
DNA methylation was
determined for several different grades and histologies of glioma
in addition to non-brain-tumor controls. The same samples were
sequenced for IDH1/2 mutations. We, and others, discovered an IDH
hypermethylator phenotype, showing a tight association between the
occurrence of IDH mutation and hypermethylation. This phenotype had
a higher prevalence in low-grade and secondary gliomas. Besides
mutation,
DNA methylation is also associated with other somatic
alterations, which can alter gene expression. To better understand
how
DNA methylation and gene expression drive glioma, we used an
integrative bioinformatics approach; our goal was to investigate
DNA methylation that modulates gene expression as well as
independent
DNA methylation (
methylation that may exert its
phenotypic effects through alternative mechanisms), assessing the
nature of their association with disease survival. Our model
supports the existing theory that
DNA methylation can work through
gene expression to influence survival outcome but also suggests
that
DNA methylation can work alone or through alternative
mechanisms to influence glioma outcome. In addition, our approach
offers an alternative method of biomarker discovery, which could
potentially be used for diagnostic and therapeutic purposes.
Overall, this work supports the hypothesis that somatic mutations
are not solely responsible for the glioma phenotype. Epigenetics,
particularly
DNA methylation, is also important in both the genesis
and outcome of the disease. Furthermore, our model provides an
alternative approach for biomarker discovery that may also be
applicable to cancers other than glioma.
Advisors/Committee Members: Kelsey, Karl (Director), Marsit, Carmen (Reader), Houseman, E. Andres (Reader), Huang, Yen-Tsung (Reader), Wiencke, John (Reader).
Subjects/Keywords: DNA methylation
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Smith, A. A. (2014). Integration of Genetic and Epigenetic Alterations in the
Discovery of Molecular Drivers of Malignancy in Glioma. (Doctoral Dissertation). Brown University. Retrieved from https://repository.library.brown.edu/studio/item/bdr:386178/
Chicago Manual of Style (16th Edition):
Smith, Ashley A. “Integration of Genetic and Epigenetic Alterations in the
Discovery of Molecular Drivers of Malignancy in Glioma.” 2014. Doctoral Dissertation, Brown University. Accessed March 01, 2021.
https://repository.library.brown.edu/studio/item/bdr:386178/.
MLA Handbook (7th Edition):
Smith, Ashley A. “Integration of Genetic and Epigenetic Alterations in the
Discovery of Molecular Drivers of Malignancy in Glioma.” 2014. Web. 01 Mar 2021.
Vancouver:
Smith AA. Integration of Genetic and Epigenetic Alterations in the
Discovery of Molecular Drivers of Malignancy in Glioma. [Internet] [Doctoral dissertation]. Brown University; 2014. [cited 2021 Mar 01].
Available from: https://repository.library.brown.edu/studio/item/bdr:386178/.
Council of Science Editors:
Smith AA. Integration of Genetic and Epigenetic Alterations in the
Discovery of Molecular Drivers of Malignancy in Glioma. [Doctoral Dissertation]. Brown University; 2014. Available from: https://repository.library.brown.edu/studio/item/bdr:386178/
3.
Cash, Haley L.
DNA Methylation of Repeat Regions in Human Cancer and
Metabolic Disease.
Degree: PhD, Pathobiology, 2011, Brown University
URL: https://repository.library.brown.edu/studio/item/bdr:11329/
► Non-communicable diseases have recently surpassed communicable diseases as the number one cause of death globally. These conditions not only lead to increased rates of mortality,…
(more)
▼ Non-communicable diseases have recently surpassed
communicable diseases as the number one cause of death globally.
These conditions not only lead to increased rates of mortality, but
also contribute to global disability that can greatly impede
development. Although many environmental and genetic risk factors
have been associated with these conditions, epigenetic mechanisms
have yet to be properly explored in these diseases. This thesis
aimed to further understand the relationships between
DNA
methylation and environmental factors as well as genetic factors in
relation to various non-communicable diseases. When examining the
relationships between LINE-1
methylation, bladder cancer, and risk
factors in the Shanghai Bladder Cancer Study, LINE-1
hypomethylation was found to be significantly associated with
increased risk of bladder cancer among non-smokers; risk was
greatest among these individuals with null
glutathione-s-transferase genoytypes. In this study we also found
that CYP1A2 phenotype among smokers, cruciferous vegetable intake,
and glutathione-s-transferase genotypes significantly influenced
LINE-1
methylation among controls. Additionally, men had
significantly higher levels of LINE-1
methylation than women. This
LINE-1 gender difference was also observed in The Samoan Family
Study of Overweight and Obese when LINE-1
methylation was measured
in this population. Additionally, LINE-1
methylation was found to
be negatively associated with age as well as HDL in men; whereas
insulin and testosterone levels were associated with LINE-1
methylation among women. Finally, the effects of bladder cancer
risk genetic variants within the PSCA gene (rs2294008) on CpG
methylation was evaluated by examining array based
DNA methylation
profiles. Upon investigation, there were not array-wide
methylation
associations with variation; however,
methylation of a CpG within
the PSCA gene was significantly associated with SNP status in a
dose-response fashion, in which there was a positive relationship
between risk allele quantity and CpG
methylation. Overall, this
work demonstrates the importance of
DNA methylation in
non-communicable diseases. Additionally, this work suggests that
complex relationships exist between environmental factors,
genetics, and epigenetics, advocating the need for further
investigations in order to more effectively understand the role of
DNA methylation in non-communicable disease.
Advisors/Committee Members: Kelsey, Karl (Director), McGarvey, Stephen (Reader), Marsit, Carmen (Reader), Houseman, E (Reader), Karagas, Margaret (Reader).
Subjects/Keywords: DNA methylation
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Cash, H. L. (2011). DNA Methylation of Repeat Regions in Human Cancer and
Metabolic Disease. (Doctoral Dissertation). Brown University. Retrieved from https://repository.library.brown.edu/studio/item/bdr:11329/
Chicago Manual of Style (16th Edition):
Cash, Haley L. “DNA Methylation of Repeat Regions in Human Cancer and
Metabolic Disease.” 2011. Doctoral Dissertation, Brown University. Accessed March 01, 2021.
https://repository.library.brown.edu/studio/item/bdr:11329/.
MLA Handbook (7th Edition):
Cash, Haley L. “DNA Methylation of Repeat Regions in Human Cancer and
Metabolic Disease.” 2011. Web. 01 Mar 2021.
Vancouver:
Cash HL. DNA Methylation of Repeat Regions in Human Cancer and
Metabolic Disease. [Internet] [Doctoral dissertation]. Brown University; 2011. [cited 2021 Mar 01].
Available from: https://repository.library.brown.edu/studio/item/bdr:11329/.
Council of Science Editors:
Cash HL. DNA Methylation of Repeat Regions in Human Cancer and
Metabolic Disease. [Doctoral Dissertation]. Brown University; 2011. Available from: https://repository.library.brown.edu/studio/item/bdr:11329/

Wake Forest University
4.
Cammarata, Michael Wesley.
DNA Methylation and Gene Expression of P2RY12 in a Multi-Ethnic Cohort.
Degree: 2015, Wake Forest University
URL: http://hdl.handle.net/10339/57275
Background: P2Y12 receptor is the target for thienopyridine mediated platelet inhibition. Epigenetic factors, including DNA methylation could influence gene expression and subsequent in vitro and clinical response to thienopyridine therapy. Our aim was to determine the relationships between DNA methylation at cis acting CpG sites and P2RY12 gene expression.
Subjects/Keywords: DNA Methylation
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Cammarata, M. W. (2015). DNA Methylation and Gene Expression of P2RY12 in a Multi-Ethnic Cohort. (Thesis). Wake Forest University. Retrieved from http://hdl.handle.net/10339/57275
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):
Cammarata, Michael Wesley. “DNA Methylation and Gene Expression of P2RY12 in a Multi-Ethnic Cohort.” 2015. Thesis, Wake Forest University. Accessed March 01, 2021.
http://hdl.handle.net/10339/57275.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Cammarata, Michael Wesley. “DNA Methylation and Gene Expression of P2RY12 in a Multi-Ethnic Cohort.” 2015. Web. 01 Mar 2021.
Vancouver:
Cammarata MW. DNA Methylation and Gene Expression of P2RY12 in a Multi-Ethnic Cohort. [Internet] [Thesis]. Wake Forest University; 2015. [cited 2021 Mar 01].
Available from: http://hdl.handle.net/10339/57275.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Cammarata MW. DNA Methylation and Gene Expression of P2RY12 in a Multi-Ethnic Cohort. [Thesis]. Wake Forest University; 2015. Available from: http://hdl.handle.net/10339/57275
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Southern California
5.
Triche, Timothy J., Jr.
Preprocessing and analysis of DNA methylation
microarrays.
Degree: PhD, Statistical Genetics and Genetic
Epidemiology, 2013, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/298429/rec/5209
► In the first chapter of this dissertation, I review the importance of cytosine methylation in vertebrate genomes. In the second chapter, I present methods which…
(more)
▼ In the first chapter of this dissertation, I review
the importance of cytosine
methylation in vertebrate genomes. In
the second chapter, I present methods which leverage a design
feature of the most widely used
DNA methylation microarrays to
ameliorate common technical artifacts. In the third chapter, I
present an investigation of sensitive methods for detecting
differential
DNA methylation. In the final chapter, I discuss the
impact of these findings for population-scale studies of
DNA
methylation. ❧ Taken together, these chapters describe versatile
and widely applicable approaches to study
DNA methylation at the
scale demanded by modern investigators. If recent years are any
indication, the size and complexity of such studies will only
increase. Changes to genomic sequence are relatively rare and
typically deleterious, thus the genomes of healthy somatic cells
from different tissues in an individual are with few exceptions
nearly identical. The epigenomes of these same cells differ
radically. Furthermore, the erasure of paternal
DNA methylation
marks at conception may be incomplete, offering a potential route
for epigenetic differences to persist across generations as well as
tissues. ❧ Unraveling the roles and functional interactions of
genomic and epigenomic changes in health and disease may thus
become one of the great scientific and informatic challenges of our
time. This dissertation presents effective analytic and informatic
practices, in an attempt to guide future investigators as they rise
to the challenge.
Advisors/Committee Members: Siegmund, Kimberly D. (Committee Chair), Laird, Peter W. (Committee Member), Lewinger, Juan Pablo (Committee Member), Gilliland, Frank D. (Committee Member).
Subjects/Keywords: DNA methylation
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Triche, Timothy J., J. (2013). Preprocessing and analysis of DNA methylation
microarrays. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/298429/rec/5209
Chicago Manual of Style (16th Edition):
Triche, Timothy J., Jr. “Preprocessing and analysis of DNA methylation
microarrays.” 2013. Doctoral Dissertation, University of Southern California. Accessed March 01, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/298429/rec/5209.
MLA Handbook (7th Edition):
Triche, Timothy J., Jr. “Preprocessing and analysis of DNA methylation
microarrays.” 2013. Web. 01 Mar 2021.
Vancouver:
Triche, Timothy J. J. Preprocessing and analysis of DNA methylation
microarrays. [Internet] [Doctoral dissertation]. University of Southern California; 2013. [cited 2021 Mar 01].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/298429/rec/5209.
Council of Science Editors:
Triche, Timothy J. J. Preprocessing and analysis of DNA methylation
microarrays. [Doctoral Dissertation]. University of Southern California; 2013. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/298429/rec/5209

