+publisher:"University of Texas – Austin" +contributor:("Iyer, Vishwanath R")

1. Polioudakis, Damon Constantine. Characterizing miRNA mediated regulation of proliferation.

Degree: PhD, Cell and Molecular Biology, 2014, University of Texas – Austin

► Cell proliferation is a fundamental biological process, and the ability of human cells to transition from a quiescent to proliferative state is essential for tissue… (more)

▼ Cell proliferation is a fundamental biological process, and the ability of human cells to transition from a quiescent to proliferative state is essential for tissue homeostasis. Most cells in eukaryotic organisms are in a quiescent state, but on appropriate physiological or pathological stimuli, many types of somatic cells may exit quiescence, re-enter the cell cycle and begin to proliferate. The ability of cells to remain viable while quiescent, exit quiescence and re-enter into the cell cycle is the basis for varied physiological processes such as wound healing, lymphocyte activation and hepatocyte regeneration, but is also a hallmark of cancer. The transition of mammalian cells from quiescence to proliferation is accompanied by the differential expression of several microRNAs (miRNAs) and transcription factors. Our understanding of miRNA biology has significantly improved, but the miRNA regulatory networks that govern cell proliferation are still largely unknown. We characterized a miR-22 Myc network that mediates proliferation through regulation of the interferon response and multiple cell cycle arrest genes. We identified several cell cycle arrest genes that regulate the effects of the tumor suppressor p53 as direct targets of miR-22, and discovered that miR-22 suppresses interferon gene expression. We go on to show that miR-22 is activated by the transcription factor Myc as quiescent cells enter proliferation, and that miR-22 represses the Myc transcriptional repressor MXD4, mediating a feed forward loop to elevate Myc expression levels. To more effectively determine miRNA targets, we utilized a combination of RNA-induced silencing complex immunoprecipitations and gene expression profiling. Using this approach for miR-191, we constructed an extensive transcriptome wide miR-191 target set. We show that miR-191 regulates proliferation, and targets multiple proto-oncogenes, including CDK9, NOTCH2, and RPS6KA3. Recent advances in determining miRNA targetomes have revealed widespread non-canonical miRNA-target pairing. We experimentally identified the transcriptome wide targets of miR-503, miR-103, and miR-494, and observed evidence of non-canonical target pairing for these miRNAs. We went on to confirm that miR-503 requires pairing outside of the canonical 5' seed region to directly target the oncogene DDHD2. Further bioinformatics analysis implicated miR-503 and DDHD2 in breast cancer tumorigenesis. Advisors/Committee Members: Iyer, Vishwanath R. (advisor).

Subjects/Keywords: miRNA; Genomics; Proliferation

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APA (6^th Edition):

Polioudakis, D. C. (2014). Characterizing miRNA mediated regulation of proliferation. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/25048

Chicago Manual of Style (16^th Edition):

Polioudakis, Damon Constantine. “Characterizing miRNA mediated regulation of proliferation.” 2014. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/25048.

MLA Handbook (7^th Edition):

Polioudakis, Damon Constantine. “Characterizing miRNA mediated regulation of proliferation.” 2014. Web. 20 Jan 2021.

Vancouver:

Polioudakis DC. Characterizing miRNA mediated regulation of proliferation. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2014. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/25048.

Council of Science Editors:

Polioudakis DC. Characterizing miRNA mediated regulation of proliferation. [Doctoral Dissertation]. University of Texas – Austin; 2014. Available from: http://hdl.handle.net/2152/25048

2. Morgan, Xochitl Chamorro. Eukaryotic transcriptional regulation : from data mining to transcriptional profiling.

Degree: PhD, Molecular Biology, 2008, University of Texas – Austin

URL: http://hdl.handle.net/2152/9709

► Survival of cells and organisms requires that each of thousands of genes is expressed at the correct time in development, in the correct tissue, and… (more)

▼ Survival of cells and organisms requires that each of thousands of genes is expressed at the correct time in development, in the correct tissue, and under the correct conditions. Transcription is the primary point of gene regulation. Genes are activated and repressed by transcription factors, which are proteins that become active through signaling, bind, sometimes cooperatively, to regulatory regions of DNA, and interact with other proteins such as chromatin remodelers. Yeast has nearly six thousand genes, several hundred of which are transcription factors; transcription factors comprise around 2000 of the 22,000 genes in the human genome. When and how these transcription factors are activated, as well as which subsets of genes they regulate, is a current, active area of research essential to understanding the transcriptional regulatory programs of organisms. We approached this problem in two divergent ways: first, an in silico study of human transcription factor combinations, and second, an experimental study of the transcriptional response of yeast mutants deficient in DNA repair. First, in order to better understand the combinatorial nature of transcription factor binding, we developed a data mining approach to assess whether transcription factors whose binding motifs were frequently proximal in the human genome were more likely to interact. We found many instances in the literature in which over-represented transcription factor pairs co-regulated the same gene, so we used co-citation to assess the utility of this method on a larger scale. We determined that over-represented pairs were more likely to be co-cited than would be expected by chance. Because proper repair of DNA is an essential and highly-conserved process in all eukaryotes, we next used cDNA microarrays to measure differentially expressed genes in eighteen yeast deletion strains with sensitivity to the DNA cross-linking agent methyl methane sulfonate (MMS); many of these mutants were transcription factors or DNA-binding proteins. Combining this data with tools such as chromatin immunoprecipitation, gene ontology analysis, expression profile similarity, and motif analysis allowed us to propose a model for the roles of Iki3 and of YML081W, a poorly-characterized gene, in DNA repair. Advisors/Committee Members: Iyer, Vishwanath R. (advisor).

Subjects/Keywords: Transcription factors; Transcriptional response; Transcriptional regulation; DNA repair; Transcription factor binding; Data mining; Human genome; Eukaryotes

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APA (6^th Edition):

Morgan, X. C. (2008). Eukaryotic transcriptional regulation : from data mining to transcriptional profiling. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/9709

Chicago Manual of Style (16^th Edition):

Morgan, Xochitl Chamorro. “Eukaryotic transcriptional regulation : from data mining to transcriptional profiling.” 2008. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/9709.

MLA Handbook (7^th Edition):

Morgan, Xochitl Chamorro. “Eukaryotic transcriptional regulation : from data mining to transcriptional profiling.” 2008. Web. 20 Jan 2021.

Vancouver:

Morgan XC. Eukaryotic transcriptional regulation : from data mining to transcriptional profiling. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2008. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/9709.

Council of Science Editors:

Morgan XC. Eukaryotic transcriptional regulation : from data mining to transcriptional profiling. [Doctoral Dissertation]. University of Texas – Austin; 2008. Available from: http://hdl.handle.net/2152/9709

3. Bhinge, Akshay Anant. A functional genomics approach to map transcriptional and post-transcriptional gene regulatory networks.

Degree: PhD, Cell and Molecular Biology, 2009, University of Texas – Austin

URL: http://hdl.handle.net/2152/6533

► It has been suggested that organismal complexity correlates with the complexity of gene regulation. Transcriptional control of gene expression is mediated by binding of regulatory… (more)

▼ It has been suggested that organismal complexity correlates with the complexity of gene regulation. Transcriptional control of gene expression is mediated by binding of regulatory proteins to cis-acting sequences on the genome. Hence, it is crucial to identify the chromosomal targets of transcription factors (TFs) to delineate transcriptional regulatory networks underlying gene expression programs. The development of ChIP-chip technology has enabled high throughput mapping of TF binding sites across the genome. However, there are many limitations to the technology including the availability of whole genome arrays for complex organisms such human or mouse. To circumvent these limitations, we developed the Sequence Tag Analysis of Genomic Enrichment (STAGE) methodology that is based on extracting short DNA sequences or “tags” from ChIP-enriched DNA. With improvements in sequencing technologies, we applied the recently developed ChIP-Seq technique i.e. ChIP followed by ultra high throughput sequencing, to identify binding sites for the TF E2F4 across the human genome. We identified previously uncharacterized E2F4 binding sites in intergenic regions and found that several microRNAs are potential E2F4 targets. Binding of TFs to their respective chromosomal targets requires access of the TF to its regulatory element, which is strongly influenced by nucleosomal remodeling. In order to understand nucleosome remodeling in response to transcriptional perturbation, we used ultra high throughput sequencing to map nucleosome positions in yeast that were subjected to heat shock or were grown normally. We generated nucleosome remodeling profiles across yeast promoters and found that specific remodeling patterns correlate with specific TFs active during the transcriptional reprogramming. Another important aspect of gene regulation operates at the post-transcriptional level. MicroRNAs (miRNAs) are ~22 nucleotide non-coding RNAs that suppress translation or mark mRNAs for degradation. MiRNAs regulate TFs and in turn can be regulated by TFs. We characterized a TF-miRNA network involving the oncofactor Myc and the miRNA miR-22 that suppresses the interferon pathway as primary fibroblasts enter a stage of rapid proliferation. We found that miR-22 suppresses the interferon pathway by inhibiting nuclear translocation of the TF NF-kappaB. Our results show how the oncogenic TF Myc cross-talks with other TF regulatory pathways via a miRNA intermediary. Advisors/Committee Members: Iyer, Vishwanath R. (advisor).

Subjects/Keywords: Gene regulatory networks; Gene regulation; Human genome; Gene mapping; Transcription factors; Transcription factor binding sites; ChIP-enriched DNA; DNA sequences; Sequence Tag Analysis of Genomic Enrichment (STAGE) methodology; Nucleosomal remodeling; MicroRNAs; Genomics

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APA (6^th Edition):

Bhinge, A. A. (2009). A functional genomics approach to map transcriptional and post-transcriptional gene regulatory networks. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/6533

Chicago Manual of Style (16^th Edition):

Bhinge, Akshay Anant. “A functional genomics approach to map transcriptional and post-transcriptional gene regulatory networks.” 2009. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/6533.

MLA Handbook (7^th Edition):

Bhinge, Akshay Anant. “A functional genomics approach to map transcriptional and post-transcriptional gene regulatory networks.” 2009. Web. 20 Jan 2021.

Vancouver:

Bhinge AA. A functional genomics approach to map transcriptional and post-transcriptional gene regulatory networks. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2009. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/6533.

Council of Science Editors:

Bhinge AA. A functional genomics approach to map transcriptional and post-transcriptional gene regulatory networks. [Doctoral Dissertation]. University of Texas – Austin; 2009. Available from: http://hdl.handle.net/2152/6533

University of Texas – Austin

4. Derryberry, Dakota Zipporah. Benchmarking of single nucleotide somatic variant calling.

Degree: MA, Cell and Molecular Biology, 2017, University of Texas – Austin

URL: http://hdl.handle.net/2152/62850

► Cancer, which affects hundreds of thousands of people worldwide every year and costs billions in treatment, is a disease caused by mutations that arise in… (more)

▼ Cancer, which affects hundreds of thousands of people worldwide every year and costs billions in treatment, is a disease caused by mutations that arise in somatic cell lines and contribute to abnormal and pathological behaviors and growth in cells. These mutations are called somatic variants and there are several types. The simplest somatic variants are single-nucleotide somatic variants, which differ between a patient’s tumor and normal DNA by only a single base pair. To better treat and understand cancer, clinicians and researchers respectively seek to identify and locate cancer-relevant mutations. The low cost and high throughput of next-generation sequencing methods has made this the preferred platform for somatic variant discovery and identification over the last five years. Despite its widespread adoption, much remains unknown about the reliability of this method. Benchmarking somatic variant calling pipelines, the topic of this thesis, is the process of attempting to fill this gap by quantifying the quality of the variant calling process in terms of the accuracy, precision, and reproducibility of results. In chapter one of this thesis, I present a review of current methods and benchmarking of single-nucleotide somatic variant calling. I begin with an overview of the variant calling process, from raw reads to high quality variant calls. Next, I discuss what is known about the quality of results produced by the computational variant discovery pipeline. Finally, I present open questions and possible areas of future research. In chapter two, I present original research concerning the filtering process at the end of the single-nucleotide somatic variant calling pipeline that attempts to distinguish between real somatic variant calls and errors. Using multiple sequencing runs from the same tumors and using concordance between runs as a measure of accuracy, I show that filters based on alignment features are the most effective at removing errors while keeping true variants. Advisors/Committee Members: Wilke, C. (Claus) (advisor), Iyer, Vishwanath R (committee member).

Subjects/Keywords: Benchmarking; Somatic mutation; Cancer; Next-gen sequencing; Variant calling; NGS

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

APA (6^th Edition):

Derryberry, D. Z. (2017). Benchmarking of single nucleotide somatic variant calling. (Masters Thesis). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/62850

Chicago Manual of Style (16^th Edition):

Derryberry, Dakota Zipporah. “Benchmarking of single nucleotide somatic variant calling.” 2017. Masters Thesis, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/62850.

