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You searched for +publisher:"U of Massachusetts : Med" +contributor:("Melissa J. Moore, PhD"). Showing records 1 – 3 of 3 total matches.

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1. Heyer, Erin E. Optimizing RNA Library Preparation to Redefine the Translational Status of 80S Monosomes: A Dissertation.

Degree: Biochemistry and Molecular Pharmacology, RNA Therapeutics Institute, 2015, U of Massachusetts : Med

Deep sequencing of strand-specific cDNA libraries is now a ubiquitous tool for identifying and quantifying RNAs in diverse sample types. The accuracy of conclusions drawn from these analyses depends on precise and quantitative conversion of the RNA sample into a DNA library suitable for sequencing. Here, we describe an optimized method of preparing strand-specific RNA deep sequencing libraries from small RNAs and variably sized RNA fragments obtained from ribonucleoprotein particle footprinting experiments or fragmentation of long RNAs. Because all enzymatic reactions were optimized and driven to apparent completion, sequence diversity and species abundance in the input sample are well preserved. This optimized method was used in an adapted ribosome-profiling approach to sequence mRNA footprints protected either by 80S monosomes or polysomes in S. cerevisiae. Contrary to popular belief, we show that 80S monosomes are translationally active as demonstrated by strong three-nucleotide phasing of monosome footprints across open reading frames. Most mRNAs exhibit some degree of monosome occupancy, with monosomes predominating on upstream ORFs, canonical ORFs shorter than ~590 nucleotides and any ORF for which the total time required to complete elongation is substantially shorter than the time required for initiation. Additionally, endogenous NMD targets tend to be monosome-enriched. Thus, rather than being inactive, 80S monosomes are significant contributors to overall cellular translation. Advisors/Committee Members: Melissa J. Moore, PhD.

Subjects/Keywords: High-Throughput Nucleotide Sequencing; Nucleotides; RNA; Gene Library; Open Reading Frames; Biochemistry; Bioinformatics; Cell Biology; Computational Biology; Genetics; Molecular Biology; Molecular Genetics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Heyer, E. E. (2015). Optimizing RNA Library Preparation to Redefine the Translational Status of 80S Monosomes: A Dissertation. (Doctoral Dissertation). U of Massachusetts : Med. Retrieved from http://escholarship.umassmed.edu/gsbs_diss/810

Chicago Manual of Style (16th Edition):

Heyer, Erin E. “Optimizing RNA Library Preparation to Redefine the Translational Status of 80S Monosomes: A Dissertation.” 2015. Doctoral Dissertation, U of Massachusetts : Med. Accessed December 02, 2020. http://escholarship.umassmed.edu/gsbs_diss/810.

MLA Handbook (7th Edition):

Heyer, Erin E. “Optimizing RNA Library Preparation to Redefine the Translational Status of 80S Monosomes: A Dissertation.” 2015. Web. 02 Dec 2020.

Vancouver:

Heyer EE. Optimizing RNA Library Preparation to Redefine the Translational Status of 80S Monosomes: A Dissertation. [Internet] [Doctoral dissertation]. U of Massachusetts : Med; 2015. [cited 2020 Dec 02]. Available from: http://escholarship.umassmed.edu/gsbs_diss/810.

Council of Science Editors:

Heyer EE. Optimizing RNA Library Preparation to Redefine the Translational Status of 80S Monosomes: A Dissertation. [Doctoral Dissertation]. U of Massachusetts : Med; 2015. Available from: http://escholarship.umassmed.edu/gsbs_diss/810

2. Anderson, Eric G. Single Molecule Visualization of the DEAH-Box ARPase Prp22 Interacting with the Spliceosome: A Dissertation.

Degree: Biochemistry and Molecular Pharmacology, RNA Therapeutics Institute, 2016, U of Massachusetts : Med

In eukaryotes, the spliceosome is a macromolecular ribonucleoprotein machine that excises introns from pre-mRNAs through two sequential transesterification reactions. The chemistry and fidelity of pre-mRNA splicing are dependent upon a series of spliceosomal rearrangements, which are mediated by trans-acting splicing factors. One key class of these factors is the DEAH-box ATPase subfamily of proteins, whose members couple ATP hydrolysis to promote RNP structural rearrangements within the spliceosome. This is typified by Prp22, which promotes release of the spliced mRNA from the spliceosome and ensures fidelity of the second step of splicing. This role is well documented through classical biochemical and yeast genetics methods. Yet very little is known regarding the comings and goings of Prp22 relative to the spliceosome. My thesis research investigated the dynamics of Prp22 during splicing by using single-molecule fluorescence methods that allowed direct observation of these events. To do this, I helped construct a toolkit that combined yeast genetics, chemical biology and Colocalization Single Molecule Spectroscopy (CoSMoS) with in vitro splicing assays. Specifically, my thesis research consisted of CoSMoS splicing experiments in which fluorescently labeled pre-mRNA, spliceosome components and Prp22 were directly visualized and analyzed. Using these methods, I found that Prp22’s interactions with the spliceosome are highly dynamic and reversible. By simultaneously monitoring Prp22 and individual spliceosome subcomplexes, I was able to frame these Prp22 binding events in context relative to specific steps in spliceosome assembly and splicing. These experiments provide insight into how Prp22 promotes mRNA release from the spliceosome and maintains splicing fidelity. Advisors/Committee Members: Melissa J. Moore, PhD.