University of Edinburgh
6.
Masalmeh, Roza Hussein Ali.
Low levels of methylation are targeted to aberrantly methylated CGIs in human colorectal cancer cells.
Degree: PhD, 2019, University of Edinburgh
URL: http://hdl.handle.net/1842/35826
► Disruption of DNA methylation patterns is a primary hallmark of cancer. One main disruption is CpG islands (CGIs) aberrant hypermethylation which is associated with transcriptional…
(more)
▼ Disruption of DNA methylation patterns is a primary hallmark of cancer. One main disruption is CpG islands (CGIs) aberrant hypermethylation which is associated with transcriptional repression of tumour suppressor genes such as BRCA1, MLH1, and CDKN2A (p16/ARF). However, the mechanism(s) underpinning this process are still unknown. One hypothesis is that high de novo methylation activity is targeted to CGIs that get aberrantly methylated in cancer. To investigate this, I used human colorectal cancer cell line (HCT116) as a model. Firstly, I have ectopically integrated representative aberrantly methylated CGIs randomly into the genome and assessed their methylation at ectopic loci. I show that integrated CGIs rarely gained methylation at ectopic locations. This suggested that the sequence doesn't program CGIs aberrant methylation at ectopic loci in HCT116 and that low de novo methylation is targeted to aberrantly methylated CGIs. Next, I wanted to confirm this result by integrating CGIs at a chosen genomic loci in order to exclude any effects from the CGI position on its methylation status. This was performed by recombinase mediated cassette exchange (RMCE). Successful targeting of a RMCE cassette to the desired chromosomal locus was achieved. However, isolating clonal cell lines with integrated CGIs was technically infeasible due to difficulty in using the thymidine kinase selection in HCT116. In order to investigate which CGIs have higher de novo methylation in HCT116 on a genome wide level, I restored DNMT3B expression in DNMTA1/DNMT3B double knockout (DKO) of HCT116. In agreement with previous reports, DNMT3B showed higher de novo methylation activity at CGIs overlapping H3K36me3. Most importantly, aberrantly methylated CGIs showed ~ 78.5% less methylation gain compared to normally methylated CGIs. To confirm results from this experiment, I treated HCT116 with 5-Aza-2'-deoxycytidine and then allowed cells to recover methylation. The rate of methylation recovery of CGIs was assessed. This showed that aberrantly methylated CGIs recover slower than normally methylated CGIs, confirming that lower de novo methylation is targeted to aberrantly methylated CGIs compared to normally methylated ones. The work carried out during the course of this thesis provides novel insights into the process of de novo methylating CGIs in cancer on a genome wide level. It suggests that low levels, rather than high levels, of methylation are targeted to aberrantly methylated CGIs in colorectal tumours.
Subjects/Keywords: DNA methylation; DNMT3B; methylation; HCT116
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Masalmeh, R. H. A. (2019). Low levels of methylation are targeted to aberrantly methylated CGIs in human colorectal cancer cells. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/35826
Chicago Manual of Style (16th Edition):
Masalmeh, Roza Hussein Ali. “Low levels of methylation are targeted to aberrantly methylated CGIs in human colorectal cancer cells.” 2019. Doctoral Dissertation, University of Edinburgh. Accessed March 01, 2021.
http://hdl.handle.net/1842/35826.
MLA Handbook (7th Edition):
Masalmeh, Roza Hussein Ali. “Low levels of methylation are targeted to aberrantly methylated CGIs in human colorectal cancer cells.” 2019. Web. 01 Mar 2021.
Vancouver:
Masalmeh RHA. Low levels of methylation are targeted to aberrantly methylated CGIs in human colorectal cancer cells. [Internet] [Doctoral dissertation]. University of Edinburgh; 2019. [cited 2021 Mar 01].
Available from: http://hdl.handle.net/1842/35826.
Council of Science Editors:
Masalmeh RHA. Low levels of methylation are targeted to aberrantly methylated CGIs in human colorectal cancer cells. [Doctoral Dissertation]. University of Edinburgh; 2019. Available from: http://hdl.handle.net/1842/35826

University of Hawaii – Manoa
7.
Song, Min-Ae.
Identification of aberrant epigenetic events in MSS/CIMP-negative colon cancer.
Degree: 2015, University of Hawaii – Manoa
URL: http://hdl.handle.net/10125/100485
► Ph.D. University of Hawaii at Manoa 2014.
My research project focused on the identification of aberrant epigenetic changes via non-coding RNAs and DNA methylation in…
(more)
▼ Ph.D. University of Hawaii at Manoa 2014.
My research project focused on the identification of aberrant epigenetic changes via non-coding RNAs and DNA methylation in MSS/CIMP-negative colon cancer, the major subtype. DNA methylation is the most well studied epigenetic event, while non-coding RNA-mediated transcriptional silencing has also an important role in cancer. My first aim was to profile microRNAs and their potential target genes in colon cancer by a study of 10 paired normal and tumor colon tissues using data from Next Generation Sequencing and Exon arrays. Nineteen miRNAs, including 6 previously colon cancer associated and 13 not previously implicated, were found aberrantly expressed in the tumor tissues. Thirty-six colon cancer related genes were significantly correlated to the expression levels of the identified miRNAs and 'Wnt/beta-catenin Signaling' was identified as the top canonical pathway for these target genes. My second aim was to identify small and long novel non-coding RNAs at the 8q24 region which contains one of the most relevant colon cancer risk variants, SNP rs6983267. Thirty-two pre-miRNAs were identified In Silico by two algorithms, but none of them were verified in further studies. However, a novel long non-coding RNA spanning the rs6983267 was recently identified, and significantly elevated expression levels were observed in 23 colon tumor tissues in our sample set. Also, one known miRNA in a cluster 400 kb away from the risk SNP showed genotype dependent expression patterns. My last aim was to elucidate the landscape of genome-wide DNA methylation in colon cancer. General hypomethylation was observed, concentrating in the intergenic regions and gene bodies, while hypermethylation was observed in promoter regions, N_Shores and CpG islands. Differentially methylated CpGs were enriched in genes with roles in cancer and gastrointestinal disease. Observations in imprinted genes suggest a more widespread dysregulation of imprinting in colon cancer than previously reported. The findings of epigenetic alterations in colon cancer will hopefully contribute to a better understanding of these aberrant events: how they are related to colon cancer development and progression, while these findings may also lead to discovery of new biomarkers that can be utilized in patient diagnosis, stratification and the follow-up of the treatment.
Subjects/Keywords: RNAs; DNA methylation
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Song, M. (2015). Identification of aberrant epigenetic events in MSS/CIMP-negative colon cancer. (Thesis). University of Hawaii – Manoa. Retrieved from http://hdl.handle.net/10125/100485
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):
Song, Min-Ae. “Identification of aberrant epigenetic events in MSS/CIMP-negative colon cancer.” 2015. Thesis, University of Hawaii – Manoa. Accessed March 01, 2021.
http://hdl.handle.net/10125/100485.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Song, Min-Ae. “Identification of aberrant epigenetic events in MSS/CIMP-negative colon cancer.” 2015. Web. 01 Mar 2021.
Vancouver:
Song M. Identification of aberrant epigenetic events in MSS/CIMP-negative colon cancer. [Internet] [Thesis]. University of Hawaii – Manoa; 2015. [cited 2021 Mar 01].
Available from: http://hdl.handle.net/10125/100485.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Song M. Identification of aberrant epigenetic events in MSS/CIMP-negative colon cancer. [Thesis]. University of Hawaii – Manoa; 2015. Available from: http://hdl.handle.net/10125/100485
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Edinburgh
8.
Termanis, Ausma.
Regulators of DNA methylation in mammalian cells.
Degree: PhD, 2013, University of Edinburgh
URL: http://hdl.handle.net/1842/11749
► Although the many cells within a mammal share the same DNA sequence, their gene expression programmes are highly heterogeneous, and their functions correspondingly diverse. This…
(more)
▼ Although the many cells within a mammal share the same DNA sequence, their gene expression programmes are highly heterogeneous, and their functions correspondingly diverse. This heterogeneity within an isogenic population of cells arises in part from the ability of each cell to respond to its immediate surroundings via a network of signalling pathways. However, this is not sufficient to explain many of the transcriptional and functional differences between cells, particularly those that are more stable, or, indeed, differences in expression between parental alleles within the same cell. This conundrum lead to the emergence of the field of epigenetics - the study of heritable changes in gene expression independent of DNA sequence. Such changes are dependent on “epigenetic modifications”, of which DNA methylation is one of the best characterised, and is associated with gene silencing. The establishment of correct DNA methylation patterns is particularly important during early development, leading to cell type specific and parental allele specific gene regulation. Besides DNA methyltransferases, various other proteins have recently been implicated in DNA methylation. The absence of these proteins leads to defects in DNA methylation and development that can be even more severe than those in DNA methyltransferase knockouts themselves. In this study I focus on three such accessory proteins: LSH (a putative chromatin remodelling ATPase), G9a (a histone lysine methyltransferase) and SmcHD1 (a structural maintenance of chromosomes protein). To compare DNA methylation between WT cells and cells knocked out for each of these proteins, I used whole genome methylated DNA affinity purification and subsequent hybridization to promoter microarrays. This enabled me to compare the requirement for each protein in DNA methylation at specific genomic regions. The absence of LSH in mouse embryonic fibroblasts (MEFs) resulted in the loss of DNA methylation at 20% of usually methylated promoters, and the misregulation of associated protein coding genes. This revealed a requirement for LSH in the establishment of DNA methylation at promoters normally methylated during pre-implantation as well as post-implantation development. Secondly, I identified hypomethylation at 26% of normally methylated promoters in G9a-/- compared to WT ES cells. Strikingly, this revealed that G9a is required for maintenance of DNA methylation at maternal as well as paternal imprinting control regions (ICRs). This is accompanied by expression defects of imprinted genes regulated by these ICRs. Finally, in collaboration with the Brockdorff lab at the University of Oxford I identified a role for SmcHD1 in establishing DNA methylation at promoters on the X chromosome normally methylated slowly during X chromosome inactivation. Interestingly, SmcHD1 was also required for DNA methylation at autosomal gene promoters, contrary to previous reports that it is mainly involved in X chromosome methylation. I conclude that different accessory proteins are required to facilitate…
Subjects/Keywords: 572.8; epigenetics; DNA methylation; X chromosome methylation
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Termanis, A. (2013). Regulators of DNA methylation in mammalian cells. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/11749
Chicago Manual of Style (16th Edition):
Termanis, Ausma. “Regulators of DNA methylation in mammalian cells.” 2013. Doctoral Dissertation, University of Edinburgh. Accessed March 01, 2021.
http://hdl.handle.net/1842/11749.
MLA Handbook (7th Edition):
Termanis, Ausma. “Regulators of DNA methylation in mammalian cells.” 2013. Web. 01 Mar 2021.
Vancouver:
Termanis A. Regulators of DNA methylation in mammalian cells. [Internet] [Doctoral dissertation]. University of Edinburgh; 2013. [cited 2021 Mar 01].
Available from: http://hdl.handle.net/1842/11749.
Council of Science Editors:
Termanis A. Regulators of DNA methylation in mammalian cells. [Doctoral Dissertation]. University of Edinburgh; 2013. Available from: http://hdl.handle.net/1842/11749