MLA Handbook (7^th Edition):

Derryberry, Dakota Zipporah. “Benchmarking of single nucleotide somatic variant calling.” 2017. Web. 20 Jan 2021.

Vancouver:

Derryberry DZ. Benchmarking of single nucleotide somatic variant calling. [Internet] [Masters thesis]. University of Texas – Austin; 2017. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/62850.

Council of Science Editors:

Derryberry DZ. Benchmarking of single nucleotide somatic variant calling. [Masters Thesis]. University of Texas – Austin; 2017. Available from: http://hdl.handle.net/2152/62850

University of Texas – Austin

5. -7915-0313. From genome to genotype : regulation of the genome in glioblastoma multiforme and atrial fibrillation.

Degree: PhD, Microbiology, 2017, University of Texas – Austin

URL: http://dx.doi.org/10.26153/tsw/2199

► The modern era of genomics has made sequencing a genome nearly routine. Genomics has amassed huge amounts of somatic and disease mutation data, as a… (more)

▼ The modern era of genomics has made sequencing a genome nearly routine. Genomics has amassed huge amounts of somatic and disease mutation data, as a result, the character sequence of the human genome has been extensively studied. This information is having an impact on the standard of care in the clinical sphere, with an increasing number of patients and clinicians turning to sequencing data as a determinant of treatment regimen. Knowledge of human protein coding genes and gene expression patterns is extensive, though not absolute. Venturing outside the relatively well-defined protein-coding regions of the genome, much is undetermined. Genome wide association studies (GWAS) have identified many genetic polymorphisms in non-coding regions on the genome that contribute to disease risk. Understanding the mechanisms by which a non-coding polymorphism can cause a phenotype demands an understanding of the physical organization and structure of chromatin in the eukaryotic nucleus. Gene expression data from primary gliolbastoma multiforme tumors (GBM) has uncovered the existence of four molecular subtypes, which affects prognosis and response to treatment. With the goal of gaining an understanding of transcriptional regulation in brain cancer, we profiled post-translational modifications of histone H3 in primary GBM tumors using ChIP-seq, and profiled gene expression in these tumors as well. We used a hidden Markov Model approach to abstract common co-occurrences of histone modifications into chromatin states. We were able to identify signatures consistent with known chromatin regulatory motifs, such as enhancers, and a bivalent state, marked by an active and repressive histone modification. These states regulated expression in a subtype-specific manner, with the proneural subtype showing a protective signature, and the mesenchymal and classical subtypes presenting a signature of invasive cellular migration and angiogenesis. The bivalent and enhancer states controlled a gene expression signature strongly suggestive of glioma stem cells (GSCs), the cells thought to be self-renewing in GBM. As part of profiling gene expression in primary GBMs, we performed RNA-sequencing in primary normal human astrocytes and six GBM-derived commercially available cell lines. We identified widespread differences in expression between tumors and cell lines, as well as a gene interaction network that is common to tumors and cell lines, dominated by chromatin remodelers and Rho guanine exchange factors. Finally, in a pilot study of 400 patients with atrial fibrillation (AF), we identified several SNPs associated with probability of success of cardiac ablation, a surgical therapy for AF. We propose that examining the local topology between a SNP of interest and any long-range contacts will help identify regulatory regions that allow a non-coding SNP to have an effect on gene expression, and thus phenotype Advisors/Committee Members: Iyer, Vishwanath R. (advisor), Huibregtse, Jon (committee member), Tucker, Haley O (committee member), Ehrlich, Lauren IR (committee member), Wilke, Claus O (committee member).

Subjects/Keywords: Genomics; Glioblastoma; Atrial fibrillation; Cancer; Brain; Heart; Gene regulation

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APA (6^th Edition):

-7915-0313. (2017). From genome to genotype : regulation of the genome in glioblastoma multiforme and atrial fibrillation. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://dx.doi.org/10.26153/tsw/2199

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Chicago Manual of Style (16^th Edition):

-7915-0313. “From genome to genotype : regulation of the genome in glioblastoma multiforme and atrial fibrillation.” 2017. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://dx.doi.org/10.26153/tsw/2199.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

MLA Handbook (7^th Edition):

-7915-0313. “From genome to genotype : regulation of the genome in glioblastoma multiforme and atrial fibrillation.” 2017. Web. 20 Jan 2021.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Vancouver:

-7915-0313. From genome to genotype : regulation of the genome in glioblastoma multiforme and atrial fibrillation. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2017. [cited 2021 Jan 20]. Available from: http://dx.doi.org/10.26153/tsw/2199.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Council of Science Editors:

-7915-0313. From genome to genotype : regulation of the genome in glioblastoma multiforme and atrial fibrillation. [Doctoral Dissertation]. University of Texas – Austin; 2017. Available from: http://dx.doi.org/10.26153/tsw/2199

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

University of Texas – Austin

6. Bagchi, Dia Nicholson. The interplay between transcription, histone variants, and chromatin structure in Eukaryotes.

Degree: PhD, Cell and Molecular Biology, 2016, University of Texas – Austin

URL: http://hdl.handle.net/2152/68249

► Transcription is a fundamental process necessary for life. In Eukaryotes this process is shaped and constrained, in part, by the 3D structure of chromatin –the… (more)

Subjects/Keywords: H2A.Z; Swr1; Ino80; Nucleosomes; Histones; Transcription; TSS; NFR; NDR; Chromatin

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

APA (6^th Edition):

Bagchi, D. N. (2016). The interplay between transcription, histone variants, and chromatin structure in Eukaryotes. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/68249

Chicago Manual of Style (16^th Edition):

Bagchi, Dia Nicholson. “The interplay between transcription, histone variants, and chromatin structure in Eukaryotes.” 2016. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/68249.

MLA Handbook (7^th Edition):

Bagchi, Dia Nicholson. “The interplay between transcription, histone variants, and chromatin structure in Eukaryotes.” 2016. Web. 20 Jan 2021.

Vancouver:

Bagchi DN. The interplay between transcription, histone variants, and chromatin structure in Eukaryotes. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2016. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/68249.

Council of Science Editors:

Bagchi DN. The interplay between transcription, histone variants, and chromatin structure in Eukaryotes. [Doctoral Dissertation]. University of Texas – Austin; 2016. Available from: http://hdl.handle.net/2152/68249

University of Texas – Austin

7. Lee, Yaelim. Transcription factor networks and chromatin remodeler function in gene regulation on the eukaryotic genome.

Degree: PhD, Cell and Molecular Biology, 2018, University of Texas – Austin

URL: http://hdl.handle.net/2152/68547

► Numerous events – from histone modification and transcription factor binding to gene expression – take place on eukaryotic chromatin, while cells are constantly exposed to… (more)

▼ Numerous events – from histone modification and transcription factor binding to gene expression – take place on eukaryotic chromatin, while cells are constantly exposed to dynamic stimuli ranging from spatial and temporal cues to environmental and extracellular signals. The cell’s ability to respond and adjust accordingly is directly related to cell fitness and viability. With the advent of next-generation sequencing, investigating these events has been enabled at nucleotide resolution but across the entire genome. In this dissertation, I investigate changes on eukaryotic genomes including yeast and human, which are triggered by stress and by loss of a protein of interest, by analyzing genomics data generated mainly through next-generation sequencing. In Chapter 1, I determine how yeast cells achieve transcriptional reprogramming in response to heat stress by first identifying the complete set of transcription factors that are essential for heat stress conditions. This is further explored by identifying both the target loci bound by the transcription factors under conditions of heat-stress, as well as the genes that require the function of the transcription factor for normal transcriptional response to heat stress. In Chapter 2, I study a chromatin remodeling factor, CHD1 (Chromodomain Helicase DNA binding protein 1) with regard to two aspects: first, what factors provide specificity for Chd1 positioning on chromatin, by examining the role of proteins that physically or genetically interact with Chd1, and second, what is the relationship of Chd1 with the hallmark of chromatin modifications, histone H3 tri-methylation at Lys 4 and Lys 36, by investigating changes in these histone methylation marks in the absence of Chd1. Additionally, I show a novel functional link between Chd1 and RNA splicing through analysis of intron retention in transcripts produced in the Chd1 mutant. Lastly, I investigate Chd1 role in human glioblastoma cell line by generating a Chd1 knock-out via the CRISPR/Cas9 genome editing system. Taken together, the work presented in this dissertation provides novel approaches, discoveries, and intriguing insights into how eukaryotic chromatin experiences dynamic alterations in response to various perturbations on a genome-wide scale. Advisors/Committee Members: Iyer, Vishwanath R. (advisor), Marcotte, Edward M (committee member), Wilke, Claus O (committee member), Johnson, Arlen W (committee member), Kim, Jonghwan (committee member).

Subjects/Keywords: Transcription; Chromatin remodeler; Histone methylation; Genomics

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

APA (6^th Edition):

Lee, Y. (2018). Transcription factor networks and chromatin remodeler function in gene regulation on the eukaryotic genome. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/68547

Chicago Manual of Style (16^th Edition):

Lee, Yaelim. “Transcription factor networks and chromatin remodeler function in gene regulation on the eukaryotic genome.” 2018. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/68547.

MLA Handbook (7^th Edition):

Lee, Yaelim. “Transcription factor networks and chromatin remodeler function in gene regulation on the eukaryotic genome.” 2018. Web. 20 Jan 2021.

Vancouver:

Lee Y. Transcription factor networks and chromatin remodeler function in gene regulation on the eukaryotic genome. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2018. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/68547.

Council of Science Editors:

Lee Y. Transcription factor networks and chromatin remodeler function in gene regulation on the eukaryotic genome. [Doctoral Dissertation]. University of Texas – Austin; 2018. Available from: http://hdl.handle.net/2152/68547

University of Texas – Austin

8. Rhee, Catherine Soo. Transcriptional and epigenetic mechanisms of the first cell fate decision and reprogramming.

Degree: PhD, Cell and Molecular Biology, 2016, University of Texas – Austin

URL: http://hdl.handle.net/2152/72695

► The placenta is a transient but vital organ mediating a myriad of interactions between maternal and embryonic tissues. The cells in the trophectoderm (TE) lineage… (more)

▼ The placenta is a transient but vital organ mediating a myriad of interactions between maternal and embryonic tissues. The cells in the trophectoderm (TE) lineage are responsible for proper implantation, placentation, and immunological functions of the placenta. However, our understanding of molecular mechanisms underlying placentation and TE development is still rudimentary. Deciphering the mechanisms by which key TE-specific transcription factors (TFs) control the first cell fate decision, as well as the maintenance and differentiation of TE, is a prerequisite for understanding early embryonic development and ultimately improving healthy pregnancy. First, using a combination of functional genomics, bioinformatics, and mouse genetics, I revealed that Arid3a is a critical regulator for controlling the first cell fate decision and placental development. Ectopically expressed Arid3a induces TE-like gene expression programs in embryonic stem (ES) cells. Moreover, Arid3a is not only essential for maintaining self-renewing TS cells, but also for promoting further differentiation of trophoblastic lineages. Consistently, Arid3a-/- mice suffer from severely impaired post-implantation development, resulting in early embryonic lethality. I further showed that Arid3a directly activates TE-specific genes while repressing pluripotency genes by recruiting HDAC1. Second, I studied the mechanisms underlying TF-mediated conversion of ES to trophoblast stem (TS)-like cells. Upon overexpression of TS cell-specific TFs, Cdx2, Arid3a, and Gata3 (CAG factors) in ES cells, I performed time–course profiling of chromatin accessibility, transcriptomes, and occupancy of these reprogramming factors during reprogramming. Using an integrative analysis, I discovered that CAG factors orchestrate the conversion via a sequential two-step regulation in a timely, ordered manner, with repression of pluripotency genes by decommissioning active enhancers, followed by activation of TS cell-specific genes as pioneer factors that can access closed chromatin. Taken together, my studies unveiled that Arid3a functions as a pivotal regulator of TE and placental development by regulating the commitment to the first cell fate, as well as by executing TE lineage differentiation. I advanced our understanding of the mechanisms underlying TF-mediated reprogramming of ES to TS-like cells, in particular Arid3a-mediated transcriptional and epigenetic regulation. Thus, my studies will be beneficial for enhancing clinical applications such as disease modeling, drug screening, and regenerative therapies. Advisors/Committee Members: Kim, Jonghwan, 1971- (advisor), Tucker, Haley O. (advisor), Iyer, Vishwanath R (committee member), Vokes, Steven A (committee member), Marcotte, Edward M (committee member).

Subjects/Keywords: Arid3a; Reprogramming; Embryonic stem cells; Trophoblast stem cells

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

APA (6^th Edition):

Rhee, C. S. (2016). Transcriptional and epigenetic mechanisms of the first cell fate decision and reprogramming. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/72695

Chicago Manual of Style (16^th Edition):

Rhee, Catherine Soo. “Transcriptional and epigenetic mechanisms of the first cell fate decision and reprogramming.” 2016. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/72695.