Subjects/Keywords: Spliceosomes; DEAH-Box ARPase Prp22; Biochemistry, Biophysics, and Structural Biology; Structural Biology

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Anderson, E. G. (2016). Single Molecule Visualization of the DEAH-Box ARPase Prp22 Interacting with the Spliceosome: A Dissertation. (Doctoral Dissertation). U of Massachusetts : Med. Retrieved from http://escholarship.umassmed.edu/gsbs_diss/823

Chicago Manual of Style (16th Edition):

Anderson, Eric G. “Single Molecule Visualization of the DEAH-Box ARPase Prp22 Interacting with the Spliceosome: A Dissertation.” 2016. Doctoral Dissertation, U of Massachusetts : Med. Accessed December 02, 2020. http://escholarship.umassmed.edu/gsbs_diss/823.

MLA Handbook (7th Edition):

Anderson, Eric G. “Single Molecule Visualization of the DEAH-Box ARPase Prp22 Interacting with the Spliceosome: A Dissertation.” 2016. Web. 02 Dec 2020.

Vancouver:

Anderson EG. Single Molecule Visualization of the DEAH-Box ARPase Prp22 Interacting with the Spliceosome: A Dissertation. [Internet] [Doctoral dissertation]. U of Massachusetts : Med; 2016. [cited 2020 Dec 02]. Available from: http://escholarship.umassmed.edu/gsbs_diss/823.

Council of Science Editors:

Anderson EG. Single Molecule Visualization of the DEAH-Box ARPase Prp22 Interacting with the Spliceosome: A Dissertation. [Doctoral Dissertation]. U of Massachusetts : Med; 2016. Available from: http://escholarship.umassmed.edu/gsbs_diss/823

3. Roy, Christian K. Putting the Pieces Together: Exons and piRNAs: A Dissertation.

Degree: Biochemistry and Molecular Pharmacology, RNA Therapeutics Institute, 2014, U of Massachusetts : Med

Analysis of gene expression has undergone a technological revolution. What was impossible 6 years ago is now routine. High-throughput DNA sequencing machines capable of generating hundreds of millions of reads allow, indeed force, a major revision toward the study of the genome’s functional output—the transcriptome. This thesis examines the history of DNA sequencing, measurement of gene expression by sequencing, isoform complexity driven by alternative splicing and mammalian piRNA precursor biogenesis. Examination of these topics is framed around development of a novel RNA-templated DNA-DNA ligation assay (SeqZip) that allows for efficient analysis of abundant, complex, and functional long RNAs. The discussion focuses on the future of transcriptome analysis, development and applications of SeqZip, and challenges presented to biomedical researchers by extremely large and rich datasets. Advisors/Committee Members: Melissa J. Moore, PhD, Phillip D. Zamore, PhD.

Subjects/Keywords: DNA; Gene Expression; Gene Expression Profiling; High-Throughput Nucleotide Sequencing; Protein Isoforms; RNA; Small Interfering RNA; DNA Sequence Analysis; Transcriptome; Biochemistry; Bioinformatics; Computational Biology; Genetics; Genomics; Systems Biology

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Roy, C. K. (2014). Putting the Pieces Together: Exons and piRNAs: A Dissertation. (Doctoral Dissertation). U of Massachusetts : Med. Retrieved from http://escholarship.umassmed.edu/gsbs_diss/726

Chicago Manual of Style (16th Edition):

Roy, Christian K. “Putting the Pieces Together: Exons and piRNAs: A Dissertation.” 2014. Doctoral Dissertation, U of Massachusetts : Med. Accessed December 02, 2020. http://escholarship.umassmed.edu/gsbs_diss/726.

MLA Handbook (7th Edition):

Roy, Christian K. “Putting the Pieces Together: Exons and piRNAs: A Dissertation.” 2014. Web. 02 Dec 2020.

Vancouver:

Roy CK. Putting the Pieces Together: Exons and piRNAs: A Dissertation. [Internet] [Doctoral dissertation]. U of Massachusetts : Med; 2014. [cited 2020 Dec 02]. Available from: http://escholarship.umassmed.edu/gsbs_diss/726.

Council of Science Editors:

Roy CK. Putting the Pieces Together: Exons and piRNAs: A Dissertation. [Doctoral Dissertation]. U of Massachusetts : Med; 2014. Available from: http://escholarship.umassmed.edu/gsbs_diss/726

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