University of Oregon
9.
Storck, William.
Characterization of LSD Complex Function, Histone Exchange, and Regulation of a Tryptophan Catabolism Gene Pair in Neurospora crassa.
Degree: PhD, Department of Chemistry and Biochemistry, 2020, University of Oregon
URL: https://scholarsbank.uoregon.edu/xmlui/handle/1794/25593
► DISSERTATION ABSTRACT William K. Storck Doctor of Philosophy Department of Chemistry and Biochemistry March 2020 Title: Characterization of LSD Complex Function, Histone Exchange, and Regulation…
(more)
▼ DISSERTATION ABSTRACT
William K. Storck
Doctor of Philosophy
Department of Chemistry and Biochemistry
March 2020
Title: Characterization of LSD Complex Function, Histone Exchange, and Regulation of a Tryptophan Catabolism Gene Pair in Neurospora crassa
Gene expression is regulated by a plethora of factors associated with chromatin, such as histone proteins.
DNA can be methylated and histones can be marked with various chemical tags, which can influence expression of underlying
DNA. Chromatin is organized into distinct domains: transcriptionally-active euchromatin and transcriptionally-silent heterochromatin. My dissertation involved investigating different aspects of chromatin regulation in the filamentous fungus Neurospora crassa.
I examined heterochromatin spreading in Neurospora mutants defective in lysine-specific demethylase 1 (LSD1). Loss of either LSD1 or its associated complex members, PHF1 or BDP-1, results in variable spreading of trimethylation of H3K9 (H3K9me3) and
DNA methylation, and this spreading is dependent on
DNA methylation, which is typically not involved in H3K9me3 establishment, and on the catalytic activity of the histone deacetylase complex, HCHC. Though there are gene expression changes present in ∆lsd1 strains, these changes do not appear to be driven by spreading H3K9me3 and
DNA methylation.
Though their relative positioning within chromatin appears to be regulated, histones are not static structures embedded within
DNA, but are
subject to constant exchange. I characterized a light-inducible histone turnover reporter strain and used it to build a simple protocol for profiling
DNA replication-independent histone turnover in Neurospora. I investigated how histone turnover correlates with gene expression, and observed similarities to other models in turnover profiles over genes. I also examined turnover at heterochromatin domains in heterochromatin mutants, which revealed that loss of H3K9me3 or its binder, HP1, or histone deacetylation by HCHC results in turnover increases.
Lastly, I investigated the regulation of a pair of genes involved in tryptophan catabolism, kyn-1 and iad-1. I demonstrate that these genes are induced through the exposure of extracellular tryptophan. Though this locus is enriched for the conserved repressive mark, H3K27me3, loss of which does not appear to significantly affect the activity of this locus. Rather, I show that this locus is repressed by the H3K36 methyltransferase, ASH1, and chromatin remodelers, CRF4-1 and CRF6-1. Another H3K36 methyltransferase, SET-2, is required to overcome this repression.
This dissertation contains previously unpublished coauthored material.
Advisors/Committee Members: Selker, Eric (advisor).
Subjects/Keywords: DNA Methylation; Epigenetics; Heterochromatin; Histone Methylation
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Storck, W. (2020). Characterization of LSD Complex Function, Histone Exchange, and Regulation of a Tryptophan Catabolism Gene Pair in Neurospora crassa. (Doctoral Dissertation). University of Oregon. Retrieved from https://scholarsbank.uoregon.edu/xmlui/handle/1794/25593
Chicago Manual of Style (16th Edition):
Storck, William. “Characterization of LSD Complex Function, Histone Exchange, and Regulation of a Tryptophan Catabolism Gene Pair in Neurospora crassa.” 2020. Doctoral Dissertation, University of Oregon. Accessed March 01, 2021.
https://scholarsbank.uoregon.edu/xmlui/handle/1794/25593.
MLA Handbook (7th Edition):
Storck, William. “Characterization of LSD Complex Function, Histone Exchange, and Regulation of a Tryptophan Catabolism Gene Pair in Neurospora crassa.” 2020. Web. 01 Mar 2021.
Vancouver:
Storck W. Characterization of LSD Complex Function, Histone Exchange, and Regulation of a Tryptophan Catabolism Gene Pair in Neurospora crassa. [Internet] [Doctoral dissertation]. University of Oregon; 2020. [cited 2021 Mar 01].
Available from: https://scholarsbank.uoregon.edu/xmlui/handle/1794/25593.
Council of Science Editors:
Storck W. Characterization of LSD Complex Function, Histone Exchange, and Regulation of a Tryptophan Catabolism Gene Pair in Neurospora crassa. [Doctoral Dissertation]. University of Oregon; 2020. Available from: https://scholarsbank.uoregon.edu/xmlui/handle/1794/25593
10.
Choi, Chang-Sui.
Change of DNA methylation status in response to environmental stress : 環境に応答したDNAメチル化の変化; カンキョウ ニ オウトウシタ DNA メチルカ ノ ヘンカ.
Degree: Nara Institute of Science and Technology / 奈良先端科学技術大学院大学
URL: http://hdl.handle.net/10061/4135
Subjects/Keywords: DNA methylation
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Choi, C. (n.d.). Change of DNA methylation status in response to environmental stress : 環境に応答したDNAメチル化の変化; カンキョウ ニ オウトウシタ DNA メチルカ ノ ヘンカ. (Thesis). Nara Institute of Science and Technology / 奈良先端科学技術大学院大学. Retrieved from http://hdl.handle.net/10061/4135
Note: this citation may be lacking information needed for this citation format:
No year of publication.
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Choi, Chang-Sui. “Change of DNA methylation status in response to environmental stress : 環境に応答したDNAメチル化の変化; カンキョウ ニ オウトウシタ DNA メチルカ ノ ヘンカ.” Thesis, Nara Institute of Science and Technology / 奈良先端科学技術大学院大学. Accessed March 01, 2021.
http://hdl.handle.net/10061/4135.
Note: this citation may be lacking information needed for this citation format:
No year of publication.
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Choi, Chang-Sui. “Change of DNA methylation status in response to environmental stress : 環境に応答したDNAメチル化の変化; カンキョウ ニ オウトウシタ DNA メチルカ ノ ヘンカ.” Web. 01 Mar 2021.
Note: this citation may be lacking information needed for this citation format:
No year of publication.
Vancouver:
Choi C. Change of DNA methylation status in response to environmental stress : 環境に応答したDNAメチル化の変化; カンキョウ ニ オウトウシタ DNA メチルカ ノ ヘンカ. [Internet] [Thesis]. Nara Institute of Science and Technology / 奈良先端科学技術大学院大学; [cited 2021 Mar 01].
Available from: http://hdl.handle.net/10061/4135.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
No year of publication.
Council of Science Editors:
Choi C. Change of DNA methylation status in response to environmental stress : 環境に応答したDNAメチル化の変化; カンキョウ ニ オウトウシタ DNA メチルカ ノ ヘンカ. [Thesis]. Nara Institute of Science and Technology / 奈良先端科学技術大学院大学; Available from: http://hdl.handle.net/10061/4135
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
No year of publication.
11.
Wada, Yuko.
Biochemical properties and physiological function of DNA methyltransferases from tobacco plants : タバコDNAメチル化酵素の生化学的特徴と生理機能; タバコ DNA メチルカ コウソ ノ セイカガクテキ トクチョウ ト セイリ キノウ.
Degree: Nara Institute of Science and Technology / 奈良先端科学技術大学院大学
URL: http://hdl.handle.net/10061/2817
Subjects/Keywords: DNA methylation
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Wada, Y. (n.d.). Biochemical properties and physiological function of DNA methyltransferases from tobacco plants : タバコDNAメチル化酵素の生化学的特徴と生理機能; タバコ DNA メチルカ コウソ ノ セイカガクテキ トクチョウ ト セイリ キノウ. (Thesis). Nara Institute of Science and Technology / 奈良先端科学技術大学院大学. Retrieved from http://hdl.handle.net/10061/2817
Note: this citation may be lacking information needed for this citation format:
No year of publication.
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Wada, Yuko. “Biochemical properties and physiological function of DNA methyltransferases from tobacco plants : タバコDNAメチル化酵素の生化学的特徴と生理機能; タバコ DNA メチルカ コウソ ノ セイカガクテキ トクチョウ ト セイリ キノウ.” Thesis, Nara Institute of Science and Technology / 奈良先端科学技術大学院大学. Accessed March 01, 2021.
http://hdl.handle.net/10061/2817.
Note: this citation may be lacking information needed for this citation format:
No year of publication.
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Wada, Yuko. “Biochemical properties and physiological function of DNA methyltransferases from tobacco plants : タバコDNAメチル化酵素の生化学的特徴と生理機能; タバコ DNA メチルカ コウソ ノ セイカガクテキ トクチョウ ト セイリ キノウ.” Web. 01 Mar 2021.
Note: this citation may be lacking information needed for this citation format:
No year of publication.
Vancouver:
Wada Y. Biochemical properties and physiological function of DNA methyltransferases from tobacco plants : タバコDNAメチル化酵素の生化学的特徴と生理機能; タバコ DNA メチルカ コウソ ノ セイカガクテキ トクチョウ ト セイリ キノウ. [Internet] [Thesis]. Nara Institute of Science and Technology / 奈良先端科学技術大学院大学; [cited 2021 Mar 01].
Available from: http://hdl.handle.net/10061/2817.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
No year of publication.
Council of Science Editors:
Wada Y. Biochemical properties and physiological function of DNA methyltransferases from tobacco plants : タバコDNAメチル化酵素の生化学的特徴と生理機能; タバコ DNA メチルカ コウソ ノ セイカガクテキ トクチョウ ト セイリ キノウ. [Thesis]. Nara Institute of Science and Technology / 奈良先端科学技術大学院大学; Available from: http://hdl.handle.net/10061/2817
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
No year of publication.

University of Manchester
12.
Villalba De la pena, Mariana.
Phenotypic plasticity and DNA methylation in
arthropods.
Degree: 2020, University of Manchester
URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:323182
► In the thesis presented here a variety of methods and approaches are used to describe methylation profiles, in different tissues and stages, and its potential…
(more)
▼ In the thesis presented here a variety of methods
and approaches are used to describe
methylation profiles, in
different tissues and stages, and its potential role in plasticity
and thermal response in the cockroach Diploptera punctata and two
water flea species: Daphnia magna and Daphnia lumholtzi. In the
viviparous cockroach Diploptera punctata I studied how metabolic
rate and life-history traits respond to temperature. I found that
the metabolic rate is adaptive and highly plastic in response to
temperature. Several his- tory traits were also affected by
temperature, for example, developmental time, number of surviving
offspring and time to reach sexual maturity. In Diploptera punctata
I further describe, for the first time, tissue-specific high
methylation levels, and show hydroxymethylation presence
exclusively in the brain. I also demostrate that
DNA methylation
global levels and patterns are responsive to the environment, as
they respond to diet and temperature. However,
methylation patterns
are also shown to be linked to the genotype. In Daphnia magna, I
investigated the
methylation profiles in the oocyte and early
embryogenic stages where I found evidence of differentially
methylated sites among stages, but more importantly, we found
evidence of almost full
methylation reprogramming in this species.
Finally, high morphological plasticity in response to predator
presence is reported in the LA2 Daphnia lumholtzi clone, among with
the first draft genome and transcriptome of this
species.
Advisors/Committee Members: KNIGHT, CHRISTOPHER CG, Hager, Reinmar, Knight, Christopher.
Subjects/Keywords: DNA methylation; Diploptera punctata; Daphnia
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Villalba De la pena, M. (2020). Phenotypic plasticity and DNA methylation in
arthropods. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:323182
Chicago Manual of Style (16th Edition):
Villalba De la pena, Mariana. “Phenotypic plasticity and DNA methylation in
arthropods.” 2020. Doctoral Dissertation, University of Manchester. Accessed March 01, 2021.
http://www.manchester.ac.uk/escholar/uk-ac-man-scw:323182.
MLA Handbook (7th Edition):
Villalba De la pena, Mariana. “Phenotypic plasticity and DNA methylation in
arthropods.” 2020. Web. 01 Mar 2021.
Vancouver:
Villalba De la pena M. Phenotypic plasticity and DNA methylation in
arthropods. [Internet] [Doctoral dissertation]. University of Manchester; 2020. [cited 2021 Mar 01].
Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:323182.
Council of Science Editors:
Villalba De la pena M. Phenotypic plasticity and DNA methylation in
arthropods. [Doctoral Dissertation]. University of Manchester; 2020. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:323182