MLA Handbook (7^th Edition):

Rhee, Catherine Soo. “Transcriptional and epigenetic mechanisms of the first cell fate decision and reprogramming.” 2016. Web. 20 Jan 2021.

Vancouver:

Rhee CS. Transcriptional and epigenetic mechanisms of the first cell fate decision and reprogramming. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2016. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/72695.

Council of Science Editors:

Rhee CS. Transcriptional and epigenetic mechanisms of the first cell fate decision and reprogramming. [Doctoral Dissertation]. University of Texas – Austin; 2016. Available from: http://hdl.handle.net/2152/72695

University of Texas – Austin

9. Fu, Qiong, Ph. D. Regulation of the activity of a budding yeast DNA damage repair enzyme Sae2.

Degree: PhD, Microbiology, 2014, University of Texas – Austin

URL: http://hdl.handle.net/2152/46516

► In response to DNA damage, many repair and signaling molecules mobilize rapidly to the sites of DNA double-strand breaks (DSBs). This network of immediate responses… (more)

▼ In response to DNA damage, many repair and signaling molecules mobilize rapidly to the sites of DNA double-strand breaks (DSBs). This network of immediate responses is regulated at the level of post-translational modifications to coordinate DNA repair and checkpoint signaling. Here we investigate the DNA damage-induced oligomeric transitions of the Sae2 protein, an important enzyme in the initiation of DSB repair. Sae2 is a target of multiple phosphorylation events, which we identify and characterize in vivo in budding yeast. Both cell cycle-dependent and DNA damage-induced phosphorylation of Sae2 are important for the cell survival after DNA damage, and the cell cycle-regulated modifications are required to prime the damage-dependent events. We find that Sae2 exists in the form of inactive oligomers that are transiently released into smaller active units by these series of phosphorylation events. DNA damage also triggers removal of Sae2 through autophagy and proteasomal degradation, ensuring that active Sae2 is present only transiently in cells. This analysis provides evidence for a novel type of protein regulation where the activity of an enzyme is controlled dynamically by post-translational modifications that regulate its solubility and oligomeric state. Budding yeast Ess1 is a phosphorylation-specific prolyl isomerase. Its human homolog Pin1 is found to isomerize CtIP, the human functional ortholog of Sae2, and promote the proteasomal degradation of CtIP. However, I could neither detect any interaction between Ess1 and Sae2, nor observe any change in Sae2 protein level while overexpressing wild-type or mutant Ess1, suggesting Ess1 does not act on Sae2, like Pin1 does on CtIP. The increased DNA damage sensitivity of Ess1 mutants indicates that Ess1 is involved in DNA repair, but not related to Sae2. Since Ess1 plays an important role in transcription termination together with a RNA 3’ end processing factor Pcf11, I overexpressed wild-type Pcf11 and found it significantly increased the DNA damage resistance of either wild-type or H164R mutant Ess1 cells, and also the sae2Δ cells. These results imply that Ess1, Pcf11 and Sae2 might contribute to DNA damage repair through transcription termination, which links transcription termination and DNA damage repair together. Advisors/Committee Members: Paull, Tanya T. (advisor), Iyer, Vishwanath R (committee member), Jayaram, Makkuni (committee member), Johnson, Arlen W (committee member), Zhang, Yan (committee member).

Subjects/Keywords: DNA repair; Sae2

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APA (6^th Edition):

Fu, Qiong, P. D. (2014). Regulation of the activity of a budding yeast DNA damage repair enzyme Sae2. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/46516

Chicago Manual of Style (16^th Edition):

Fu, Qiong, Ph D. “Regulation of the activity of a budding yeast DNA damage repair enzyme Sae2.” 2014. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/46516.

MLA Handbook (7^th Edition):

Fu, Qiong, Ph D. “Regulation of the activity of a budding yeast DNA damage repair enzyme Sae2.” 2014. Web. 20 Jan 2021.

Vancouver:

Fu, Qiong PD. Regulation of the activity of a budding yeast DNA damage repair enzyme Sae2. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2014. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/46516.

Council of Science Editors:

Fu, Qiong PD. Regulation of the activity of a budding yeast DNA damage repair enzyme Sae2. [Doctoral Dissertation]. University of Texas – Austin; 2014. Available from: http://hdl.handle.net/2152/46516

University of Texas – Austin

10. Gong, Fade. Role of bromodomain containing proteins in the DNA damage response.

Degree: PhD, Cell and Molecular Biology, 2016, University of Texas – Austin

URL: http://hdl.handle.net/2152/68576

► Chromatin-based DNA damage response (DDR) mechanisms are fundamental for preventing genome and epigenome instability, which are hallmarks of cancer. How chromatin promotes genome-epigenome integrity in… (more)

▼ Chromatin-based DNA damage response (DDR) mechanisms are fundamental for preventing genome and epigenome instability, which are hallmarks of cancer. How chromatin promotes genome-epigenome integrity in response to DNA damage is a critical question. Chromatin acetylation is a key signaling event involved in detecting, signaling and repairing DNA damage. The bromodomain (BRD) containing protein is the primary reader of acetylation. Thus, BRD proteins represent attractive candidates for reading damaged chromatin to mediate genome-epigenome integrity. In the first part of this project, I performed a screen to analyze the dynamics of BRD protein at DNA damage sites. I identified one-third of BRD proteins relocalized upon DNA damage, a phenomenon common to DNA damage factors. In the second part of my thesis work, I functionally studied the BRD protein ZMYND8 in a novel transcription-dependent DNA damage recognition pathway. Upon DNA damage specifically within actively transcribing chromatin, ZMYND8 is recruited through its BRD to TIP60 mediated H4 acetylations. ZMYND8 associates with the NuRD complex and promotes its accumulation at damage sites to facilitate transcriptional repression and promote repair by homologous recombination (HR). To investigate mechanisms regulating this novel ZMYND8-NuRD pathway, I performed another screen to check the recruitment of ZMYND8 interacting factors as well as their effects on ZMYND8 recruitment. I identified the H3K4me3 specific histone demethylase KDM5A is a key upstream regulator of this transcription-dependent DNA damage recognition pathway. Upon DNA damage, KDM5A mediates the removal of H3K4me3 around active chromatin near damage sites, which is an essential step to facilitate recruitment of ZMYND8 and NuRD complex to DNA damage. Similar to ZMYND8 and NuRD, depletion of KDM5A also impairs damage induced transcriptional silencing and DNA double-strand break (DSB) repair by homologous recombination (HR). The DDR is not only a dynamic process focusing that regulates protein factor interaction at DNA damage sites, but also promotes transcriptional changes of some genes upon DNA damage. In another part of this project, I screened the functional role of BRD proteins in regulating transcription in response to different types of damage. I identified two novel p53 target genes SP110 and SP140. In response to treatment with the DNA damaging chemotherapeutic agent, Doxorubicin, in U2OS cells, SP110 and SP140 are upregulated in a p53 dependent manner. In summary, this study provides a comprehensive view for BRD reader proteins in promoting the DDR within acetylated chromatin to preserve genome-epigenome stability. Advisors/Committee Members: Miller, Kyle M. (advisor), Iyer, Vishwanath R (committee member), Paull, Tanya T (committee member), Vasquez, Karen M (committee member), Xhemalce, Blerta (committee member).

Subjects/Keywords: DNA damage response; DNA repair; Chromatin; Acetylation; Bromodomain

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

APA (6^th Edition):

Gong, F. (2016). Role of bromodomain containing proteins in the DNA damage response. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/68576

Chicago Manual of Style (16^th Edition):

Gong, Fade. “Role of bromodomain containing proteins in the DNA damage response.” 2016. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/68576.

MLA Handbook (7^th Edition):

Gong, Fade. “Role of bromodomain containing proteins in the DNA damage response.” 2016. Web. 20 Jan 2021.

Vancouver:

Gong F. Role of bromodomain containing proteins in the DNA damage response. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2016. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/68576.

Council of Science Editors:

Gong F. Role of bromodomain containing proteins in the DNA damage response. [Doctoral Dissertation]. University of Texas – Austin; 2016. Available from: http://hdl.handle.net/2152/68576

University of Texas – Austin

11. Zhou, Yi, Ph. D. Regulation of DNA damage response by ATM and DNA-PKcs.

Degree: PhD, Cell and Molecular Biology, 2015, University of Texas – Austin

URL: http://hdl.handle.net/2152/63857

► The 5’ strand resection of DNA double strand breaks (DSBs) initiates homologous recombination (HR) and is critical for genomic stability. To date there is no… (more)

▼ The 5’ strand resection of DNA double strand breaks (DSBs) initiates homologous recombination (HR) and is critical for genomic stability. To date there is no quantitative method to measure single-stranded DNA (ssDNA) intermediates of resection in mammalian cells. In this study I develop a quantitative PCR (qPCR)-based assay to quantitate ssDNA intermediates, specifically, the 3’ ssDNA product of resection at specific DSBs induced by AsiSI restriction enzyme in human cells. I protect the large mammalian genome from shearing by embedding the cells in low-gelling-point agar during genomic DNA extraction, and measure the levels of ssDNA intermediates by qPCR following restriction enzyme digestion. This assay is more quantitative and precise compared with existing protein foci-based methods. Using this assay I quantitatively measure ssDNA intermediates of resection in human cells and find that the 5' strand at endonuclease-generated break sites is resected up to 3.5 kb in a cell cycle dependent manner. Depletion of CtIP, Mre11, Exo1, or SOSS1 blocks resection, while depletion of 53BP1, Ku or DNA-dependent protein kinase catalytic subunit (DNA-PKcs) leads to increased resection as measured by this method. While 53BP1 negatively regulates DNA end processing, depletion of BRCA1 does not, suggesting that the role of BRCA1 in HR is primarily to promote RAD51 filament formation, not to regulate end resection. Using direct measurement of resection in human cells and reconstituted assays of resection with purified proteins in vitro, I also show that DNA-PKcs, a classic non-homologous end joining (NHEJ) factor, antagonizes DSB resection by blocking the recruitment of resection enzymes such as exonuclease 1 (Exo1). Autophosphorylation of DNA-PKcs promotes DNA-PKcs dissociation and consequently Exo1 binding. ATM kinase activity can compensate for DNA-PKcs autophosphorylation and promote resection under conditions where DNA-PKcs catalytic activity is inhibited. The Mre11/Rad50/Nbs1 (MRN) complex further stimulates resection in the presence of Ku and DNA-PKcs by recruiting Exo1 and enhancing DNA-PKcs autophosphorylation. This work suggests that, in addition to its key role in NHEJ, DNA-PKcs also acts in concert with MRN and ATM to regulate resection and thus DNA repair pathway choice. In addition, I find that MRN strongly suppresses DNA Ligase IV/XRCC4-mediated end rejoining, whereas it dramatically promotes DNA end ligation by the DNA Ligase III/XRCC1 complex. The Ataxia-Telangiectasia mutated (ATM) protein is a key regulator of checkpoint activation and HR in response to DSBs. The MRN complex acts as a DSB sensor and is essential for ATM recruitment to broken DNA ends and ATM activation. However, the precise mechanism for ATM activation upon DNA damage and ATM inactivation after DNA repair has remained poorly understood. Phosphorylation of ATM has been suggested to play important roles in this process. Autophosphorylation of ATM at four sites (S1981, S367, S1893, and S2996) has been shown to be essential for ATM activation and… Advisors/Committee Members: Paull, Tanya T. (advisor), Finkelstein, Ilya J (committee member), Iyer, Vishwanath R (committee member), Miller, Kyle M (committee member), Lee, Seongmin (committee member).

Subjects/Keywords: DNA repair; DNA damage response; Double strand breaks; ATM; DNA-PKcs; MRN; Exo1; DNA end resection

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

APA (6^th Edition):

Zhou, Yi, P. D. (2015). Regulation of DNA damage response by ATM and DNA-PKcs. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/63857

Chicago Manual of Style (16^th Edition):

Zhou, Yi, Ph D. “Regulation of DNA damage response by ATM and DNA-PKcs.” 2015. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/63857.

MLA Handbook (7^th Edition):

Zhou, Yi, Ph D. “Regulation of DNA damage response by ATM and DNA-PKcs.” 2015. Web. 20 Jan 2021.

Vancouver:

Zhou, Yi PD. Regulation of DNA damage response by ATM and DNA-PKcs. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2015. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/63857.

Council of Science Editors:

Zhou, Yi PD. Regulation of DNA damage response by ATM and DNA-PKcs. [Doctoral Dissertation]. University of Texas – Austin; 2015. Available from: http://hdl.handle.net/2152/63857

University of Texas – Austin

12. Laurent, Jon Michael. Evolutionary conservation of protein abundance and function.

Degree: PhD, Cellular and Molecular Biology, 2016, University of Texas – Austin

URL: http://hdl.handle.net/2152/68224

► Conservation lies at the heart of biology. All organisms on earth are descended from a common ancestor, resulting in the preservation of many biological properties,… (more)

▼ Conservation lies at the heart of biology. All organisms on earth are descended from a common ancestor, resulting in the preservation of many biological properties, from genotype to gene function and phenotype. The advent of next generation nucleic acid sequencing, mass-spectrometry proteomics, and other global measurement technologies, along with the emergence of computational and systems biology, have facilitated huge strides in our ability to make meaningful observations at all levels of biological phenomena. As a result, we can now make comparative assessments of the degree to which various processes are conserved and connected between species. Additionally, newly developed techniques for highly efficient genome manipulation enable us to test these comparative observations experimentally. As an example, global measurement technologies have enabled observation of the abundances of nearly all proteins and mRNAs in the cells in many organisms, and further determine to what extent proteins levels are controlled by the levels of mRNA. In chapter one, I utilize these data to investigate the conservation of protein and mRNA abundance levels across a diverse set of organisms. Expression levels, while important for proper cell functioning, are only one observable property between genotype and phenotype. Evolutionary conservation can be seen all the way to phenotype, as in the identification of orthologous phenotypes, or ‘phenologs’, described in further detail in the introduction. Given these conserved phenomena, we asked a simple question: ’To what extent can an organisms genes function in the context of another organism?’. To address this question, we systematically replaced hundreds of yeast genes with their human orthologs. In chapters two and three I present these replacements, and further discuss what features of the genes or ortholog groups can explain their ability to replace or not. Chapter four includes a presentation of an ongoing effort to extend the replacement studies by replacing a complete yeast protein complex with its human counterpart. I will end with a discussion of the current state of relevant work, and where I see additional efforts going into the future. Advisors/Committee Members: Marcotte, Edward M. (advisor), Ellington, Andrew D (committee member), Iyer, Vishwanath R (committee member), Browning, Karen S (committee member), Appling, Dean R (committee member).

Subjects/Keywords: Humanization; Yeast genetics; Systems biology; Humanized yeast

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APA (6^th Edition):

Laurent, J. M. (2016). Evolutionary conservation of protein abundance and function. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/68224

Chicago Manual of Style (16^th Edition):

Laurent, Jon Michael. “Evolutionary conservation of protein abundance and function.” 2016. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/68224.

MLA Handbook (7^th Edition):

Laurent, Jon Michael. “Evolutionary conservation of protein abundance and function.” 2016. Web. 20 Jan 2021.

Vancouver:

Laurent JM. Evolutionary conservation of protein abundance and function. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2016. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/68224.

Council of Science Editors:

Laurent JM. Evolutionary conservation of protein abundance and function. [Doctoral Dissertation]. University of Texas – Austin; 2016. Available from: http://hdl.handle.net/2152/68224

University of Texas – Austin

13. -4913-7238. Genetic and bioinformatic approaches to characterize ethanol teratogenesis.

Degree: PhD, Cell and Molecular Biology, 2019, University of Texas – Austin

URL: http://dx.doi.org/10.26153/tsw/7506

► Alcohol consumption during pregnancy is the most preventable cause of birth defects, yet approximately 2-5% of children are afflicted with Fetal Alcohol Spectrum Disorders (FASD).… (more)

▼ Alcohol consumption during pregnancy is the most preventable cause of birth defects, yet approximately 2-5% of children are afflicted with Fetal Alcohol Spectrum Disorders (FASD). FASD describes the complex and highly variable deleterious phenotypes caused by prenatal alcohol exposure. Twin studies suggest a genetic predisposition, contributing to the variation in risk for FASD. Despite this, we lack a basic understanding of 1) the factors that protect or predispose an individual to FASD and 2) how these genetic factors interact in ethanol teratogenesis. Results from a genetic “shelf” screen revealed vangl2, a member of the Wnt/planar cell polarity (PCP) pathway that mediates convergent extension movements that narrow and elongate the body axis, as an ethanol-sensitive genetic locus. Untreated vangl2 mutants displayed a relatively intact craniofacial skeleton. Ethanol-exposed vangl2 heterozygotes and mutants, displayed cyclopean and midfacial defects. To assess the relative level of variation of the transcriptional response to ethanol, I performed single embryo RNA-seq during early embryonic stages. Individual zebrafish embryos were exposed to a subteratogenic dose of 1% ethanol in embryo media. My data suggests that the effect of ethanol is subtle; time is the most important variable driving variation in fold coverage across all samples. Despite this, I find a number of differentially expressed genes in response to ethanol. Transcriptional changes due to ethanol are indicative of increased oxidative stress and ion transport and reduced DNA replication and cell division. Using a bioinformatic approach, I find cyclopamine, a Hedgehog pathway inhibitor, interacts with ethanol. Further genetic analyses shows that ethanol disrupts convergent extension of the mesoderm, which in turn disrupts localization of shh in the axial mesoderm, a signal necessary to separate the eye field. I find this effect to be further exacerbated in the vangl2 mutant background. Together these data yield important insight necessary to advance understanding and treatment for FASD Advisors/Committee Members: Eberhart, Johann K. (advisor), Harris, R. A (committee member), Iyer, Vishwanath R (committee member), Sullivan, Christopher S (committee member), Wallingford, John B (committee member).

Subjects/Keywords: Ethanol; Fetal Alcohol Spectrum Disorders; Fetal Alcohol Syndrome; Wnt/planar cell polarity pathway; vangl2; Convergent extension; Cyclopia; Cyclopamine; Sonic hedgehog

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APA (6^th Edition):

-4913-7238. (2019). Genetic and bioinformatic approaches to characterize ethanol teratogenesis. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://dx.doi.org/10.26153/tsw/7506

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Chicago Manual of Style (16^th Edition):

-4913-7238. “Genetic and bioinformatic approaches to characterize ethanol teratogenesis.” 2019. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://dx.doi.org/10.26153/tsw/7506.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

MLA Handbook (7^th Edition):

-4913-7238. “Genetic and bioinformatic approaches to characterize ethanol teratogenesis.” 2019. Web. 20 Jan 2021.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Vancouver:

-4913-7238. Genetic and bioinformatic approaches to characterize ethanol teratogenesis. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2019. [cited 2021 Jan 20]. Available from: http://dx.doi.org/10.26153/tsw/7506.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Council of Science Editors:

-4913-7238. Genetic and bioinformatic approaches to characterize ethanol teratogenesis. [Doctoral Dissertation]. University of Texas – Austin; 2019. Available from: http://dx.doi.org/10.26153/tsw/7506

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

University of Texas – Austin

14. Sorenson, Matthew Richard. Exploring the eukaryotic gene expression machinery using a single-cell yeast gene expression reporter.

Degree: PhD, Microbiology, 2014, University of Texas – Austin

URL: http://hdl.handle.net/2152/31557

► It has become increasingly evident that gene expression processes in eukaryotes involve communication and coordination between many complex, independent macromolecular machines. To query these processes… (more)

▼ It has become increasingly evident that gene expression processes in eukaryotes involve communication and coordination between many complex, independent macromolecular machines. To query these processes and to explore the potential relationships between them in the budding yeast Saccharomyces cerevisiae, we designed a versatile reporter employing multicolor high-throughput flow cytometry. Due to its design, this single reporter exhibits a distinctive signature for many defects in gene expression including transcription, histone modification, pre-mRNA splicing, mRNA export, nonsense-mediated decay, and mRNA degradation. Analysis of the reporter in 4967 non-essential yeast genes not only revealed striking phenotypic overlaps between similar functions, but also provided us a dataset in which to compare additional genetic or chemical perturbations. Utilizing a binning and clustering algorithm we developed we are able to compare reporter expression data from thousands of mutants in a semi-automated fashion, essentially grouping mutants or conditions based on the levels of reporter signal. I further utilized our reporter to screen a vast library of in vivo produced cyclic peptides using fluorescence-activated cell sorting (FACS), identifying a cyclic peptide that resulted in mild gene-specific pre-mRNA splicing inhibition. Additionally, I adapted our reporter assay to perform a high-throughput small molecule screen to identify inhibitors or modulators of specific gene expression processes. Our efforts led to the identification of a small molecule that inhibits pre-mRNA splicing in a dose-dependent manner. Moreover, I utilized our reporter system to quickly identify loss-of-function mutants in the poorly characterized gene SWM2. The three mutants of interest have reduced interaction with Tgs1p, the conserved trimethylguanosine synthase, which we believe leads to decreased hypermethylation of the 5’ caps of spliceosomal snRNAs. Altogether this work describes the development, validation and utility of the versatile gene expression reporter system we developed, providing our lab and others a valuable tool to interrogate a wide-range of gene expression processes in yeast. Advisors/Committee Members: Stevens, Scott W. (advisor), Ellington, Andrew D (committee member), Iyer, Vishwanath R (committee member), Johnson, Arlen W (committee member), Marcotte, Edward M (committee member).

Subjects/Keywords: Gene expression; Reporter; Screening; Flow cytometry

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

APA (6^th Edition):

Sorenson, M. R. (2014). Exploring the eukaryotic gene expression machinery using a single-cell yeast gene expression reporter. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/31557

Chicago Manual of Style (16^th Edition):

Sorenson, Matthew Richard. “Exploring the eukaryotic gene expression machinery using a single-cell yeast gene expression reporter.” 2014. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/31557.

MLA Handbook (7^th Edition):

Sorenson, Matthew Richard. “Exploring the eukaryotic gene expression machinery using a single-cell yeast gene expression reporter.” 2014. Web. 20 Jan 2021.

Vancouver:

Sorenson MR. Exploring the eukaryotic gene expression machinery using a single-cell yeast gene expression reporter. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2014. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/31557.

Council of Science Editors:

Sorenson MR. Exploring the eukaryotic gene expression machinery using a single-cell yeast gene expression reporter. [Doctoral Dissertation]. University of Texas – Austin; 2014. Available from: http://hdl.handle.net/2152/31557

University of Texas – Austin

15. Park, Daechan. Genome-wide approaches to explore transcriptional regulation in eukaryotes.

Degree: PhD, Cellular and Molecular Biology, 2014, University of Texas – Austin

URL: http://hdl.handle.net/2152/30443

► Transcriptional regulation is a complicated process controlled by numerous factors such as transcription factors (TFs), chromatin remodeling enzymes, nucleosomes, post-transcriptional machineries, and cis-acting DNA sequence.… (more)

▼ Transcriptional regulation is a complicated process controlled by numerous factors such as transcription factors (TFs), chromatin remodeling enzymes, nucleosomes, post-transcriptional machineries, and cis-acting DNA sequence. I explored the complex transcriptional regulation in eukaryotes through three distinct studies to comprehensively understand the functional genomics at various steps. Although a variety of high throughput approaches have been developed to understand this complex system on a genome wide scale with high resolution, a lack of accurate and comprehensive annotation transcription start sites (TSS) and polyadenylation sites (PAS) has hindered precise analyses even in Saccharomyces cerevisiae, one of the simplest eukaryotes. We developed Simultaneous Mapping Of RNA Ends by sequencing (SMORE-seq) and identified the strongest TSS and PAS of over 90% of yeast genes with single nucleotide resolution. Owing to the high accuracy of TSS identified by SMORE-seq, we detected possibly mis-annotated 150 genes that have a TSS downstream of the annotated start codon. Furthermore, SMORE-seq showed that 5’-capped non-coding RNAs were highly transcribed divergently from TATA-less promoters in wild-type cells under normal conditions. Mapping of DNA-protein interactions is essential to understanding the role of TFs in transcriptional regulation. ChIP-seq is the most widely used method for this purpose. However, careful attention has not been given to technical bias reflected in final target calling due to many experimental steps of ChIP-seq including fixation and shearing of chromatin, immunoprecipitation, sequencing library construction, and computational analysis. While analyzing large-scale ChIP-seq data, we observed that unrelated proteins appeared to bind to the gene bodies of highly transcribed genes across datasets. Control experiments including input, IgG ChIP in untagged cells, and the Golgi factor Mnn10 ChIP also showed the strong binding at the same loci, indicating that the signals were obviously derived from bias that is devoid of biological meaning. In addition, the appearance of nucleosomal periodicity in ChIP-seq data for proteins localizing to gene bodies is another bias that can be mistaken for false interactions with nucleosomes. We alleviated these biases by correcting data with proper negative controls, but the biases could not be completely removed. Therefore, caution is warranted in interpreting the results from ChIP-seq. Nucleosome positioning is another critical mechanism of transcriptional regulation. Global mapping of nucleosome occupancy in S. cerevisiae strains deleted for chromatin remodeling complexes has elucidated the role of these complexes on a genome wide scale. In this study, loss of chromodomain helicase DNA binding protein 1 (Chd1) resulted in severe disorganization of nucleosome positioning. Despite the difficulties of performing ChIP-seq for chromatin remodeling complexes due to their transient and dynamic localization on chromatin, we successfully mapped the genome-wide… Advisors/Committee Members: Iyer, Vishwanath R. (advisor), Marcotte, Edward M (committee member), Paull, Tanya T (committee member), Miller, Kyle M (committee member), Stevens, Scott W (committee member).