Vanderbilt University
13.
Whitley, Brent Tyler.
Aflatoxin B1 adducts with d(ATCGAT)2 and d(ATGCAT)2: Do methylation and hydroxymethylation influence reaction stoichiometry?.
Degree: MS, Chemistry, 2013, Vanderbilt University
URL: http://hdl.handle.net/1803/12018
► Aflatoxin B1 (AFB1), a carcinogenic mycotoxin produced by the common agricultural contaminant A. flavus, has been implicated in the high rates of hepatocellular carcinoma observed…
(more)
▼ Aflatoxin B1 (AFB1), a carcinogenic mycotoxin produced by the common agricultural contaminant A. flavus, has been implicated in the high rates of hepatocellular carcinoma observed in some developing countries. Upon ingestion, AFB1 is metabolized by liver monooxygenases to AFB1-exo-8,9-epoxide prior to reacting with
DNA. AFB1 epoxide preferentially reacts at CpG islands, where it is attacked by the N7 atom of dG. The primary lesion found in vitro is trans-8,9-dihydro-(N7-guanyl)-9-hydroxy AFB1. The stoichiometry of this reaction has been characterized for the two oligonucleotide sequence isomers 5’-ATCGAT-3’ and 5’-ATGCAT-3’. In the sequence 5’-ATCGAT-3’, the AFB1 adduct occupies the 5’ side of dG, blocking the addition of a second equivalent of epoxide to the complementary strand. This results in a 1:1 AFB1:oligonucleotide limiting stoichiometry in the formation of the 5’-ATC(AFB)GAT-3’. However, a second equivalent of epoxide is free to bind to the complementary strand of 5’-ATGCAT-3’, giving a 2:1 stoichiometry. Since CpG islands are frequently
subject to epigenetic regulation, it is important to know whether the reaction stoichiometry is altered by cytosine
methylation or hydroxymethylation. In this work, 5’-[AT(5-methyl-dC)GAT]2-3’, 5’-[ATG(5-methyl-dC)AT]2-3’, 5’-[AT(5-hydroxymethyl-dC)GAT]2-3’, and 5’-[ATG(5-hydroxymethyl-dC)AT]2-3’ were each reacted with an excess of AFB1 epoxide and analyzed by HPLC. The equilibrium concentrations of the unreacted oligonucleotide and the adduct were used to calculate the limiting stoichiometry of the reaction.
Methylation and hydroxymethylation did not influence reaction stoichiometry.
Advisors/Committee Members: Carmelo Rizzo (committee member), Michael Stone (Committee Chair).
Subjects/Keywords: methylation; DNA adducts; Aflatoxin; carcinogen
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Whitley, B. T. (2013). Aflatoxin B1 adducts with d(ATCGAT)2 and d(ATGCAT)2: Do methylation and hydroxymethylation influence reaction stoichiometry?. (Thesis). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/12018
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):
Whitley, Brent Tyler. “Aflatoxin B1 adducts with d(ATCGAT)2 and d(ATGCAT)2: Do methylation and hydroxymethylation influence reaction stoichiometry?.” 2013. Thesis, Vanderbilt University. Accessed March 01, 2021.
http://hdl.handle.net/1803/12018.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Whitley, Brent Tyler. “Aflatoxin B1 adducts with d(ATCGAT)2 and d(ATGCAT)2: Do methylation and hydroxymethylation influence reaction stoichiometry?.” 2013. Web. 01 Mar 2021.
Vancouver:
Whitley BT. Aflatoxin B1 adducts with d(ATCGAT)2 and d(ATGCAT)2: Do methylation and hydroxymethylation influence reaction stoichiometry?. [Internet] [Thesis]. Vanderbilt University; 2013. [cited 2021 Mar 01].
Available from: http://hdl.handle.net/1803/12018.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Whitley BT. Aflatoxin B1 adducts with d(ATCGAT)2 and d(ATGCAT)2: Do methylation and hydroxymethylation influence reaction stoichiometry?. [Thesis]. Vanderbilt University; 2013. Available from: http://hdl.handle.net/1803/12018
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University
14.
Abu Bakar, Nur Suhada.
Transgenerational inheritance of epigenetic regulation by Unstable factor for orange1 in maize.
Degree: 2013, Penn State University
URL: https://submit-etda.libraries.psu.edu/catalog/18226
► Epigenetics is the study of heritable changes in gene expression or cellular phenotype that are attributable to mechanisms other than changes in DNA sequence. In…
(more)
▼ Epigenetics is the study of heritable changes in gene expression or cellular phenotype that are attributable to mechanisms other than changes in
DNA sequence. In plants, epigenetic regulation plays a key role in various biological processes such as paramutation, genomic imprinting, and gene silencing. Although numerous studies have been done to elucidate the underlying mechanism behind epigenetic regulation, many questions are yet to be answered. In this study, the maize pericarp color1 (p1) gene is used as a reporter to study the nature of epigenetic inheritance of stable tissue-specific gene expression. An allele of p1, P1-wr was used as a phenotypic marker to investigate the transgenerational inheritance of Unstable factor for orange1 (Ufo1-1)-induced changes in maize. Ufo1-1 activates p1 expression and thus phlobaphenes are ectopically accumulated throughout the plant body indicating loss of tissue-specificity of p1 expression. Previous study has shown that Ufo1-1-induced pigmentation phenotypes are only observed in a subset of P1-wr; Ufo1-1 plants. Interestingly, within this subset, pigmentation level is highly variable. Also, it has been shown that this increased pigmentation is associated with changes of
DNA methylation pattern in the P1-wr distal enhancer and intron sequences. Moreover, the increased pigmentation phenotypes in the backcross population are accompanied by progressive loss of P1-wr
methylation from one generation to the next. Thus, the objective of this study was to investigate the inheritance of Ufo1-1 through genotyping using linked markers. This information was then compared to the Ufo1-1-induced phenotypes to verify the epigenetic regulation of P1-wr by Ufo1-1. The second objective of this study was to establish a qRT-PCR based assay to investigate
DNA methylation level at p1 in different genotypes of P1-wr; Ufo1-1 plants. The relative
methylation levels provided better understanding of the correlation between the range of pericarp pigmentation in P1-wr; Ufo1-1 plants and their respective
DNA methylation states at p1.
Advisors/Committee Members: Surinder Chopra, Thesis Advisor/Co-Advisor, Majid R Foolad, Thesis Advisor/Co-Advisor, Dawn S Luthe, Thesis Advisor/Co-Advisor.
Subjects/Keywords: epigenetics; DNA methylation; inheritance
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Abu Bakar, N. S. (2013). Transgenerational inheritance of epigenetic regulation by Unstable factor for orange1 in maize. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/18226
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):
Abu Bakar, Nur Suhada. “Transgenerational inheritance of epigenetic regulation by Unstable factor for orange1 in maize.” 2013. Thesis, Penn State University. Accessed March 01, 2021.
https://submit-etda.libraries.psu.edu/catalog/18226.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Abu Bakar, Nur Suhada. “Transgenerational inheritance of epigenetic regulation by Unstable factor for orange1 in maize.” 2013. Web. 01 Mar 2021.
Vancouver:
Abu Bakar NS. Transgenerational inheritance of epigenetic regulation by Unstable factor for orange1 in maize. [Internet] [Thesis]. Penn State University; 2013. [cited 2021 Mar 01].
Available from: https://submit-etda.libraries.psu.edu/catalog/18226.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Abu Bakar NS. Transgenerational inheritance of epigenetic regulation by Unstable factor for orange1 in maize. [Thesis]. Penn State University; 2013. Available from: https://submit-etda.libraries.psu.edu/catalog/18226
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Newcastle
15.
Barzideh, Jaleh.
Epigenetic modification in human male germ line.
Degree: MPhil, 2010, University of Newcastle
URL: http://hdl.handle.net/1959.13/923302
► Masters Research - Master of Philosophy (MPhil)
The purpose of this study was to examine the methylation status of human sperm DNA in relation to…
(more)
▼ Masters Research - Master of Philosophy (MPhil)
The purpose of this study was to examine the methylation status of human sperm DNA in relation to the functional competence of these cells. In order to achieve this aim discontinuous Percoll gradient density centrifugation was used to generate sperm populations that were either normal (high-density Percoll fraction) or functionally impaired (low density Percoll fraction). The methylation status of these cells was then examined using HPLC, immunocytochemistry or flow cytometry and ultimately correlated with additional markers reflecting the tendency of these cells to default to an intrinsic apoptotic pathway. The results of this study suggest that the mitochondrial genome is heavily methylated during spermatogenesis possibly as a means of suppressing expression of the paternal mitochondrial genome following fertilization. Extensive methylation of the mitochondrial genome appeared to be a ubiquitous, consistent feature of these cells and was present in both the high and low quality sperm populations. By contrast, the methylation status of the nuclear genome appeared to change dramatically in relation to the functional competence of the spermatozoa, such that defective cells exhibited a statistically significant increase in nuclear DNA methylation. Such hypermethylation of defective cells was confirmed by all 3 of the techniques used in this study (HPLC, immunocytochemistry and flow cytometry). Different patterns of 5-methylcytosine expression were observed sperm nuclei by immunocytochemistry and possible interpretations offered in terms of the packaging of chromosomes into the nucleus during sperm differentiation. Furthermore, the methylation status of these cells was negatively correlated with various aspects of sperm function including sperm motility and the tendency of these cells to become apoptotic as reflected by the expression of activated caspases and Annexin-V binding. In addition the hypermethylation of human spermatozoa was highly correlated with their capacity to bind chromomycin3A, a marker that reflects the efficiency of sperm chromatin protamination. These results clearly suggest that defective human spermatozoa are associated with hypermethylation of their nuclear genome, possibly as a consequence of the defective control of DNA methyltransferase activity during spermiogenesis. These hypermethylated cells are functionally defective and exhibit a tendency to default to an apoptotic cascade that features activation of endogenous caspases, phosphatidylserine exteriorization and DNA damage. These results have important implications for the safety of assisted conception procedures that frequently involve the forced fertilization of oocytes with defective spermatozoa
Advisors/Committee Members: University of Newcastle. Faculty of Health, School of Biomedical Sciences and Pharmacy.
Subjects/Keywords: DNA; methylation; human sperm
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Barzideh, J. (2010). Epigenetic modification in human male germ line. (Masters Thesis). University of Newcastle. Retrieved from http://hdl.handle.net/1959.13/923302
Chicago Manual of Style (16th Edition):
Barzideh, Jaleh. “Epigenetic modification in human male germ line.” 2010. Masters Thesis, University of Newcastle. Accessed March 01, 2021.
http://hdl.handle.net/1959.13/923302.
MLA Handbook (7th Edition):
Barzideh, Jaleh. “Epigenetic modification in human male germ line.” 2010. Web. 01 Mar 2021.
Vancouver:
Barzideh J. Epigenetic modification in human male germ line. [Internet] [Masters thesis]. University of Newcastle; 2010. [cited 2021 Mar 01].
Available from: http://hdl.handle.net/1959.13/923302.
Council of Science Editors:
Barzideh J. Epigenetic modification in human male germ line. [Masters Thesis]. University of Newcastle; 2010. Available from: http://hdl.handle.net/1959.13/923302

Oregon State University
16.
Vargason, Jeffrey M.
The effect of cytosine methylation on DNA structure.
Degree: PhD, Biochemistry and Biophysics, 2002, Oregon State University
URL: http://hdl.handle.net/1957/32388
► DNA methylation is common in prokaryotes and eukaryotes and has been implicated in various biological roles including gene silencing, X-chromosome inactivation, and genomic imprinting. 5-methylcytosine…
(more)
▼ DNA methylation is common in prokaryotes and eukaryotes and has been
implicated in various biological roles including gene silencing, X-chromosome
inactivation, and genomic imprinting. 5-methylcytosine the "fifth base" of the
genetic code comprises 1-3% of the human genome and is primarily found on
cytosines within the context of the CpG sequence. Although progress has been
made in understanding the biological roles of 5-methylcytosine, we are only
beginning to uncover how it changes the local structure and global conformation of
DNA. This thesis deals with the local perturbations in structure and hydration and
the global conformational changes induced by the presence of 5-methylcytosine in
DNA as determined by single crystal x-ray diffraction.
5-methylcytosine induces a novel conformation in the structure of duplex
DNA. This conformation has characteristics of both the A-
DNA and B-
DNA
conformations as well as some unique defining characteristics. This distinct duplex
provides a structural rationale for the increased rate of deamination in 5-methylcytosine relative to cytosine. In addition to this novel conformation, 5-methylcytosine stabilizes intermediates within the B-
DNA to A-
DNA transition pathway, thus providing a crystallographic map of the transition from B-
DNA to A-
DNA.
5-methylcytosine was also used as a tool to probe the stabilizing features of
the
DNA four-way junction (known as the Holliday junction). The first crystal
structures of Holliday junctions were found serendipitously while studying duplex
DNA. The
DNA four-way junction formation in these crystals was thought to be
stabilized by a network of sequence dependent hydrogen bonds at the junction
crossover. In this thesis, 5-methylcytosine was used to perturb these hydrogen
bonds; however, the junction persisted, suggesting that there is flexibility in the
types of sequences that can accommodate junction formation in the crystal, as well
as, flexibility in the global structure of the junction. Overall, this work describes
the effects of 5-methylcytosine on the local and global structure and hydration of
DNA structure, as well as raising some interesting questions regarding the
biological impact of
methylation induced
DNA structure.
Advisors/Committee Members: Ho, Pui Shing (advisor).
Subjects/Keywords: DNA – Methylation
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APA (6th Edition):
Vargason, J. M. (2002). The effect of cytosine methylation on DNA structure. (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/32388
Chicago Manual of Style (16th Edition):
Vargason, Jeffrey M. “The effect of cytosine methylation on DNA structure.” 2002. Doctoral Dissertation, Oregon State University. Accessed March 01, 2021.
http://hdl.handle.net/1957/32388.
MLA Handbook (7th Edition):
Vargason, Jeffrey M. “The effect of cytosine methylation on DNA structure.” 2002. Web. 01 Mar 2021.
Vancouver:
Vargason JM. The effect of cytosine methylation on DNA structure. [Internet] [Doctoral dissertation]. Oregon State University; 2002. [cited 2021 Mar 01].
Available from: http://hdl.handle.net/1957/32388.
Council of Science Editors:
Vargason JM. The effect of cytosine methylation on DNA structure. [Doctoral Dissertation]. Oregon State University; 2002. Available from: http://hdl.handle.net/1957/32388

Oregon State University
17.
Bononi, Judy.
Effect of hemi-methylated CG dinucleotide on Z-DNA stability : crystallographic and solution studies.
Degree: MS, Biochemistry and Biophysics, 1994, Oregon State University
URL: http://hdl.handle.net/1957/35264
Subjects/Keywords: DNA – Methylation
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Bononi, J. (1994). Effect of hemi-methylated CG dinucleotide on Z-DNA stability : crystallographic and solution studies. (Masters Thesis). Oregon State University. Retrieved from http://hdl.handle.net/1957/35264
Chicago Manual of Style (16th Edition):
Bononi, Judy. “Effect of hemi-methylated CG dinucleotide on Z-DNA stability : crystallographic and solution studies.” 1994. Masters Thesis, Oregon State University. Accessed March 01, 2021.
http://hdl.handle.net/1957/35264.
MLA Handbook (7th Edition):
Bononi, Judy. “Effect of hemi-methylated CG dinucleotide on Z-DNA stability : crystallographic and solution studies.” 1994. Web. 01 Mar 2021.
Vancouver:
Bononi J. Effect of hemi-methylated CG dinucleotide on Z-DNA stability : crystallographic and solution studies. [Internet] [Masters thesis]. Oregon State University; 1994. [cited 2021 Mar 01].
Available from: http://hdl.handle.net/1957/35264.
Council of Science Editors:
Bononi J. Effect of hemi-methylated CG dinucleotide on Z-DNA stability : crystallographic and solution studies. [Masters Thesis]. Oregon State University; 1994. Available from: http://hdl.handle.net/1957/35264
18.
Gentil, Marie-Véronique.
Contrôle épigénétique du risque de montaison chez une plante de grande culture : la betterave sucrière : mise au point d'une stratégie de caractérisation d'épiallèles associés à la sensibilité à la montaison en vue de l'élaboration d'un test de sélection : Epigenetic control of the bolting risk in a crop plant : sugar-beet : the development of a strategy to characterize epialleles associated with bolting sensivity, with a view to implementation as a selection tool.
Degree: Docteur es, Physiologie et biologie des organismes et des populations, 2009, Université d'Orléans
URL: http://www.theses.fr/2009ORLE2005
► Chez les plantes, les processus de développement global et de plasticité développementale sont contrôlés par des mécanismes épigénétiques. La méthylation de l’ADN peut présenter un…
(more)
▼ Chez les plantes, les processus de développement global et de plasticité développementale sont contrôlés par des mécanismes épigénétiques. La méthylation de l’ADN peut présenter un polymorphisme (épiallèles) qui est une source possible de biomarqueurs pour la sélection de génotypes d’intérêt agronomique. Pourtant, la recherche de tels biomarqueurs n’a pas encore été initiée. Dans ce contexte, nos objectifs ont concerné l'élaboration d'une stratégie pour la mise en évidence d’un contrôle épigénétique lors d’un processus développemental chez la betterave sucrière (Beta vulgaris altissima), ainsi que la recherche des biomarqueurs épigénétiques associés. Cette stratégie a d’abord été appliquée à la morphogenèse in vitro, sur trois lignées cellulaires de betterave sucrière. Une relation a pu être établie entre le niveau de méthylation de l’ADN et les propriétés morphogénétiques des lignées. Des biomarqueurs de morphogenèse in vitro ont ainsi été identifiés. La même stratégie a ensuite été appliquée in planta à la même espèce. L'existence d'un contrôle épigénétique lors de la vernalisation et de la dévernalisation chez plusieurs hybrides de betterave sucrière, avec des sensibilités à la montaison différentes, a été démontrée. Nous suggérons que l’amplitude et la cinétique des variations épigénétiques contrôlent l’induction de la montaison et sa rapidité, confirmant ainsi le rôle de la méthylation de l’ADN dans ce processus. Les loci cibles de ces remaniements de la méthylation de l'ADN lors de la vernalisation ont été définis. Un criblage a enfin permis d’identifier de potentiels biomarqueurs épigénétiques de la sensibilité à la montaison en vue de la mise au point d’un futur test de sélection agronomique.
In plants, the processes of global development and of developmental plasticity are controlled by epigenetic mechanisms. Polymorphism in DNA methylation (leading to epialleles) is a possible source of biomarkers for the selection of genotypes of agronomic interest. Until now, however, the search for such biomarkers has not been undertaken. Against this background, our objectives were to develop a strategy to investigate the existence of epigenetic control during a developmental process in sugar-beet (Beta vulgaris altissima) and to search for associated epigenetic biomarkers. The strategy was first applied to three sugar-beet cell lines, where we were able to established a relationship between the level of DNA methylation and the morphogenetic statue of the lines, and thus to identified a number of biomarkers for in vitro morphogenesis. We then applied the same strategy in planta in the same species and demonstrated the existence of epigenetic control (DNA methylation) during vernalization and devernalization in several sugar-beet hybrids that differed for bolting susceptibility. We propose that the scale and kinetics of epigenetic modifications control the induction and the rapidity of bolting, confirming the role of DNA methylation in this process. We have identified a number of target loci for these changes in DNA…
Advisors/Committee Members: Hagège, Daniel (thesis director), Maury, Stéphane (thesis director).
Subjects/Keywords: Méthylation de l'ADN; DNA methylation
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Gentil, M. (2009). Contrôle épigénétique du risque de montaison chez une plante de grande culture : la betterave sucrière : mise au point d'une stratégie de caractérisation d'épiallèles associés à la sensibilité à la montaison en vue de l'élaboration d'un test de sélection : Epigenetic control of the bolting risk in a crop plant : sugar-beet : the development of a strategy to characterize epialleles associated with bolting sensivity, with a view to implementation as a selection tool. (Doctoral Dissertation). Université d'Orléans. Retrieved from http://www.theses.fr/2009ORLE2005
Chicago Manual of Style (16th Edition):
Gentil, Marie-Véronique. “Contrôle épigénétique du risque de montaison chez une plante de grande culture : la betterave sucrière : mise au point d'une stratégie de caractérisation d'épiallèles associés à la sensibilité à la montaison en vue de l'élaboration d'un test de sélection : Epigenetic control of the bolting risk in a crop plant : sugar-beet : the development of a strategy to characterize epialleles associated with bolting sensivity, with a view to implementation as a selection tool.” 2009. Doctoral Dissertation, Université d'Orléans. Accessed March 01, 2021.
http://www.theses.fr/2009ORLE2005.
MLA Handbook (7th Edition):
Gentil, Marie-Véronique. “Contrôle épigénétique du risque de montaison chez une plante de grande culture : la betterave sucrière : mise au point d'une stratégie de caractérisation d'épiallèles associés à la sensibilité à la montaison en vue de l'élaboration d'un test de sélection : Epigenetic control of the bolting risk in a crop plant : sugar-beet : the development of a strategy to characterize epialleles associated with bolting sensivity, with a view to implementation as a selection tool.” 2009. Web. 01 Mar 2021.
Vancouver:
Gentil M. Contrôle épigénétique du risque de montaison chez une plante de grande culture : la betterave sucrière : mise au point d'une stratégie de caractérisation d'épiallèles associés à la sensibilité à la montaison en vue de l'élaboration d'un test de sélection : Epigenetic control of the bolting risk in a crop plant : sugar-beet : the development of a strategy to characterize epialleles associated with bolting sensivity, with a view to implementation as a selection tool. [Internet] [Doctoral dissertation]. Université d'Orléans; 2009. [cited 2021 Mar 01].
Available from: http://www.theses.fr/2009ORLE2005.
Council of Science Editors:
Gentil M. Contrôle épigénétique du risque de montaison chez une plante de grande culture : la betterave sucrière : mise au point d'une stratégie de caractérisation d'épiallèles associés à la sensibilité à la montaison en vue de l'élaboration d'un test de sélection : Epigenetic control of the bolting risk in a crop plant : sugar-beet : the development of a strategy to characterize epialleles associated with bolting sensivity, with a view to implementation as a selection tool. [Doctoral Dissertation]. Université d'Orléans; 2009. Available from: http://www.theses.fr/2009ORLE2005