Subjects/Keywords: Transcription; Genomics; Next generation sequencing; ChIP-seq; RNA-seq; MNase-seq; TSS; Non-coding RNA; Nucleosome

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

APA (6^th Edition):

Park, D. (2014). Genome-wide approaches to explore transcriptional regulation in eukaryotes. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/30443

Chicago Manual of Style (16^th Edition):

Park, Daechan. “Genome-wide approaches to explore transcriptional regulation in eukaryotes.” 2014. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/30443.

MLA Handbook (7^th Edition):

Park, Daechan. “Genome-wide approaches to explore transcriptional regulation in eukaryotes.” 2014. Web. 20 Jan 2021.

Vancouver:

Park D. Genome-wide approaches to explore transcriptional regulation in eukaryotes. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2014. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/30443.

Council of Science Editors:

Park D. Genome-wide approaches to explore transcriptional regulation in eukaryotes. [Doctoral Dissertation]. University of Texas – Austin; 2014. Available from: http://hdl.handle.net/2152/30443

University of Texas – Austin

16. -5005-7182. Single molecule peptide sequencing.

Degree: PhD, Cell and Molecular Biology, 2015, University of Texas – Austin

URL: http://hdl.handle.net/2152/47208

► The proteome is a highly dynamic and complex set of proteins, specific not only to a particular organism, but to cell types and environmental conditions.… (more)

▼ The proteome is a highly dynamic and complex set of proteins, specific not only to a particular organism, but to cell types and environmental conditions. Understanding proteome changes as they occur is especially important for molecular diagnostics and developing biomarkers. Currently, the primary technology for proteome wide identification and quantification is shotgun mass spectrometry; while powerful, it lacks high sensitivity and coverage. In this dissertation, I discuss my work in the development of a new technology, termed “fluorosequencing”, for sequencing peptides from a complex protein sample at the level of single molecules. The concept is to generate a positional information pattern of an amino acid(s) (such as xKxxK, where K is lysine and x can be any of the other amino acid residues). In order to obtain such a pattern, we proposed a scheme of (i) selectively labeling one or more amino acid(s) in the peptides, (ii) immobilizing millions of these individual fluorescently labeled peptides on a glass surface, (iii) monitoring their changing fluorescent pattern by TIRF microscopy as the (iv) N-terminal amino acid is sequentially cleaved by Edman chemistry and (v) using the resulting fluorescent signature (fluorosequences) to uniquely identify individual single molecule peptides in the mixture. We began by developing a computational framework to justify the feasibility of the concept. By modeling different sources of anticipated errors, we showed that the errors do not greatly affect the identification of proteins in the human proteome. Secondly, after screening fluorophores for their solvent stability, we used fluorescently labeled synthetic peptides covalently immobilized on beads to experimentally demonstrate the ability of the technique to determine the position of the fluorescently labeled residue in peptides. Finally, we translated the bead optimized chemistry procedures to a single molecule setup. We implemented the fluorosequencing method to sequence synthetic peptide molecules and provided evidence for the technique’s utility to discriminate peptides in a peptide mixture with single molecule sensitivity. By establishing the foundational work towards the proof-of-principle for fluorosequencing, we can now scale the method in order to realize the idea of single molecule proteome wide sequencing. Advisors/Committee Members: Marcotte, Edward M. (advisor), Ellington, Andrew (committee member), Russell, Rick (committee member), Iyer, Vishwanath R (committee member), Finkelstein, Ilya J (committee member), Anslyn, Eric V (committee member).

Subjects/Keywords: Peptide sequencing; Single molecule; Proteomics; Proteomes; Proteome changes; Fluorosequencing

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APA (6^th Edition):

-5005-7182. (2015). Single molecule peptide sequencing. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/47208

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Chicago Manual of Style (16^th Edition):

-5005-7182. “Single molecule peptide sequencing.” 2015. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/47208.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

MLA Handbook (7^th Edition):

-5005-7182. “Single molecule peptide sequencing.” 2015. Web. 20 Jan 2021.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Vancouver:

-5005-7182. Single molecule peptide sequencing. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2015. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/47208.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Council of Science Editors:

-5005-7182. Single molecule peptide sequencing. [Doctoral Dissertation]. University of Texas – Austin; 2015. Available from: http://hdl.handle.net/2152/47208

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

University of Texas – Austin

17. Qin, Yidan. Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine.

Degree: PhD, Microbiology, 2016, University of Texas – Austin

URL: http://hdl.handle.net/2152/41602

► Thermostable group II intron reverse transcriptases (TGIRTs) from thermophilic bacteria are advantageous for biotechnological applications that require cDNA synthesis, such as RT-qPCR and RNA-seq. TGIRTs… (more)

▼ Thermostable group II intron reverse transcriptases (TGIRTs) from thermophilic bacteria are advantageous for biotechnological applications that require cDNA synthesis, such as RT-qPCR and RNA-seq. TGIRTs have higher thermostability, processivity and fidelity than conventional retroviral RTs, along with a novel end-to-end template-switching activity that attaches RNA-seq adapters to target RNAs without RNA ligation. First, I optimized the TGIRT template-switching method for RNA-seq analysis of small non-coding RNAs (ncRNAs). I showed that TGIRT-seq gives full-length reads of tRNAs, which are refractory to retroviral RTs, and enables identification of a variety of base modifications in tRNAs by distinctive patterns of misincorporated nucleotides. With collaborators, I developed an efficient and quantitative high-throughput tRNA sequencing method, identified RNAs bound by the human interferon-induced protein IFIT5, yielding new insights into its functions in tRNA quality control and innate immunity, and uncovered a novel mRNA-independent mechanism for elongation of nascent peptides. Second, I developed a new, streamlined TGIRT-seq method for comprehensive analysis of all RNA size classes in a single RNA-seq. This method enables RNA-seq library construction from <1 ng of fragmented RNAs in <5 h. By using the method, I showed that human plasma contains large numbers of protein-coding and long ncRNAs together with diverse classes of small ncRNAs, which are mostly present as full-length transcripts. With collaborators, I showed that TGIRT-seq analysis of circulating RNAs identified potential biomarkers at different stages of multiple myeloma and may provide a sensitive, non-invasive diagnostic tool for a variety of human diseases. Finally, I adapted TGIRTs for use in mapping of RNA structures and RNA-protein interaction sites, and identification of RNA targets of cellular RNA-binding proteins. My research led to a series of new biological insights, which would have been difficult or impossible to obtain by current methods, and established TGIRTs as a tool for a broad range of applications in RNA research and diagnostics. Advisors/Committee Members: Lambowitz, Alan (advisor), Iyer, Vishwanath R (committee member), Krug, Robert M (committee member), Russell, Rick (committee member), Stevens, Scott W (committee member), Sullivan, Christopher S (committee member).

Subjects/Keywords: RNA-seq; Diagnostics; Precision medicine; Non-coding RNA; Circulating RNA

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APA (6^th Edition):

Qin, Y. (2016). Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/41602

Chicago Manual of Style (16^th Edition):

Qin, Yidan. “Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine.” 2016. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/41602.

MLA Handbook (7^th Edition):

Qin, Yidan. “Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine.” 2016. Web. 20 Jan 2021.

Vancouver:

Qin Y. Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2016. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/41602.

Council of Science Editors:

Qin Y. Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine. [Doctoral Dissertation]. University of Texas – Austin; 2016. Available from: http://hdl.handle.net/2152/41602

University of Texas – Austin

18. Kim, Jonghwan. Genome-wide mapping of DNA-protein interactions in eukaryotes.

Degree: PhD, Cell and Molecular Biology, 2005, University of Texas – Austin

URL: http://hdl.handle.net/2152/2250

► The genome of an organism encodes thousands of genes, and their expression needs to be precisely controlled at the right place and time for normal… (more)

▼ The genome of an organism encodes thousands of genes, and their expression needs to be precisely controlled at the right place and time for normal cellular functioning. Control of gene expression occurs predominantly at the level of transcription and the transcription of a particular gene is determined by the interactions between diverse regulatory proteins and their specific cis-acting binding elements. However, our understanding about how and when transcription factors function in the context of the whole genome is limited. Hundreds to thousands of transcription factors can potentially interact with DNA in the genome and modulate the level of transcription of protein coding genes into mRNAs in response to regulatory signals. Identifying the chromosomal targets of regulatory transcription factors in various conditions is crucial for reconstructing the transcriptional regulatory networks underlying global gene expression programs. Recently-developed chromatin immunoprecipitation (ChIP)-based genome-wide studies such as ChIP-microarrays allow us to identify the genomic loci occupied by transcription factors in vivo. In combination with expression profiling analysis, the ChIP-microarray method is a powerful tool to study DNA-protein interactions in vivo. However, there are some limitations to applying this ChIP-microarray method to every sequenced large genome due to the complexity and size of large genomes such as human or mouse. To gain a better understanding of the functions of transcription factors in mediating eukaryotic gene regulation, we performed ChIP-microarray analysis in yeast and human systems. First, we determined the role of the yeast TATA-box binding protein (TBP) in controlling global gene expression and revealed that PolIII genes are the strongest targets of TBP in yeast. Second, we determined that the human oncogenic transcription factor Myc has more than a thousand target genes in human cells. Finally, to address some of the current limitations in ChIP-microarrays, we developed an alternative method, sequence tag analysis of genomic enrichment (STAGE), to study genome-wide mapping of DNA-protein interactions. Advisors/Committee Members: Iyer, Vishwanath R. (advisor).

Subjects/Keywords: Eukaryotic cells; DNA-protein interactions; Genetic transcription

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APA (6^th Edition):

Kim, J. (2005). Genome-wide mapping of DNA-protein interactions in eukaryotes. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/2250

Chicago Manual of Style (16^th Edition):

Kim, Jonghwan. “Genome-wide mapping of DNA-protein interactions in eukaryotes.” 2005. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/2250.

MLA Handbook (7^th Edition):

Kim, Jonghwan. “Genome-wide mapping of DNA-protein interactions in eukaryotes.” 2005. Web. 20 Jan 2021.

Vancouver:

Kim J. Genome-wide mapping of DNA-protein interactions in eukaryotes. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2005. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/2250.

Council of Science Editors:

Kim J. Genome-wide mapping of DNA-protein interactions in eukaryotes. [Doctoral Dissertation]. University of Texas – Austin; 2005. Available from: http://hdl.handle.net/2152/2250

University of Texas – Austin

19. Hu, Zhanzhi. Functional transcription regulatory network reconstruction and characterization.

Degree: PhD, Microbiology, 2005, University of Texas – Austin

URL: http://hdl.handle.net/2152/2450

► The genome of yeast Saccharomyces cerevisiae encodes more than 5,800 genes with well controlled and coordinated expression patterns for normal cellular functions. Control of gene… (more)

▼ The genome of yeast Saccharomyces cerevisiae encodes more than 5,800 genes with well controlled and coordinated expression patterns for normal cellular functions. Control of gene expression occurs primarily at the transcriptional level via transcription factors. In response to various conditions, these regulators bind to promoters of target genes and recruit additional factors and the transcription machinery to activate or repress transcription. However, the genome-wide details of the transcriptional regulatory networks are largely unknown. We first mapped the genome-wide in vivo DNA binding distribution of Heat Shock Factor (HSF), one of the most highly conserved transcriptional regulators in eukaryotes. HSF mediates the response of cells to many stresses including heat shock, but little is known about its full range of biological targets. We used whole genome analyses to identify virtually all of the direct transcriptional targets of yeast HSF. The majority of the identified loci were heat-inducibly bound by HSF. The target genes encode proteins with a broad range of biological functions. This study provides novel insights into the role of HSF in growth, development, disease and aging, and in the complex metabolic reprogramming in cells in response to stress. Together with a recent study using a similar approach, this has provided a view of the potential regulatory network composed of transcription factors and their binding sites. However, it has been implicated that the binding of a transcription factor does not necessarily lead to an expression change. We therefore profiled the transcriptional response of yeast upon the individual deletion of more than 250 transcriptional regulators under normal growth as well as under heat shock for a subset of those. This enabled us to construct a functional transcription network. Solid support of the network was established. Known and novel roles of transcription factors were inferred and quantitatively verified. From the promoter regions of the target gene sets, we discovered many novel sequence motifs in addition to many previously characterized ones. In conclusion, the present study provides important insights for elucidating the specific roles of transcription factors in mediating the responses of the cells under different conditions. Advisors/Committee Members: Iyer, Vishwanath R. (advisor).