University of Tasmania
19.
De Paoli-Iseppi, R.
Molecular biomarkers for seabird age estimation : implications for ecological monitoring.
Degree: 2019, University of Tasmania
URL: https://eprints.utas.edu.au/32756/3/De_Paoli_Iseppi_whole_thesis.pdf
;
https://eprints.utas.edu.au/32756/2/De%20Paoli%20open%20articles.zip
;
https://eprints.utas.edu.au/32756/1/De%20Paoli%20restricted%20article.zip
;
De
Paoli-Iseppi,
R
ORCID:
0000-0001-7724-9144
<https://orcid.org/0000-0001-7724-9144>
2019
,
'Molecular
biomarkers
for
seabird
age
estimation
:
implications
for
ecological
monitoring',
PhD
thesis,
University
of
Tasmania.
► Seabirds are widely used as an indicator species to track important changes in ecosystems. The key data required for monitoring include (i) population trends (ii)…
(more)
▼ Seabirds are widely used as an indicator species to track important changes in ecosystems. The key data required for monitoring include (i) population trends (ii) status, including demographic properties such as age structure and reproductive performance. Most seabirds have no outward or easily identifiable marks to age individuals and there are currently no robust molecular methods for age estimation in birds. Instead, individuals must be marked by leg rings as chicks to establish known-age populations, which is a labour intensive and expensive process. Long-term monitoring of some populations of birds has produced only small numbers of individuals for which there is a known age, highlighting the urgent need to identify alternative aging techniques.
In this thesis, I describe the development and testing of age-related differentially methylated positions (aDMPs) as a minimally invasive method for the estimation of chronological age in the Short-tailed shearwater (Ardenna tenuirostris). Recent studies have revealed novel examples of DNA methylation (DNAm) age association in several mammalian species, indicating the potential for developing DNAm age biomarkers for a broad range of wild animals. Emerging technologies for measuring epigenetic signals have also enhanced our ability to study age-related DNAm changes.
I assessed DNAm in several shearwater genes that have shown age-related DNAm changes in mammals. In birds ranging in age from chicks (months old) to 21 years, bisulphite treated blood and feather DNA was sequenced. The sequences allowed DNAm analysis across 67 CpG sites in 13 target gene regions. Despite the identification of some weakly correlated aDMPs, the majority had no clear association with age and statistical analysis using a penalised lasso approach did not produce an accurate ageing model. Our data indicated that some age-related signatures identified in orthologous mammalian genes are not conserved in the shearwater and that an alternative technique would be required to progress in this area.
The alternative approach that I tried was digital restriction enzyme analysis of methylation (DREAM). I quantified DNAm in whole blood samples from a total of 71 known-age shearwater using DREAM. This method measures DNAm levels at thousands of CpG dinucleotides throughout the genome. We identified seven CpG sites with DNAm levels that correlated with age. A model based on these relationships estimated age within a mean of 2.8 years of known age, based on validation estimates from models created by repeated sampling of training and validation data subsets. Longitudinal observation of individuals re-sampled over 1 or 2 years generally showed an increase in estimated age (6/7 cases). These seven aDMPs were then selected for use in a more cost-effective, targeted approach using a next generation sequencing assay. I validated and then generated chronological age estimates in a large set of known, minimum and unknown age individuals sourced from our study population.
Using targeted NGS we confirmed…
Subjects/Keywords: DNA; methylation; seabirds; epigenetics; ageing
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
De Paoli-Iseppi, R. (2019). Molecular biomarkers for seabird age estimation : implications for ecological monitoring. (Thesis). University of Tasmania. Retrieved from https://eprints.utas.edu.au/32756/3/De_Paoli_Iseppi_whole_thesis.pdf ; https://eprints.utas.edu.au/32756/2/De%20Paoli%20open%20articles.zip ; https://eprints.utas.edu.au/32756/1/De%20Paoli%20restricted%20article.zip ; De Paoli-Iseppi, R ORCID: 0000-0001-7724-9144 <https://orcid.org/0000-0001-7724-9144> 2019 , 'Molecular biomarkers for seabird age estimation : implications for ecological monitoring', PhD thesis, University of Tasmania.
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):
De Paoli-Iseppi, R. “Molecular biomarkers for seabird age estimation : implications for ecological monitoring.” 2019. Thesis, University of Tasmania. Accessed March 01, 2021.
https://eprints.utas.edu.au/32756/3/De_Paoli_Iseppi_whole_thesis.pdf ; https://eprints.utas.edu.au/32756/2/De%20Paoli%20open%20articles.zip ; https://eprints.utas.edu.au/32756/1/De%20Paoli%20restricted%20article.zip ; De Paoli-Iseppi, R ORCID: 0000-0001-7724-9144 <https://orcid.org/0000-0001-7724-9144> 2019 , 'Molecular biomarkers for seabird age estimation : implications for ecological monitoring', PhD thesis, University of Tasmania..
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
De Paoli-Iseppi, R. “Molecular biomarkers for seabird age estimation : implications for ecological monitoring.” 2019. Web. 01 Mar 2021.
Vancouver:
De Paoli-Iseppi R. Molecular biomarkers for seabird age estimation : implications for ecological monitoring. [Internet] [Thesis]. University of Tasmania; 2019. [cited 2021 Mar 01].
Available from: https://eprints.utas.edu.au/32756/3/De_Paoli_Iseppi_whole_thesis.pdf ; https://eprints.utas.edu.au/32756/2/De%20Paoli%20open%20articles.zip ; https://eprints.utas.edu.au/32756/1/De%20Paoli%20restricted%20article.zip ; De Paoli-Iseppi, R ORCID: 0000-0001-7724-9144 <https://orcid.org/0000-0001-7724-9144> 2019 , 'Molecular biomarkers for seabird age estimation : implications for ecological monitoring', PhD thesis, University of Tasmania..
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
De Paoli-Iseppi R. Molecular biomarkers for seabird age estimation : implications for ecological monitoring. [Thesis]. University of Tasmania; 2019. Available from: https://eprints.utas.edu.au/32756/3/De_Paoli_Iseppi_whole_thesis.pdf ; https://eprints.utas.edu.au/32756/2/De%20Paoli%20open%20articles.zip ; https://eprints.utas.edu.au/32756/1/De%20Paoli%20restricted%20article.zip ; De Paoli-Iseppi, R ORCID: 0000-0001-7724-9144 <https://orcid.org/0000-0001-7724-9144> 2019 , 'Molecular biomarkers for seabird age estimation : implications for ecological monitoring', PhD thesis, University of Tasmania.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Columbia University
20.
Wang, Ya.
Statistical Methods for Epigenetic Data.
Degree: 2019, Columbia University
URL: https://doi.org/10.7916/d8-9z87-ts07
► DNA methylation plays a crucial role in human health, especially cancer. Traditional DNA methylation analysis aims to identify CpGs/genes with differential methylation (DM) between experimental…
(more)
▼ DNA methylation plays a crucial role in human health, especially cancer. Traditional DNA methylation analysis aims to identify CpGs/genes with differential methylation (DM) between experimental groups. Differential variability (DV) was recently observed that contributes to cancer heterogeneity and was also shown to be essential in detecting early DNA methylation alterations, notably epigenetic field defects. Moreover, studies have demonstrated that environmental factors may modify the effect of DNA methylation on health outcomes, or vice versa. Therefore, this dissertation seeks to develop new statistical methods for epigenetic data focusing on DV and interactions when efficient analytical tools are lacking. First, as neighboring CpG sites are usually highly correlated, we introduced a new method to detect differentially methylated regions (DMRs) that uses combined DM and DV signals between diseased and non-diseased groups. Next, using both DM and DV signals, we considered the problem of identifying epigenetic field defects, when CpG-site-level DM and DV signals are minimal and hard to be detected by existing methods. We proposed a weighted epigenetic distance-based method that accumulates CpG-site-level DM and DV signals in a gene. Here DV signals were captured by a pseudo-data matrix constructed using centered quadratic methylation measures. CpG-site-level association signal annotations were introduced as weights in distance calculations to up-weight signal CpGs and down-weight noise CpGs to further boost the study power. Lastly, we extended the weighted epigenetic distance-based method to incorporate DNA methylation by environment interactions in the detection of overall association between DNA methylation and health outcomes. A pseudo-data matrix was constructed with cross-product terms between DNA methylation and environmental factors that is able to capture their interactions. The superior performance of the proposed methods were shown through intensive simulation studies and real data applications to multiple DNA methylation data.
Subjects/Keywords: Biometry; Epigenetics; DNA – Methylation; Statistics
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Wang, Y. (2019). Statistical Methods for Epigenetic Data. (Doctoral Dissertation). Columbia University. Retrieved from https://doi.org/10.7916/d8-9z87-ts07
Chicago Manual of Style (16th Edition):
Wang, Ya. “Statistical Methods for Epigenetic Data.” 2019. Doctoral Dissertation, Columbia University. Accessed March 01, 2021.
https://doi.org/10.7916/d8-9z87-ts07.
MLA Handbook (7th Edition):
Wang, Ya. “Statistical Methods for Epigenetic Data.” 2019. Web. 01 Mar 2021.
Vancouver:
Wang Y. Statistical Methods for Epigenetic Data. [Internet] [Doctoral dissertation]. Columbia University; 2019. [cited 2021 Mar 01].
Available from: https://doi.org/10.7916/d8-9z87-ts07.
Council of Science Editors:
Wang Y. Statistical Methods for Epigenetic Data. [Doctoral Dissertation]. Columbia University; 2019. Available from: https://doi.org/10.7916/d8-9z87-ts07
21.
Pollak, Adam Jacob.
Rethinking How Proteins Move Along DNA.
Degree: 2014, University of California – eScholarship, University of California
URL: http://www.escholarship.org/uc/item/1nc2s6fx
► Site-specific DNA binding by proteins is critical for diverse biological processes, including gene regulation, DNA repair, DNA replication, immune response, and others. In most cases,…
(more)
▼ Site-specific DNA binding by proteins is critical for diverse biological processes, including gene regulation, DNA repair, DNA replication, immune response, and others. In most cases, this binding is preceded by facilitated diffusion, where the protein passively moves along nonspecific DNA (DNA lacking particular binding sites) in search of its site(s). Details concerning the mechanisms of how proteins move along DNA remain unclear yet actively investigated. Several reports claim that facilitated diffusion relies primarily on sliding and hopping processes, where the protein moves along the trajectory of the DNA helix. However, these mechanisms involve redundant searches over local regions (up to hundreds of base pairs), while site finding in vivo requires searches of hundreds of thousands of base pairs. We "rethink" facilitated diffusion in two ways: 1) what are the mechanisms available for facilitated diffusion? And 2) how are these mechanisms driven by proteins' specific biological context? We investigate the facilitated diffusion properties of E. coli DNA adenine methyltransferase (Dam), which methylates palindromic 5'-GATC-3' sites on the N6 position of adenine. We use an in vitro steady-state processivity assay, where the ability of the enzyme to catalyze multiple methylations within a single binding event is quantified. Our results are suggestive of a new mechanism, intersegmental hopping, where proteins hop between regions of a single DNA molecule that are looped together. This mechanism allows for efficient long-range movements, and is similar to other ambiguously described looping mechanisms proposed in recent reports. Dam's low cellular copy number and need to move along the entire bacterial chromosome (i.e. its biological context) is ideally accommodated by this mechanism, as we imagine will be true for other proteins with low copy numbers and rare sites. We also demonstrate that EcoRI ENase uses an extreme sliding mechanism, previously hypothesized to be unlikely. EcoRI ENase and EcoRV ENase both cut incoming phage DNA as part of type II restriction modification systems, and are shown here to use distinct facilitated diffusion mechanisms. We argue that their site finding mechanisms are complimentary, ensuring robust phage defense, again demonstrating the connection between facilitated diffusion and biological context. Furthermore, we show that Dam is able to move along DNA in spite of pre-incubated protein roadblocks. Provocatively, DNA-loop inducing roadblocks, such as the histone-like Lrp, can improve the translocation process by specifically enhancing intersegmental hopping. Therefore, this mechanism is proposed as a general way for proteins to move along the crowded, compacted genomic DNA landscape. Dam was previously demonstrated to undergo intrasite processivity, where the methylation of both strands within a single GATC site proceeds by a single Dam enzyme dramatically reorienting itself while switching between strands. Here, we show that intrasite processivity is only possible on long stretches…
Subjects/Keywords: Chemistry; Biochemistry; DNA; Enzymes; Methylation
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Pollak, A. J. (2014). Rethinking How Proteins Move Along DNA. (Thesis). University of California – eScholarship, University of California. Retrieved from http://www.escholarship.org/uc/item/1nc2s6fx
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):
Pollak, Adam Jacob. “Rethinking How Proteins Move Along DNA.” 2014. Thesis, University of California – eScholarship, University of California. Accessed March 01, 2021.
http://www.escholarship.org/uc/item/1nc2s6fx.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Pollak, Adam Jacob. “Rethinking How Proteins Move Along DNA.” 2014. Web. 01 Mar 2021.
Vancouver:
Pollak AJ. Rethinking How Proteins Move Along DNA. [Internet] [Thesis]. University of California – eScholarship, University of California; 2014. [cited 2021 Mar 01].
Available from: http://www.escholarship.org/uc/item/1nc2s6fx.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Pollak AJ. Rethinking How Proteins Move Along DNA. [Thesis]. University of California – eScholarship, University of California; 2014. Available from: http://www.escholarship.org/uc/item/1nc2s6fx
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of North Carolina – Greensboro
22.
Rumph, Candie.
Aberrant DNA methylation and patterns of histone
modifications at the WNT5A Promoter B in osteosarcoma cells.
Degree: 2014, University of North Carolina – Greensboro
URL: http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=16604
► WNT5A is a secreted ligand involved in differentiation, proliferation, cell movement and apoptosis. WNT5A is often misregulated in cancer and is known to be involved…
(more)
▼ WNT5A is a secreted ligand involved in
differentiation, proliferation, cell movement and apoptosis. WNT5A
is often misregulated in cancer and is known to be involved in
cancer metastasis. The focus of this study was on the possible
epigenetic regulation of WNT5A expression in osteosarcoma cells. In
this study, I analyzed WNT5A regulation from its two major
transcription start sites, termed Promoter A and Promoter B. The
levels of promoter B transcripts were reduced in the osteosarcoma
cell line, U20S, and in primary osteosarcoma tissue of three
individuals, compared to normal osteoblasts. To determine if this
decrease in Promoter B activity in U20S is due to
DNA methylation,
I analyzed six CpG islands associated with Promoter B by bisulfite
sequencing. Results show that Regions 1 and 2 are unmethylated,
Regions 3, 4, 5 are methylated and Region 6, which includes the
Promoter B start of transcription, is partially methylated. The
DNA
methylation pattern is similar to the pattern determined in another
osteosarcoma cell line SaOS-2. However, Region 6 of U20S is only
25% methylated, whereas Region 6 of SaOS-2 is 62% methylated. The
level of
methylation is negatively correlated with Promoter B
transcript levels, indicating that Region 6
methylation affects
transcription. Histone modifications were examined for their
involvement in Promoter A and Promoter B activity by chromatin
immunoprecipitation (ChIP) assays. H3K4me3, an activating histone
mark, showed high enrichment in Promoter A and reduced enrichment
in Promoter B Region 6 of U20S cells, indicating that H3K4me3 has a
role in the reduction of Promoter B activity. H3K27me3 and H3K9me3,
repressive histone marks, were not differentially enriched on
Promoters A and B. H3K27me3 was enriched on Regions 3 and 4 located
upstream of the Promoter B start of transcription. Overall, these
results suggest that WNT5A Promoter B activity is reduced in
osteosarcoma by both histone modification and
DNA methylation.;
WNT5A, Osteosarcoma Cells,
DNA methylation
Advisors/Committee Members: Karen Katula (advisor).
Subjects/Keywords: Wnt proteins; DNA – Methylation; Osteosarcoma
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Chicago ·
MLA ·
Vancouver ·
CSE |
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to Zotero / EndNote / Reference
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APA (6th Edition):
Rumph, C. (2014). Aberrant DNA methylation and patterns of histone
modifications at the WNT5A Promoter B in osteosarcoma cells. (Masters Thesis). University of North Carolina – Greensboro. Retrieved from http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=16604
Chicago Manual of Style (16th Edition):
Rumph, Candie. “Aberrant DNA methylation and patterns of histone
modifications at the WNT5A Promoter B in osteosarcoma cells.” 2014. Masters Thesis, University of North Carolina – Greensboro. Accessed March 01, 2021.
http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=16604.
MLA Handbook (7th Edition):
Rumph, Candie. “Aberrant DNA methylation and patterns of histone
modifications at the WNT5A Promoter B in osteosarcoma cells.” 2014. Web. 01 Mar 2021.
Vancouver:
Rumph C. Aberrant DNA methylation and patterns of histone
modifications at the WNT5A Promoter B in osteosarcoma cells. [Internet] [Masters thesis]. University of North Carolina – Greensboro; 2014. [cited 2021 Mar 01].
Available from: http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=16604.
Council of Science Editors:
Rumph C. Aberrant DNA methylation and patterns of histone
modifications at the WNT5A Promoter B in osteosarcoma cells. [Masters Thesis]. University of North Carolina – Greensboro; 2014. Available from: http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=16604

University of Toronto
23.
Strong, Emma.
Rearrangements of 7q11.23: disorders of the epigenome.
Degree: PhD, 2017, University of Toronto
URL: http://hdl.handle.net/1807/93053
► Rearrangements of a 1.5 Mb region on chromosome 7q11.23 produce two distinct multisystem developmental disorders. Deletion of this region causes Williams-Beuren syndrome (WS; MIM 194050)…
(more)
▼ Rearrangements of a 1.5 Mb region on chromosome 7q11.23 produce two distinct multisystem developmental disorders. Deletion of this region causes Williams-Beuren syndrome (WS; MIM 194050) and the reciprocal duplication causes 7q11.23 duplication syndrome (Dup7; MIM 609757). Individuals with WS and Dup7 show an array of contrasting and overlapping phenotypes, including variable intellectual disability, Attention Deficit Hyperactivity Disorder, social disinhibition and anxiety. Rearrangements at 7q11.23 provide an excellent model for studying gene dosage sensitivity in neurodevelopment and the molecular mechanism of related neuropsychiatric disorders.
Little is known about how rearrangements at 7q11.23 contribute to the manifestation of specific phenotypes in these disorders. Several genes at this locus have been associated with epigenetic mechanisms and parent-of-origin dependent expression of specific phenotypes have been noted. To understand the impact of rearrangements at 7q11.23 on the epigenome, I have studied parent-of-origin dependent expression of individual genes at this locus, as well as genome-wide DNA methylation.
Here I provide the first evidence to show that rearrangements of 7q11.23 result in dose-dependent changes to DNA methylation in peripheral blood from children with WS and Dup7. Aberrant DNA methylation was also identified in cortical neurons from a mouse model of WS, suggesting that DNA methylation is likely disrupted in neural tissue from individuals with 7q11.23 rearrangements. Using a combination of rare atypical deletions and duplications of 7q11.23 and mice with hemizygous deletions of Gtf2i and Gtf2ird1, I provide the first evidence that the TFII-I family of transcription factors contribute to aberrant DNA methylation when deleted or duplicated. Lastly, I identified monoallelic expression of Fkbp6, a gene involved in meiosis and piRNA biogenesis, in mouse and human cortical tissue, which may contribute to parent-of-origin dependent expression of phenotypes in WS. These data suggest WS and Dup7 are disorders of the epigenome, and that DNA methylation may be an important mechanism in the pathogenesis of these disorders.
2018-12-19 00:00:00
Advisors/Committee Members: Osborne, Lucy R, Molecular and Medical Genetics.
Subjects/Keywords: 7q11.23; DNA methylation; Imprinting; 0369
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Strong, E. (2017). Rearrangements of 7q11.23: disorders of the epigenome. (Doctoral Dissertation). University of Toronto. Retrieved from http://hdl.handle.net/1807/93053
Chicago Manual of Style (16th Edition):
Strong, Emma. “Rearrangements of 7q11.23: disorders of the epigenome.” 2017. Doctoral Dissertation, University of Toronto. Accessed March 01, 2021.
http://hdl.handle.net/1807/93053.
MLA Handbook (7th Edition):
Strong, Emma. “Rearrangements of 7q11.23: disorders of the epigenome.” 2017. Web. 01 Mar 2021.
Vancouver:
Strong E. Rearrangements of 7q11.23: disorders of the epigenome. [Internet] [Doctoral dissertation]. University of Toronto; 2017. [cited 2021 Mar 01].
Available from: http://hdl.handle.net/1807/93053.
Council of Science Editors:
Strong E. Rearrangements of 7q11.23: disorders of the epigenome. [Doctoral Dissertation]. University of Toronto; 2017. Available from: http://hdl.handle.net/1807/93053

University of Melbourne
24.
NOVAKOVIC, BORIS.
Epigenetics of human placental development and pregnancy-associated disease.
Degree: 2013, University of Melbourne
URL: http://hdl.handle.net/11343/38191
► INTRODUCTION: Epigenetics literally means ‘above DNA’ and refers to the study of molecular modifications that control gene expression and chromatin structure. DNA methylation, the most…
(more)
▼ INTRODUCTION: Epigenetics literally means ‘above DNA’ and refers to the study of molecular modifications that control gene expression and chromatin structure. DNA methylation, the most extensively studied epigenetic modification, is involved in both the maintenance of chromosome stability and gene expression. Due to its role in gene expression, tissue specific DNA methylation patterns are assumed to reflect the function of a specific gene in a particular tissue.
The human placenta facilitates the interaction between the mother and the fetus, including nutrient and oxygen exchange, waste removal and the protection of the fetus from the maternal immune response. Due to its role at the feto-maternal interface, the placenta is exposed to several environmental factors with the capacity to alter placental function and fetal development. Many of these effects are likely to be mediated by epigenetic change. Linking specific environmental exposures, genetic, and epigenetic variation to maternal and neonatal outcomes may provide valuable mechanistic insights into the role of placental dysfunction in pregnancy-associated disease and later health. Therefore, DNA methylation studies in healthy and disease placentas have the potential to identify new genes associated with placental function. The aim of this PhD was to take a genome-scale approach to characterise gene promoter methylation in the normal human placenta.
MATERIALS AND METHODS: Several different tissues, primary cells and cell lines were used in this study. These included placental villi from first, second and third trimester, purified first trimester villous and extravillous cytotrophoblasts, choriocarcinoma and trophoblast-derived cell lines. Placental tissue, neonatal cord blood and maternal peripheral blood serum from twin births, collected as part of the Peri/post-natal Epigenetic Twins Study (PETS) cohort, were used for two aims of this project. Environmental data on maternal nutrition and supplementation during pregnancy were collected through questionnaires or measured in maternal blood serum.
DNA methylation levels were analysed on the genome-scale level using the Illumina Infinium HumanMethylation27 BeadChip, and at the gene-specific level using the SEQUENOM MassARRAY EpiTYPER platform.
RESULTS: Genome-scale DNA methylation analysis of normal human placenta from first to third trimester identified dynamic changes in DNA methylation patterns in response to increasing gestation and environmental/stochastic factors. Most of the changes were observed at genes involved in immune cell communication and signalling, which likely reflects the change in cell composition as well as the differing immunological interactions between the mother and the fetus as the pregnancy progresses. Furthermore, increasing inter-individual variation in methylation level at certain CpG sites over gestation…
Subjects/Keywords: epigenetics; DNA methylation; placenta; environment
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
NOVAKOVIC, B. (2013). Epigenetics of human placental development and pregnancy-associated disease. (Doctoral Dissertation). University of Melbourne. Retrieved from http://hdl.handle.net/11343/38191
Chicago Manual of Style (16th Edition):
NOVAKOVIC, BORIS. “Epigenetics of human placental development and pregnancy-associated disease.” 2013. Doctoral Dissertation, University of Melbourne. Accessed March 01, 2021.
http://hdl.handle.net/11343/38191.
MLA Handbook (7th Edition):
NOVAKOVIC, BORIS. “Epigenetics of human placental development and pregnancy-associated disease.” 2013. Web. 01 Mar 2021.
Vancouver:
NOVAKOVIC B. Epigenetics of human placental development and pregnancy-associated disease. [Internet] [Doctoral dissertation]. University of Melbourne; 2013. [cited 2021 Mar 01].
Available from: http://hdl.handle.net/11343/38191.
Council of Science Editors:
NOVAKOVIC B. Epigenetics of human placental development and pregnancy-associated disease. [Doctoral Dissertation]. University of Melbourne; 2013. Available from: http://hdl.handle.net/11343/38191

University of Southern California
25.
Hinoue, Toshinori.
DNA hypermethylation: its role in colorectal tumorigenesis
and potential clinical applications.
Degree: PhD, Biochemistry & Molecular Biology, 2011, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/238424/rec/2066
► Aberrant DNA hypermethylation of CpG islands is a common and early event in colorectal tumorigenesis. Promoter DNA hypermethylation is associated with transcriptional gene silencing, and…
(more)
▼ Aberrant
DNA hypermethylation of CpG islands is a
common and early event in colorectal tumorigenesis. Promoter
DNA
hypermethylation is associated with transcriptional gene silencing,
and can contribute to tumorigenesis when it occurs at a critical
tumor suppressor gene. A distinct subset of colorectal cancers
display the CpG island methylator phenotype (CIMP), characterized
by an exceptionally high frequency of cancer-specific
DNA
hypermethylation. Recent studies have shown that an activating
mutation of BRAF (BRAFV600E) is specifically associated with CIMP.
We used colorectal cancer cell lines and primary tumors to
elucidate the molecular mechanisms for the association. We first
examined whether expression of BRAFV600E causes CIMP-specific
DNA
hypermethylation in the CIMP-negative, BRAF wild-type COLO 320DM
colorectal cancer cell line. We found that stable expression of
BRAFV600E is not sufficient to induce CIMP in our system. Secondly,
considering the alternative possibility, we searched for genes
whose
DNA hypermethylation was tightly linked to BRAFV600E and CIMP
in colorectal cancer. Intriguingly, we identified CIMP-dependent
DNA hypermethylation and transcriptional inactivation of IGFBP7, a
mediator of BRAFV600E-induced cellular senescence and apoptosis.
Inactivation of IGFBP7 by
DNA hypermethylation may accommodate
BRAFV600E by blocking the senescence pathway. Therefore, our work
provides a mechanistic rationale for the association between
BRAFV600E and CIMP. Moreover, in an attempt to further characterize
CIMP-associated
DNA hypermethylation, we have quantitatively
determined
DNA methylation status of 27,578 CpG sites located in
14,495 gene promoters in 100 colorectal tumors and 8 normal
mucosae. Through stringent statistical methods, we have identified
cancer-specific
DNA hypermethylation of 1,036 genes, of which 601
show CIMP-specific
DNA hypermethylation. We have also generated
gene expression data.; Our most comprehensive list of CIMP targets
and their expression data will help us understand the role of
CIMP-associated
DNA hypermethylation in colorectal tumorigenesis,
and provide the opportunity to study structural and sequence
characteristics of affected CpG islands. The latter might
ultimately give us insights into the underlying basis of
CIMP-associated
DNA hypermethylation. Finally, we have developed a
panel of novel cancer-specific
DNA methylation markers, which would
potentially be useful for early diagnosis of colorectal cancer
using a noninvasive stool
DNA test or a minimally invasive
blood-based assay.
Advisors/Committee Members: Laird, Peter W. (Committee Chair), Coetzee, Gerhard A. (Committee Member), Dubeau, Louis (Committee Member), Rice, Judd C. (Committee Member).
Subjects/Keywords: colorectal cancer; DNA methylation; CIMP
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Hinoue, T. (2011). DNA hypermethylation: its role in colorectal tumorigenesis
and potential clinical applications. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/238424/rec/2066
Chicago Manual of Style (16th Edition):
Hinoue, Toshinori. “DNA hypermethylation: its role in colorectal tumorigenesis
and potential clinical applications.” 2011. Doctoral Dissertation, University of Southern California. Accessed March 01, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/238424/rec/2066.
MLA Handbook (7th Edition):
Hinoue, Toshinori. “DNA hypermethylation: its role in colorectal tumorigenesis
and potential clinical applications.” 2011. Web. 01 Mar 2021.
Vancouver:
Hinoue T. DNA hypermethylation: its role in colorectal tumorigenesis
and potential clinical applications. [Internet] [Doctoral dissertation]. University of Southern California; 2011. [cited 2021 Mar 01].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/238424/rec/2066.
Council of Science Editors:
Hinoue T. DNA hypermethylation: its role in colorectal tumorigenesis
and potential clinical applications. [Doctoral Dissertation]. University of Southern California; 2011. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/238424/rec/2066

University of Hong Kong
26.
關駿傑.
Development and
application of a single mouse embryo DNA methylation-detection
assay.
Degree: 2014, University of Hong Kong
URL: http://hdl.handle.net/10722/197532
► During preimplantation embryonic development, imprinting genes are susceptible to methylation changes by artificial manipulation, which may lead to developmental abnormalities. In addition, environmental endocrine disruptors…
(more)
▼ During preimplantation embryonic development,
imprinting genes are susceptible to methylation changes by
artificial manipulation, which may lead to developmental
abnormalities. In addition, environmental endocrine disruptors
(EDs) in everyday household products are also found to perturb
fertility development and cause epigenetic aberrations. While
embryo supply is scarce and conventional epigenetic studies require
embryos in vast amount, an assay was developed in this study to
examine the methylation statuses of imprinting genes using DNA from
single mouse blastocysts cultured in-vitro or exposed to EDs.
Promoter CpG methylation patterns of three imprinting genes, small
nuclear ribonucleoprotein polypeptide N (SNRPN), paternally
expressed 3 (Peg3), and potassium voltage-gated channel 1
overlapping transcript 1 (Kcnq1ot1), were examined from genomic DNA
of a single mouse blastocyst. The genomic DNA was isolated and
treated with bisulfite modification to preserve the methylation
statuses. Afterwards, the DNA was subjected to whole genome
amplification (WGA). Methylation-specific polymerase chain reaction
(methyl-PCR) was performed with allele-specific primers; the
amplicons were cloned and sequenced. CpG methylations in SNRPN,
Peg3 and Kcnq1ot1 showed no statistical significant difference
(P>0.05; Mann Whitney U test) in both parental alleles between a
single genomic-amplified blastocyst and 20 non-amplified
blastocysts, indicating no artifact was being introduced during the
WGA procedure. Using the assay, it was revealed that blastocysts
cultured in-vitro expressed slight but nonsignificant deviation in
methylation rates to both parental alleles of SNRPN and Kcnq1ot1
except in single blastocysts, which displayed significant loss in
maternal methylation on SNRPN upon culturing. On the other hand,
paternal methylation profile of Peg3 appeared unaffected,
suggesting resistance to methylation perturbations induced by
in-vitro culturing. Despite that there was no significant
difference in overall methylation rates between in-vivo or in-vitro
developed blastocysts, certain CpG residues appeared to displayed
significant loss of methylation (LOM) or gain of methylation (GOM)
induced by in-vitro culture in all three genes being studied.
Furthermore, using the developed, assay the epigenetic effects of
three endocrine disruptors, simazine, propiconazole, and cadmium
chloride (CdCl2) on in-vitro cultured single blastocysts were
revealed. When compared to blastocysts cultured with KSOM+AA medium
as controls, CdCl2-treated blastocysts displayed the most
methylation aberrations in both alleles and within particular CpG
residues, possibly due to its dual effect in both hypermethylation
and hypomethylation across the methylome. Both simazine- and
propiconazole -treated blastocysts displayed overall methylation
significant defects were observed within particular CpG residues.
Overall, the assay used in this study allowed the comprehensive
investigation of methylome from the DNA extracted from a single
blastocyst.defects resembled to…
Subjects/Keywords: DNA -
Methylation
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
關駿傑. (2014). Development and
application of a single mouse embryo DNA methylation-detection
assay. (Thesis). University of Hong Kong. Retrieved from http://hdl.handle.net/10722/197532
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):
關駿傑. “Development and
application of a single mouse embryo DNA methylation-detection
assay.” 2014. Thesis, University of Hong Kong. Accessed March 01, 2021.
http://hdl.handle.net/10722/197532.
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):
關駿傑. “Development and
application of a single mouse embryo DNA methylation-detection
assay.” 2014. Web. 01 Mar 2021.
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Vancouver:
關駿傑. Development and
application of a single mouse embryo DNA methylation-detection
assay. [Internet] [Thesis]. University of Hong Kong; 2014. [cited 2021 Mar 01].
Available from: http://hdl.handle.net/10722/197532.
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:
關駿傑. Development and
application of a single mouse embryo DNA methylation-detection
assay. [Thesis]. University of Hong Kong; 2014. Available from: http://hdl.handle.net/10722/197532
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Not specified: Masters Thesis or Doctoral Dissertation
27.
Playfoot, Christopher James.
Genome defence in hypomethylated developmental contexts.
Degree: PhD, 2017, University of Edinburgh
URL: http://hdl.handle.net/1842/28783
► Retrotransposons constitute around 40% of the mammalian genome and their aberrant activation can have wide ranging detrimental consequences, both throughout development and into somatic lineages.…
(more)
▼ Retrotransposons constitute around 40% of the mammalian genome and their aberrant activation can have wide ranging detrimental consequences, both throughout development and into somatic lineages. DNA methylation is one of the major epigenetic mechanisms in mammals, and is essential in repressing retrotransposons throughout mammalian development. Yet during normal mouse embryonic development some cell lineages become extensively DNA hypomethylated and it is not clear how these cells maintain retrotransposon silencing in a globally hypomethylated genomic context. In this thesis I determine that hypomethylation in multiple contexts results in the consistent activation of only one gene in the mouse genome - Tex19.1. Thus if a generic compensatory mechanism for loss of DNA methylation exists in mice, it must function through this gene. Tex19.1-/- mice de-repress retrotransposons in the hypomethylated component of the placenta and in the mouse germline, and have developmental defects in these tissues. In this thesis I examine the mechanism of TEX19.1 mediated genome defence and the developmental consequences upon its removal. I show that TEX19.1 functions in repressing retrotransposons, at least in part, through physically interacting with the transcriptional co-repressor, KAP1. Tex19.1-/- ES cells have reduced levels of KAP1 bound retrotransposon chromatin and reduced levels of the repressive H3K9me3 modification at these loci. Furthermore, these subsets of retrotransposon loci are de-repressed in Tex19.1-/- placentas. Thus, my data indicates that mouse cells respond to hypomethylation by activating expression of Tex19.1, which in turn augments compensatory, repressive histone modifications at retrotransposon sequences, thereby helping developmentally hypomethylated cells to maintain genome stability. I next aimed to further elucidate the role of Tex19.1 in the developing hypomethylated placenta. I determine that Tex19.1-/- placental defects precede intrauterine growth restriction of the embryo and that alterations in mRNA abundance in E12.5 Tex19.1-/- placentas is likely in part due to genic transcriptional changes. De-repression of LINE- 1 is evident in these placentas and elements of the de-repressed subfamily are associated with significantly downregulated genes. If retrotransposon de-repression is contributing to developmental defects by interfering with gene expression remains to be determined, however I identify a further possible mechanism leading to placental developmental defects. I determine that Tex19.1-/- placentas have an increased innate immune response and I propose that this is contributing to the developmental defects observed. Developmental defects and retrotransposon de-repression are also observed in spermatogenesis in Tex19.1-/- testes, the molecular basis for which is unclear. I therefore investigate the possibility that the TEX19.1 interacting partners, the E3 ubiquitin ligase proteins, may be contributing to the phenotypes observed in Tex19.1- /- testes. I show that repression of MMERVK10C in the…
Subjects/Keywords: DNA methylation; Tex19.1; retrotransposons
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Playfoot, C. J. (2017). Genome defence in hypomethylated developmental contexts. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/28783
Chicago Manual of Style (16th Edition):
Playfoot, Christopher James. “Genome defence in hypomethylated developmental contexts.” 2017. Doctoral Dissertation, University of Edinburgh. Accessed March 01, 2021.
http://hdl.handle.net/1842/28783.
MLA Handbook (7th Edition):
Playfoot, Christopher James. “Genome defence in hypomethylated developmental contexts.” 2017. Web. 01 Mar 2021.
Vancouver:
Playfoot CJ. Genome defence in hypomethylated developmental contexts. [Internet] [Doctoral dissertation]. University of Edinburgh; 2017. [cited 2021 Mar 01].
Available from: http://hdl.handle.net/1842/28783.
Council of Science Editors:
Playfoot CJ. Genome defence in hypomethylated developmental contexts. [Doctoral Dissertation]. University of Edinburgh; 2017. Available from: http://hdl.handle.net/1842/28783