Subjects/Keywords: Genetic transcription – Regulation

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

APA (6^th Edition):

Hu, Z. (2005). Functional transcription regulatory network reconstruction and characterization. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/2450

Chicago Manual of Style (16^th Edition):

Hu, Zhanzhi. “Functional transcription regulatory network reconstruction and characterization.” 2005. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/2450.

MLA Handbook (7^th Edition):

Hu, Zhanzhi. “Functional transcription regulatory network reconstruction and characterization.” 2005. Web. 20 Jan 2021.

Vancouver:

Hu Z. Functional transcription regulatory network reconstruction and characterization. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2005. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/2450.

Council of Science Editors:

Hu Z. Functional transcription regulatory network reconstruction and characterization. [Doctoral Dissertation]. University of Texas – Austin; 2005. Available from: http://hdl.handle.net/2152/2450

University of Texas – Austin

20. Gu, Jian. Exploring the global gene expression programs and regulation in the response of quiescent human fibroblasts to distinct proliferative stimuli.

Degree: PhD, Cell and Molecular Biology, 2005, University of Texas – Austin

URL: http://hdl.handle.net/2152/2435

► Serum treatment of quiescent human dermal fibroblasts induces proliferation coupled with a complex physiological response that is indicative of their normal role in wound-healing. However,… (more)

▼ Serum treatment of quiescent human dermal fibroblasts induces proliferation coupled with a complex physiological response that is indicative of their normal role in wound-healing. However, it is not known to what extent such complex transcriptional events are specific to a given cell type and signal, and to what extent these changes are innate programmed responses that are activated in a range of related cell types in response to a variety of stimuli. We have profiled the global transcriptional program of human fibroblasts from two distinct tissue sources to four different growth stimuli and identified a striking conservation in their gene expression signatures. However, there were specific differences among different stimuli with regard to signaling pathways that mediate these transcriptional programs. The use of a specific PI3-kinase pathway inhibitor suggested that this pathway is differentially involved in mediating the responses of cells to serum as compared to individual peptide growth factors. By applying siRNA knockdown technique, we demonstrated that putative targets of two important immediate early transcription factors, Myc and SRF, served functions related to cell cycle progression/cell survival and wound healing, indicating that these two transcription factors may serve as master transcription controllers during the transition of fibroblasts from quiescence to proliferation. In addition, different Myc targets were identified either between different cell types (Hela vs. foreskin fibroblasts) or between different cell states (unsynchronized vs. synchronized), while SRF targets included a group of genes only induced at certain time points during cell cycle progression, which was not observed in the Myc data. MicroRNA (miRNA) expression profiling indicated that let7 and other miRNAs with similar expression profiles may be involved in regulating the transcriptional program in response to proliferative signals. Our results indicate that conservation of transcriptional programs and their regulation among different cell types may be much broader than previously appreciated. Advisors/Committee Members: Iyer, Vishwanath R. (advisor).

Subjects/Keywords: Gene expression; Genetic regulation; Fibroblasts

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

APA (6^th Edition):

Gu, J. (2005). Exploring the global gene expression programs and regulation in the response of quiescent human fibroblasts to distinct proliferative stimuli. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/2435

Chicago Manual of Style (16^th Edition):

Gu, Jian. “Exploring the global gene expression programs and regulation in the response of quiescent human fibroblasts to distinct proliferative stimuli.” 2005. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/2435.

MLA Handbook (7^th Edition):

Gu, Jian. “Exploring the global gene expression programs and regulation in the response of quiescent human fibroblasts to distinct proliferative stimuli.” 2005. Web. 20 Jan 2021.

Vancouver:

Gu J. Exploring the global gene expression programs and regulation in the response of quiescent human fibroblasts to distinct proliferative stimuli. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2005. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/2435.

Council of Science Editors:

Gu J. Exploring the global gene expression programs and regulation in the response of quiescent human fibroblasts to distinct proliferative stimuli. [Doctoral Dissertation]. University of Texas – Austin; 2005. Available from: http://hdl.handle.net/2152/2435

University of Texas – Austin

21. Killion, Patrick J., 1974-. Fungus to fibroblast: a functional genomic exploration of eukaryotic transcriptional regulation: Functional genomic exploration of eukaryotic transcriptional regulation.

Degree: PhD, Cell and Molecular Biology, 2007, University of Texas – Austin

URL: http://hdl.handle.net/2152/3616

► I have pursued a breadth of research that explored the functional genomic study of eukaryotic transcriptional regulation. I have utilized two model organisms, many experimental… (more)

▼ I have pursued a breadth of research that explored the functional genomic study of eukaryotic transcriptional regulation. I have utilized two model organisms, many experimental methodologies, and have developed a suite of computational resources to study the interaction of transcription factors with regulated targets. In Saccharomyces cerevisiae I worked with my collaborator Dr. Zhanzhi (Mike) Hu to characterize the whole-genome transcriptional response of 263 individual transcription factor deletions. We utilized a sophisticated error model and directed-weighted graphs to model a network of high-confidence targets for each transcription factor profiled. We then used regulatory epistasis to elucidate the true set of primary KO-regulated targets and construct a functional transcriptional regulatory network. This network was analyzed for ontological and sequence motif enrichment in order to gain insight into the biological functions represented by transcription factors studied. Functional validation was performed to evaluate the probability of novel functional characterizations. Significant insight was gained from this study with regard to the nature of regulatory cascades and the inability for DNA binding events to predict regulation. This set of analysis was performed with a novel bioinformatic server called ArrayPlex. ArrayPlex is a software package that centrally provides a large number of flexible toolsets useful for functional genomics including microarray data storage, quality assessments, data visualization, gene annotation retrieval, statistical tests, genomic sequence retrieval and motif analysis. It uses a client-server architecture based on open source components, provides graphical, command-line, as well as programmatic access to all needed resources, and is extensible by virtue of a documented API. Using many of the techniques and computational resources developed, I pursued the study of microRNA transcriptional abundance and targeting in H. sapiens cell cultures. Utilizing custom-fabricated microarrays, I measured the whole-genome response of both mRNAs and microRNAs under serum stimulation, c-Myc overexpression, and c-Myc siRNA-mediated knockdown. I then characterized the regulatory interactions between the sets of regulated microRNAs and coordinately regulated transcription factors. Using analytical methods sensitive to regulatory directionality of both populations I was able to determine high-confidence relationships between transcription factors and regulated microRNAs as well as microRNAs and regulated gene targets. Advisors/Committee Members: Iyer, Vishwanath R. (advisor).

Subjects/Keywords: Genetic transcription – Regulation

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APA (6^th Edition):

Killion, Patrick J., 1. (2007). Fungus to fibroblast: a functional genomic exploration of eukaryotic transcriptional regulation: Functional genomic exploration of eukaryotic transcriptional regulation. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/3616

Chicago Manual of Style (16^th Edition):

Killion, Patrick J., 1974-. “Fungus to fibroblast: a functional genomic exploration of eukaryotic transcriptional regulation: Functional genomic exploration of eukaryotic transcriptional regulation.” 2007. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/3616.

MLA Handbook (7^th Edition):

Killion, Patrick J., 1974-. “Fungus to fibroblast: a functional genomic exploration of eukaryotic transcriptional regulation: Functional genomic exploration of eukaryotic transcriptional regulation.” 2007. Web. 20 Jan 2021.

Vancouver:

Killion, Patrick J. 1. Fungus to fibroblast: a functional genomic exploration of eukaryotic transcriptional regulation: Functional genomic exploration of eukaryotic transcriptional regulation. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2007. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/3616.

Council of Science Editors:

Killion, Patrick J. 1. Fungus to fibroblast: a functional genomic exploration of eukaryotic transcriptional regulation: Functional genomic exploration of eukaryotic transcriptional regulation. [Doctoral Dissertation]. University of Texas – Austin; 2007. Available from: http://hdl.handle.net/2152/3616

22. Lee, Bum Kyu. Genome-wide target identification of sequence-specific transcription factors through ChIP sequencing.

Degree: PhD, Microbiology, 2011, University of Texas – Austin

URL: http://hdl.handle.net/2152/ETD-UT-2011-05-3038

► The regulation of gene expression at the right time, place, and degree is crucial for many cellular processes such as proliferation and development. In addition,… (more)

▼ The regulation of gene expression at the right time, place, and degree is crucial for many cellular processes such as proliferation and development. In addition, in order to maintain cellular life, cells must rapidly and appropriately respond to various environmental stimuli. Sequence-specific transcription factors (TFs) can recognize functional regulatory DNA elements in a sequence-specific manner so that they can regulate only a specific group of genes, a process which enables cells to cope with diverse internal and external stimuli. Human has approximately 1,400 sequence-specific TFs whose aberrant expression causes a wide range of detrimental consequences including developmental disorders, diseases, and cancers; therefore, it is pivotal to identify the binding sites of each sequence-specific TF in order to unravel its roles in and mechanisms of gene regulation. Even though some TFs have been intensively studied, the majority of TFs still remain to be studied, particularly the tasks of identifying their genome-wide target genes and deciphering their biological roles in specific cellular contexts. Many questions remain unanswered: how many sites on the human genome a sequence-specific TF can bind; whether all TF-bound sites are functional; how a TF achieves binding specificity onto its targets; how and to what extent a TF is involved in gene regulation. Comprehensive identification of the binding sites of sequence-specific TFs and follow-up molecular studies including gene expression microarrays will provide close answers to these questions. Chromatin Immunoprecipitation coupled with recently developed high-throughput sequencing (ChIP-seq) allows us to perform genome-scale unbiased identification of the binding sites of sequence-specific TFs. Here, to gain insight into gene regulatory functions of TFs as well as their influences on gene expression, we conducted, in diverse cell lines, genome-wide identification of the binding sites of several sequence-specific TFs (CTCF, E2F4, MYC, Pol II) that are involved in a wide range of biological functions, including cell proliferation, development, apoptosis, genome stability, and DNA repair. Analysis of ChIP-seq data provided not only comprehensive binding profiles of those TF across the genome in diverse cell lines, but also revealed tissue-specific binding of CTCF, MYC, and Pol II as well as combinatorial usage among these three factors. Analyses also showed that some CTCF binding sites were inherited from parents to children and regulated in an individual-specific as well as allele-specific manner. Finally, genome-wide target identification of several TFs will broaden our understanding of the gene regulatory roles of these sequence-specific TFs. Advisors/Committee Members: Iyer, Vishwanath R. (advisor), DeLozanne, Arturo (committee member), Marcotte, Edward (committee member), Tucker, Philip (committee member), Stevens, Scott (committee member).

Subjects/Keywords: Sequence-specific transcription factors; Genome-wide target genes; Cellular contexts; Binding sites; Chromatin Immunopracipitation; ChIP-seq data; E2F4; CTCF; MYC; RNAPII

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APA (6^th Edition):

Lee, B. K. (2011). Genome-wide target identification of sequence-specific transcription factors through ChIP sequencing. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/ETD-UT-2011-05-3038

Chicago Manual of Style (16^th Edition):

Lee, Bum Kyu. “Genome-wide target identification of sequence-specific transcription factors through ChIP sequencing.” 2011. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/ETD-UT-2011-05-3038.

MLA Handbook (7^th Edition):

Lee, Bum Kyu. “Genome-wide target identification of sequence-specific transcription factors through ChIP sequencing.” 2011. Web. 20 Jan 2021.

Vancouver:

Lee BK. Genome-wide target identification of sequence-specific transcription factors through ChIP sequencing. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2011. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/ETD-UT-2011-05-3038.

Council of Science Editors:

Lee BK. Genome-wide target identification of sequence-specific transcription factors through ChIP sequencing. [Doctoral Dissertation]. University of Texas – Austin; 2011. Available from: http://hdl.handle.net/2152/ETD-UT-2011-05-3038

23. Malur, Meghana. Host innate immune response to influenza A virus infection : role of LGP2 and importance of NS1:CPSF30 interaction for virulence.