University of Edinburgh
28.
Perricone, Sara Maria.
The role of DNA methylation in transcriptional regulation.
Degree: PhD, 2015, University of Edinburgh
URL: http://hdl.handle.net/1842/17866
► In mammals, the correct spatio-temporal patterns of gene expression are coordinated by transcription factor networks in combination with epigenetic signalling pathways. CpG methylation is an…
(more)
▼ In mammals, the correct spatio-temporal patterns of gene expression are coordinated by transcription factor networks in combination with epigenetic signalling pathways. CpG methylation is an epigenetic modification of DNA involved in the heritable transmission of gene silencing patterns. Increasing evidence suggest a primary role for CpG methylation in the direct regulation of gene expression, at least for a subset of promoters. An example of this direct regulation is represented by the ectopic expression of genes involved in genome defence pathways upon global loss of methylation. However, the mechanistic relationship between CpG methylation and transcriptional regulation is not well understood. To explore this, we have applied Cap Analysis of Gene Expression (CAGE), to cells deficient in CpG methylation (Mouse Embryonic Fibroblasts with hypomorphic mutation of Dnmt1 ) and matched controls. This provides a quantitative, single nucleotide resolution, genome wide map of methylation responsive transcription initiation. Integrating this with RNA-seq, genome wide measures of CpG methylation and ChIP-seq for histone modifications in the same system, provides a detailed view of how reduced CpG methylation alters the chromatin and transcriptional landscape of the genome. Our results show dramatic shifts in the cellular RNA pool, with the pronounced up-regulation or de-repression of promoters in a specific sub-family of transposable elements. Tens of other genic and non-coding RNA promoters similarly show dramatic inductions. Contrary to a prior hypothesis, we found no evidence for increased rates of transcriptional initiation from anonymous genomic sites not previously implicated in promoter activity. Transcription initiation at CpG island promoters is generally unaffected by hypomethylation, however a set of TSSs located in CpG island shores and a class to transposable element overlapping TSSs do appear to be sensitive to methylation and are significantly up-regulated upon hypomethylation.
Subjects/Keywords: 572.8; DNA methylation; transcription; hypomethylation
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Perricone, S. M. (2015). The role of DNA methylation in transcriptional regulation. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/17866
Chicago Manual of Style (16th Edition):
Perricone, Sara Maria. “The role of DNA methylation in transcriptional regulation.” 2015. Doctoral Dissertation, University of Edinburgh. Accessed March 01, 2021.
http://hdl.handle.net/1842/17866.
MLA Handbook (7th Edition):
Perricone, Sara Maria. “The role of DNA methylation in transcriptional regulation.” 2015. Web. 01 Mar 2021.
Vancouver:
Perricone SM. The role of DNA methylation in transcriptional regulation. [Internet] [Doctoral dissertation]. University of Edinburgh; 2015. [cited 2021 Mar 01].
Available from: http://hdl.handle.net/1842/17866.
Council of Science Editors:
Perricone SM. The role of DNA methylation in transcriptional regulation. [Doctoral Dissertation]. University of Edinburgh; 2015. Available from: http://hdl.handle.net/1842/17866

University of Guelph
29.
Templeman, Colbey Jane.
Differential DNA Methylation of Seed Yield QTL in Intercontinental Mega-Environments in a Canadian x Chinese Soybean Population.
Degree: MS, Department of Plant Agriculture, 2019, University of Guelph
URL: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/16964
► DNA methylation is an epigenetic modification that can produce phenotypic changes that impact a plant’s adaptation to the environment. Sodium bisulfite sequencing was carried out…
(more)
▼ DNA methylation is an epigenetic modification that can produce phenotypic changes that impact a plant’s adaptation to the environment. Sodium bisulfite sequencing was carried out on the genomic regions associated with seed yield in multiple (QTLU) and specific (QTLSP) mega-environments (ME). One QTLU (Satt139) and one QTLSP (Satt063) were evaluated on source seed grown in three MEs (Canada, USA, and China in 2010) of four selected RILs (28, 47, 4 and 90) derived from OAC Millennium x Heinong 38, and the parents. The source seed was grown in two field locations (Woodstock and Elora, ON) in both 2012 and 2013. Demethylation was observed in RIL 47 (China) in the Satt063 (QTLSP) region when grown in Elora and Woodstock in 2013. Due to methodology limitations, further research on
DNA methylation is warranted to determine its role in the expression of yield QTL across different ME.
Advisors/Committee Members: Rajcan, Istvan (advisor).
Subjects/Keywords: Soybean; DNA methylation; Mega-environments
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Templeman, C. J. (2019). Differential DNA Methylation of Seed Yield QTL in Intercontinental Mega-Environments in a Canadian x Chinese Soybean Population. (Masters Thesis). University of Guelph. Retrieved from https://atrium.lib.uoguelph.ca/xmlui/handle/10214/16964
Chicago Manual of Style (16th Edition):
Templeman, Colbey Jane. “Differential DNA Methylation of Seed Yield QTL in Intercontinental Mega-Environments in a Canadian x Chinese Soybean Population.” 2019. Masters Thesis, University of Guelph. Accessed March 01, 2021.
https://atrium.lib.uoguelph.ca/xmlui/handle/10214/16964.
MLA Handbook (7th Edition):
Templeman, Colbey Jane. “Differential DNA Methylation of Seed Yield QTL in Intercontinental Mega-Environments in a Canadian x Chinese Soybean Population.” 2019. Web. 01 Mar 2021.
Vancouver:
Templeman CJ. Differential DNA Methylation of Seed Yield QTL in Intercontinental Mega-Environments in a Canadian x Chinese Soybean Population. [Internet] [Masters thesis]. University of Guelph; 2019. [cited 2021 Mar 01].
Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/16964.
Council of Science Editors:
Templeman CJ. Differential DNA Methylation of Seed Yield QTL in Intercontinental Mega-Environments in a Canadian x Chinese Soybean Population. [Masters Thesis]. University of Guelph; 2019. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/16964

University of Manchester
30.
Villalba De La Pena, Mariana.
Phenotypic plasticity and DNA methylation in arthropods.
Degree: PhD, 2019, University of Manchester
URL: https://www.research.manchester.ac.uk/portal/en/theses/phenotypic-plasticity-and-dna-methylation-in-arthropods(018d01cd-8fcc-496d-8856-1ea59e5c3200).html
;
https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.799391
► In the thesis presented here a variety of methods and approaches are used to describe methylation profiles, in different tissues and stages, and its potential…
(more)
▼ In the thesis presented here a variety of methods and approaches are used to describe methylation profiles, in different tissues and stages, and its potential role in plasticity and thermal response in the cockroach Diploptera punctata and two water flea species: Daphnia magna and Daphnia lumholtzi. In the viviparous cockroach Diploptera punctata I studied how metabolic rate and life-history traits respond to temperature. I found that the metabolic rate is adaptive and highly plastic in response to temperature. Several his- tory traits were also affected by temperature, for example, developmental time, number of surviving offspring and time to reach sexual maturity. In Diploptera punctata I further describe, for the first time, tissue-specific high methylation levels, and show hydroxymethylation presence exclusively in the brain. I also demostrate that DNA methylation global levels and patterns are responsive to the environment, as they respond to diet and temperature. However, methylation patterns are also shown to be linked to the genotype. In Daphnia magna, I investigated the methylation profiles in the oocyte and early embryogenic stages where I found evidence of differentially methylated sites among stages, but more importantly, we found evidence of almost full methylation reprogramming in this species. Finally, high morphological plasticity in response to predator presence is reported in the LA2 Daphnia lumholtzi clone, among with the first draft genome and transcriptome of this species.
Subjects/Keywords: DNA methylation; Diploptera punctata; Daphnia
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APA (6th Edition):
Villalba De La Pena, M. (2019). Phenotypic plasticity and DNA methylation in arthropods. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/phenotypic-plasticity-and-dna-methylation-in-arthropods(018d01cd-8fcc-496d-8856-1ea59e5c3200).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.799391
Chicago Manual of Style (16th Edition):
Villalba De La Pena, Mariana. “Phenotypic plasticity and DNA methylation in arthropods.” 2019. Doctoral Dissertation, University of Manchester. Accessed March 01, 2021.
https://www.research.manchester.ac.uk/portal/en/theses/phenotypic-plasticity-and-dna-methylation-in-arthropods(018d01cd-8fcc-496d-8856-1ea59e5c3200).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.799391.
MLA Handbook (7th Edition):
Villalba De La Pena, Mariana. “Phenotypic plasticity and DNA methylation in arthropods.” 2019. Web. 01 Mar 2021.
Vancouver:
Villalba De La Pena M. Phenotypic plasticity and DNA methylation in arthropods. [Internet] [Doctoral dissertation]. University of Manchester; 2019. [cited 2021 Mar 01].
Available from: https://www.research.manchester.ac.uk/portal/en/theses/phenotypic-plasticity-and-dna-methylation-in-arthropods(018d01cd-8fcc-496d-8856-1ea59e5c3200).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.799391.
Council of Science Editors:
Villalba De La Pena M. Phenotypic plasticity and DNA methylation in arthropods. [Doctoral Dissertation]. University of Manchester; 2019. Available from: https://www.research.manchester.ac.uk/portal/en/theses/phenotypic-plasticity-and-dna-methylation-in-arthropods(018d01cd-8fcc-496d-8856-1ea59e5c3200).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.799391
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