Degree: PhD, Microbiology, 2011, University of Texas – Austin

URL: http://hdl.handle.net/2152/19827

► Influenza A viruses can cause a highly contagious respiratory illness in humans. Immediately after virus infection the innate immune response is initiated by binding of… (more)

▼ Influenza A viruses can cause a highly contagious respiratory illness in humans. Immediately after virus infection the innate immune response is initiated by binding of viral RNA species to RIG-I that leads to activation of IRF3 and NF-κB transcription factors and activation of interferon (IFN) transcription. LGP2 is a member of the RIG-I like receptor (RLR) family and is induced after virus infection. The role of LGP2 in virus infection is controversial: it has been reported to either positively or negatively affect RIG-I mediated signaling. The goal of this study was to determine whether LGP2 has a role during infection with influenza A viruses that have circulated in humans. We focused on two viruses expressing NS1 proteins that differ in their ability to inhibit IRF3 activation and IFN transcription; a H1N1 virus (Tx91) that inhibits IRF3 activation and a H3N2 virus (Ud) that does not. This study revealed that LGP2 has strikingly different roles during infection of mouse embryonic fibroblasts and human cells with these viruses. Specifically, LGP2 has no detectable role in H1N1 virus-infected cells, whereas it downregulates IFN synthesis in H3N2 virus-infected cells. Our results indicate that LGP2 acts as a negative regulator of the IFN response in influenza A viruses that activate IRF3. The NS1 protein also binds the 30kDa-subunit of the cleavage and polyadenylation specificity factor-CPSF30, a protein required for 3′-end processing of cellular pre-mRNAs, thereby inhibiting production of mature IFN-β mRNA. The NS1 proteins of pathogenic 1997 H5N1 viruses lack two highly conserved residues (F103 and M106) that are needed to stabilize the NS1-CPSF30 complex. Instead their NS1 proteins have L at 103 and I at 106, resulting in non-optimal CPSF30 binding in infected cells. We demonstrated that strengthening CPSF30 binding by changing L and I to the consensus residues (F and M respectively) leads to a dramatic (300-fold) increase in lethality of the virus in mice. This increased virulence is associated with faster systemic spread of the virus. Microarray analyses revealed increased cytokine levels in extrapulmonary tissues, particularly the brain. These results highlight the importance of NS1:CPSF30 binding in modulating virulence in H5N1 viruses. Advisors/Committee Members: Krug, Robert M. (advisor), Huibregtse, Jon M (committee member), Iyer, Vishwanath R (committee member), Sullivan, Christopher S (committee member), Russell, Rick (committee member).

Subjects/Keywords: IRF3; Interferon regulatory factor 3; IFN; Interferon; LGP2; Laboratory of genetics and physiology

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APA (6^th Edition):

Malur, M. (2011). Host innate immune response to influenza A virus infection : role of LGP2 and importance of NS1:CPSF30 interaction for virulence. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/19827

Chicago Manual of Style (16^th Edition):

Malur, Meghana. “Host innate immune response to influenza A virus infection : role of LGP2 and importance of NS1:CPSF30 interaction for virulence.” 2011. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/19827.

MLA Handbook (7^th Edition):

Malur, Meghana. “Host innate immune response to influenza A virus infection : role of LGP2 and importance of NS1:CPSF30 interaction for virulence.” 2011. Web. 20 Jan 2021.

Vancouver:

Malur M. Host innate immune response to influenza A virus infection : role of LGP2 and importance of NS1:CPSF30 interaction for virulence. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2011. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/19827.

Council of Science Editors:

Malur M. Host innate immune response to influenza A virus infection : role of LGP2 and importance of NS1:CPSF30 interaction for virulence. [Doctoral Dissertation]. University of Texas – Austin; 2011. Available from: http://hdl.handle.net/2152/19827

24. Popowski, Melissa Ann. Role of Bright/ARID3A in mouse development, somatic cell reprogramming, and pluripotency.

Degree: PhD, Cell and Molecular Biology, 2012, University of Texas – Austin

URL: http://hdl.handle.net/2152/ETD-UT-2012-08-6316

► Bright/ARID3A was initially discovered for its role in immunoglobulin heavy chain transcription in the mouse. Bright has also been implicated as a target of p53… (more)

▼ Bright/ARID3A was initially discovered for its role in immunoglobulin heavy chain transcription in the mouse. Bright has also been implicated as a target of p53 and as an E2F binding partner. We have previously shown that Bright is necessary for hematopoietic stem cell development in the embryo. In this work, we show that Bright has a much broader role in development than previously appreciated. Loss of Bright in mice usually results in embryonic lethality due to lack of hematopoietic stem cells. Rare survivor mice initially appear smaller in size than either wildtype or heterozygous littermates, but as they age, these differences diminish. We show that adult Bright null mice have age-dependent kidney defects. Previous work in the adult mouse has not indicated a role for Bright in kidney function. We observed an increase in cellular proliferation in Bright null kidneys, indicating a possible mechanism behind our observation. Loss of Bright has recently been implicated in causing developmental plasticity in somatic cells. Our data indicate that loss of Bright is sufficient to fully reprogram mouse embryonic fibroblasts (MEFs) back to a pluripotent state. We term these cells Bright repression induced pluripotent stem cells (BriPS). BriPS derived from Bright knockout MEFs can be stably maintained in standard embryonic stem cell culture conditions: they express pluripotency markers and can form teratomas in vivo. We further viii show that Bright is active during embryonic stem cell differentiation. Bright represses key pluripotency genes, suggesting the mechanism of reprogramming may be Bright’s direct repression of key pluripotency factors in somatic cells. Recent advances in inducing pluripotency in somatic cells (iPS cells) have created a new field of disease modeling, increased our knowledge of how pluripotency is regulated, and introduced the hope that they can be adapted to treat disease. However, current methods for producing iPS involve overexpression of potentially oncogenic transcription factors, leaving a large gap between the lab and the clinic. Our results mark the first demonstration of an alternative method to reprograming somatic cells that is not mediated by overexpression of pluripotency factors. Advisors/Committee Members: Tucker, Philip W. (advisor), Huibregtse, Jon M. (committee member), Iyer, Vishwanath R. (committee member), Marcotte, Edward M. (committee member), Sanders, Bob G. (committee member).

Subjects/Keywords: Bright; ARID3A; Cell reprogramming; Induced pluripotency

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APA (6^th Edition):

Popowski, M. A. (2012). Role of Bright/ARID3A in mouse development, somatic cell reprogramming, and pluripotency. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/ETD-UT-2012-08-6316

Chicago Manual of Style (16^th Edition):

Popowski, Melissa Ann. “Role of Bright/ARID3A in mouse development, somatic cell reprogramming, and pluripotency.” 2012. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/ETD-UT-2012-08-6316.

MLA Handbook (7^th Edition):

Popowski, Melissa Ann. “Role of Bright/ARID3A in mouse development, somatic cell reprogramming, and pluripotency.” 2012. Web. 20 Jan 2021.

Vancouver:

Popowski MA. Role of Bright/ARID3A in mouse development, somatic cell reprogramming, and pluripotency. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2012. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/ETD-UT-2012-08-6316.

Council of Science Editors:

Popowski MA. Role of Bright/ARID3A in mouse development, somatic cell reprogramming, and pluripotency. [Doctoral Dissertation]. University of Texas – Austin; 2012. Available from: http://hdl.handle.net/2152/ETD-UT-2012-08-6316

25. Batista, Bianca Stella. Glycomic insights into microvesicle biogenesis.

Degree: PhD, Cell and Molecular Biology, 2011, University of Texas – Austin

URL: http://hdl.handle.net/2152/ETD-UT-2011-08-4240

► Cells can mediate intercellular communication by the secretion and uptake of microvesicles, nano-sized membranous particles that carry signaling molecules, antigens, lipids, mRNA and miRNA between… (more)

▼ Cells can mediate intercellular communication by the secretion and uptake of microvesicles, nano-sized membranous particles that carry signaling molecules, antigens, lipids, mRNA and miRNA between cells. The biological function of these vesicles is dependent upon their composition and cellular origin which is regulated by mechanisms that are not well understood. Based on their molecular content, microvesicles may play a role in immune regulation, cancer progression, the spread of infectious agents and numerous other important normal and pathogenic processes. The proteomic content of microvesicles from diverse sources has been intensely studied. In contrast, little is known about their glycomic content. The glycosylation pattern of a protein or lipid plays a key role in determining its functional properties in several ways. Glycans can determine the trafficking of a protein to particular regions of the cell as well as the protein’s half life. In addition, the glycan-dervied oligomerization of glycolipids and glycoproteins is a known mechanism for the activation of receptors and recognition of ligands on the surface of the cell. Glycomic analysis may thus provide valuable insights into microvesicle function. I utilized lectin microarray technology to compare the glycosylation patterns of microvesicles derived from a variety of biological sources. When compared to cellular membranes, microvesicles were enriched in high mannose, polylactosamine, α2-6 sialic acid, and complex N-linked glycans but exclude terminal blood group A and B antigens. The polylactosamine signature in microvesicles from different cell lines derives from distinct glycoprotein cohorts. After treatment of Sk-Mel-5 cells with lactose to inhibit lectin-glycan interactions, secretion of microvesicle resident proteins was severely reduced. Taken together, this work provides evidence for a role of glycosylation in microvesicle-directed protein sorting. Advisors/Committee Members: Stein, David S. (advisor), Mahal, Lara K. (advisor), Iyer, Vishwanath R. (committee member), Sullivan, Christopher S. (committee member), Liu, Hung-Wen (committee member).

Subjects/Keywords: Lectin microarray; Glycosylation; Microvesicles; Exosomes; Ectosomes; Glycomics; Lectins; Microparticles

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APA (6^th Edition):

Batista, B. S. (2011). Glycomic insights into microvesicle biogenesis. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/ETD-UT-2011-08-4240

Chicago Manual of Style (16^th Edition):

Batista, Bianca Stella. “Glycomic insights into microvesicle biogenesis.” 2011. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/ETD-UT-2011-08-4240.

MLA Handbook (7^th Edition):

Batista, Bianca Stella. “Glycomic insights into microvesicle biogenesis.” 2011. Web. 20 Jan 2021.

Vancouver:

Batista BS. Glycomic insights into microvesicle biogenesis. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2011. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/ETD-UT-2011-08-4240.

Council of Science Editors:

Batista BS. Glycomic insights into microvesicle biogenesis. [Doctoral Dissertation]. University of Texas – Austin; 2011. Available from: http://hdl.handle.net/2152/ETD-UT-2011-08-4240

26. Zhao, Alice. Cytoplasmic foci at the crossroads of artifactual science and biological function.

Degree: PhD, Cell and molecular biology, 2016, University of Texas – Austin

URL: http://hdl.handle.net/2152/39610

► Deciphering protein interaction and compartmentalization is crucial to understanding the molecular mechanisms that drive biological processes. Using various high throughput approaches, we have managed to… (more)

Subjects/Keywords: Protein; Foci; Fiber; Filament; Macrostructure; Immunofluorescence; Immunoprecipitation; Microscopy; Protein tag; TTC4; Purinosome; Co-fractionation; Cell chip; Transfection; High-throughput; Aggregation; CTP synthase; Glutamine synthetase; Purine biosynthesis

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APA (6^th Edition):

Zhao, A. (2016). Cytoplasmic foci at the crossroads of artifactual science and biological function. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/39610

Chicago Manual of Style (16^th Edition):

Zhao, Alice. “Cytoplasmic foci at the crossroads of artifactual science and biological function.” 2016. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/39610.

MLA Handbook (7^th Edition):

Zhao, Alice. “Cytoplasmic foci at the crossroads of artifactual science and biological function.” 2016. Web. 20 Jan 2021.

Vancouver:

Zhao A. Cytoplasmic foci at the crossroads of artifactual science and biological function. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2016. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/39610.

Council of Science Editors:

Zhao A. Cytoplasmic foci at the crossroads of artifactual science and biological function. [Doctoral Dissertation]. University of Texas – Austin; 2016. Available from: http://hdl.handle.net/2152/39610

27. -8320-6789. Functional analysis of DNA methylation and hydroxymethylation during eye development.

Degree: PhD, Cell and Molecular Biology, 2018, University of Texas – Austin

URL: http://hdl.handle.net/2152/65697

► DNA methylation is an epigenetic mechanism known to play roles in regulating gene expression in various developmental and disease contexts. However, little is known about… (more)

▼ DNA methylation is an epigenetic mechanism known to play roles in regulating gene expression in various developmental and disease contexts. However, little is known about its function during eye development. Two types of methylation marks, 5- methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), are thought to serve as silencing and activating signals for gene regulation, respectively. De novo methyltransferases (dnmt3 family) are responsible for the establishment of 5mC, while cytosine dioxygenases (tet family) convert 5mC into 5hmC, a stable epigenetic mark that can either remain on the genome or undergo subsequent demethylation. Here I performed gene expression and functional tests to elucidate the roles for both of these cytosine-modifying enzyme families during development, with an emphasis on the eye. All dnmt3-family and tet-family genes are expressed tissue-specifically in relevant domains during eye development. Single and double mutants for genes within dnmt3 family develop normally without any overt eye phenotype, indicating that these genes possess redundant functions during eye development. In contrast, in tet2-/-;tet3-/- mutants, retinal neurons are specified but most fail to terminally differentiate. Retinal ganglion cells lack a proper retino-tectal projection, and photoreceptors fail to generate outer segments. Mechanistically, mosaic analyses revealed a surprising cell non-autonomous requirement for tet activity during retinal neurogenesis. Through a combination of candidate gene analysis, transcriptomics and pharmacological manipulations, I identified candidate cell-extrinsic pathways regulated by tet2 and tet3. Additionally, genome-wide 5mC and 5hmC distribution profiles for retinal progenitor cells (RPCs) and differentiated retinal neurons are still currently unknown. To this end, I performed parallel bisulfite and oxidative bisulfite reactions followed by next-generation sequencing (BS/OXBS-seq) to generate the first nucleotide-resolution combined methylome/hydroxymethylome map of retinal cells during development and correlated these with gene expression. This genome- wide approach revealed expected 5mC/5hmC profiles of candidate retinal developmental genes, and identified several novel, uncharacterized genes with potential roles during RPC differentiation. These genes are candidates for further investigation to determine their functions during retinal neurogenesis. Data presented in this Dissertation uncover the role of DNA methylation and hydroxymethylation during eye development and provide the first epigenomic maps of 5mC/5hmC dynamics during retina formation. Advisors/Committee Members: Vokes, Steven Alexander (advisor), Gross, Jeffrey Martin (advisor), Chen, Zengjian (committee member), Stein, David (committee member), Iyer, Vishwanath R (committee member).

Subjects/Keywords: DNA; Methylation; Hydroxymethylation; 5mC; 5hmC; Retina; Development; Zebrafish; Oxidative; Bisulfite; Epigenetic

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APA (6^th Edition):

-8320-6789. (2018). Functional analysis of DNA methylation and hydroxymethylation during eye development. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/65697

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Chicago Manual of Style (16^th Edition):

-8320-6789. “Functional analysis of DNA methylation and hydroxymethylation during eye development.” 2018. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/65697.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

MLA Handbook (7^th Edition):

-8320-6789. “Functional analysis of DNA methylation and hydroxymethylation during eye development.” 2018. Web. 20 Jan 2021.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Vancouver:

-8320-6789. Functional analysis of DNA methylation and hydroxymethylation during eye development. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2018. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/65697.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Council of Science Editors:

-8320-6789. Functional analysis of DNA methylation and hydroxymethylation during eye development. [Doctoral Dissertation]. University of Texas – Austin; 2018. Available from: http://hdl.handle.net/2152/65697

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

28. Ki, Sanghee. Thymocytes require stromal-derived signals, incluiding activation of chemokine receptors EBI2 and GRP146, for proper differentiation and selection.

Degree: PhD, Cell and molecular biology, 2016, University of Texas – Austin

URL: http://hdl.handle.net/2152/41590

► The thymus is the primary lymphoid organ where immature thymocytes differentiate and mature to become functional T cells that are self-MHC restricted and self-tolerant. In… (more)

▼ The thymus is the primary lymphoid organ where immature thymocytes differentiate and mature to become functional T cells that are self-MHC restricted and self-tolerant. In addition to developing T cells, the thymus is comprised of stromal cells, subdivided into cortical and medullary regions, which form a component of the microenvironment for thymocyte development. Throughout their development, thymocytes undergo bidirectional crosstalk with the thymic epithelial cells, which is essential for proper development of both the thymocyte and epithelial subsets. Thymic involution is a detrimental process of aging which results in degeneration of the thymic microenvironment, reduction in T cell output, and contraction of the naïve T cell pool, thus contributing to impaired immune responses in aging individuals. Molecular and cellular changes that drive thymic atrophy during aging are not well understood. To address this gap in knowledge, I analyzed transcriptional changes in purified thymic stromal subsets early in the process of age-associated thymic involution (Chapter 2). These studies revealed that there is gradual down-regulation of cell cycle genes and E2F3 transcriptional targets in thymic epithelial cell subsets as the thymus begins to involute. This suggests that diminished proliferative activity in a subset of thymic epithelial cells is a major contributing factor to age-associated involution. I also identified an increasingly proinflmamatory signature in thymic dendritic cells early in the involution process. These results have provided novel insights into the mechanisms behind thymic atrophy and identify cellular targets for thymic rebound strategies. Chemokine receptors, a subset of G protein coupled receptors (GPCRs), have been implicated in guiding thymocytes between different thymic regions, thus enabling interactions with local stromal subsets that support T cell differentiation. For example, chemokine receptors play an essential role in driving thymocyte migration into the medulla, where thymocytes scan numerous self-antigens to establish central tolerance. Importantly, failure of thymocytes to enter the thymic medulla results in impaired self-tolerance, leading to autoimmunity. We have identified EBI2 and GPR146 as candidate GPCRs that could contribute to thymocyte accumulation in the medulla, interactions with antigen presenting cells therein, and thus the induction of tolerance. In chapter 3, I report that EBI2 is essential for negative selection toward some self-antigens and restrains regulatory T cell generation in the thymus. Through two-photon imaging, I identified reduced motility and medullary accumulation as mechanisms by which EBI2 deficiency could impair negative selection. In chapter 4, I describe generation of a GPR146 deficient mouse strain, and initial studies indicating GPR146 is involved in thymocyte differentiation and selection. Through these studies we have revealed novel functions for GPCRs in promoting thymocyte migration and the induction of self-tolerance. Advisors/Committee Members: Ehrlich, Lauren (advisor), Marcotte, Edward M. (committee member), Tucker, Haley (committee member), Vokes, Steven (committee member), Iyer, Vishwanath R. (committee member).

Subjects/Keywords: Thymocyte; G-protein coupled receptor; Thymocyte development; Negative selection; Thymic stroma cells; Thymic involution; EBI2; GPR146

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APA (6^th Edition):

Ki, S. (2016). Thymocytes require stromal-derived signals, incluiding activation of chemokine receptors EBI2 and GRP146, for proper differentiation and selection. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/41590

Chicago Manual of Style (16^th Edition):

Ki, Sanghee. “Thymocytes require stromal-derived signals, incluiding activation of chemokine receptors EBI2 and GRP146, for proper differentiation and selection.” 2016. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/41590.

MLA Handbook (7^th Edition):

Ki, Sanghee. “Thymocytes require stromal-derived signals, incluiding activation of chemokine receptors EBI2 and GRP146, for proper differentiation and selection.” 2016. Web. 20 Jan 2021.

Vancouver:

Ki S. Thymocytes require stromal-derived signals, incluiding activation of chemokine receptors EBI2 and GRP146, for proper differentiation and selection. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2016. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/41590.

Council of Science Editors:

Ki S. Thymocytes require stromal-derived signals, incluiding activation of chemokine receptors EBI2 and GRP146, for proper differentiation and selection. [Doctoral Dissertation]. University of Texas – Austin; 2016. Available from: http://hdl.handle.net/2152/41590

29. Agarwal, Poonam. Understanding chromatin mechanisms involved in DNA damage and chemotherapeutic responses.

Degree: PhD, Cell and Molecular Biology, 2018, University of Texas – Austin

URL: http://hdl.handle.net/2152/63290

► One of the hallmarks of cancer is genomic instability driven by DNA damage. Cells respond to these genetic insults through chromatin-based mechanisms that repair the… (more)

▼ One of the hallmarks of cancer is genomic instability driven by DNA damage. Cells respond to these genetic insults through chromatin-based mechanisms that repair the damage. Chromatin plays a pivotal role in protecting cells from genome and epigenome instability that drive cancer progression. Chromatin, a highly dynamic complex of DNA and proteins, undergoes structural and functional changes in response to cellular factors that are essential for replication, transcription, DNA damage responses (DDR) and repair. Chromatin structure and function are highly dependent on histone modifications. Histones are modified on distinct amino acids by post-translational modifications (PTMs). Delineating chromatin-regulated processes are fundamental for understanding the nuclear pathways that regulate access to, and protection of, our genetic and epigenetic information. The first part of my project focused on analyzing the contribution of a chromatin domain, the nucleosome acidic patch in regulating histone H2A/X ubiquitination and the DDR using in vitro and in vivo approaches. I established techniques to biochemically purify human recombinant histones and reconstituted nucleosome core particles (NCPs) containing WT or acidic patch mutant H2A/X for in vitro Ub assays with purified E3 ligases, RNF168 and RING1B/BMI1. Both E3s ubiquitinated H2A/X within WT NCPs but not mutant NCPs. Thus, this assay confirmed our hypothesis that the effect of the acidic patch mutation on H2AX/ H2Aub is direct and that it mediates site-specific ubiquitinations. I showed that the acidic patch interacting peptide LANA could compete with RNF168 and RING1B/BMI1 dependent H2AX/H2A Ub. In the second project, I tested how chromatin alters targeting of an anticancer drug using a cisplatin derivative that acts on the genome. I identified that cotreatment of cisplatin and the clinically approved drug Vorinostat/SAHA generated clusters of lesions that co-localized with translesion synthesis factors. However, I found that activated translesion synthesis no longer acted as a bypass mechanism but instead promoted apoptosis. These results demonstrated that pharmacological alterations of chromatin reprograms genome targeting with platinum drugs and, concomitantly, drug response. The third project for my thesis work involves functional analysis of the bromodomain containing TRIM proteins in DDR. These proteins belong to the bromodomain (BRD) family, which are the readers of PTM acetylation. I identified specific domains in TRIM24 required for its recruitment to damaged DNA and its dependency on other chromatin associated factors, namely, SUV39H1, KAT6B, TRIM28, TRIM33 that regulate TRIM24 dynamics in the context of DNA damage. I validated some interactors of TRIM24, TRIM28 and TRIM33 including the FACT and MCM complex. In summary, knowledge gained from these studies will help to understand how these BRD reader proteins promote the DDR within acetylated chromatin to preserve genome stability. Advisors/Committee Members: Miller, Kyle M. (advisor), Iyer, Vishwanath R (committee member), Paull, Tanya T (committee member), Vasquez, Karen M (committee member), Xhemalce, Blerta (committee member).

Subjects/Keywords: DNA damage; Chromatin

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APA (6^th Edition):

Agarwal, P. (2018). Understanding chromatin mechanisms involved in DNA damage and chemotherapeutic responses. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/63290

Chicago Manual of Style (16^th Edition):

Agarwal, Poonam. “Understanding chromatin mechanisms involved in DNA damage and chemotherapeutic responses.” 2018. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/63290.

MLA Handbook (7^th Edition):

Agarwal, Poonam. “Understanding chromatin mechanisms involved in DNA damage and chemotherapeutic responses.” 2018. Web. 20 Jan 2021.

Vancouver:

Agarwal P. Understanding chromatin mechanisms involved in DNA damage and chemotherapeutic responses. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2018. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/63290.

Council of Science Editors:

Agarwal P. Understanding chromatin mechanisms involved in DNA damage and chemotherapeutic responses. [Doctoral Dissertation]. University of Texas – Austin; 2018. Available from: http://hdl.handle.net/2152/63290

30. Zhou, Li, doctor of microbiology. Mechanistic analysis of selective inhibition of RNA processing in Escherichia coli.

Degree: PhD, Microbiology, 2010, University of Texas – Austin

URL: http://hdl.handle.net/2152/ETD-UT-2010-08-1691

► In Escherichia coli, the RNA degradosome is a protein complex involved in the general degradation of mRNA and in post-transcriptional gene regulation. The principal components… (more)

Subjects/Keywords: RNA Degradosome; RNase E; RraA; RraB

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APA (6^th Edition):

Zhou, Li, d. o. m. (2010). Mechanistic analysis of selective inhibition of RNA processing in Escherichia coli. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/ETD-UT-2010-08-1691

Chicago Manual of Style (16^th Edition):

Zhou, Li, doctor of microbiology. “Mechanistic analysis of selective inhibition of RNA processing in Escherichia coli.” 2010. Doctoral Dissertation, University of Texas – Austin. Accessed January 20, 2021. http://hdl.handle.net/2152/ETD-UT-2010-08-1691.

MLA Handbook (7^th Edition):

Zhou, Li, doctor of microbiology. “Mechanistic analysis of selective inhibition of RNA processing in Escherichia coli.” 2010. Web. 20 Jan 2021.

Vancouver:

Zhou, Li dom. Mechanistic analysis of selective inhibition of RNA processing in Escherichia coli. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2010. [cited 2021 Jan 20]. Available from: http://hdl.handle.net/2152/ETD-UT-2010-08-1691.

Council of Science Editors:

Zhou, Li dom. Mechanistic analysis of selective inhibition of RNA processing in Escherichia coli. [Doctoral Dissertation]. University of Texas – Austin; 2010. Available from: http://hdl.handle.net/2152/ETD-UT-2010-08-1691

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