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Biochemical Studies On The Role Of Rna Polymerase Ii Phosphorylation During Transcription Initiation
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Book Synopsis Biochemical Studies on the Role of RNA Polymerase II Phosphorylation During Transcription Initiation by : Hua Lü
Download or read book Biochemical Studies on the Role of RNA Polymerase II Phosphorylation During Transcription Initiation written by Hua Lü and published by . This book was released on 1993 with total page 286 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis The Role of RNA Polymerase II Phosphorylation in the Early Stages of Transcription by : Jonathan Donald Chesnut
Download or read book The Role of RNA Polymerase II Phosphorylation in the Early Stages of Transcription written by Jonathan Donald Chesnut and published by . This book was released on 1994 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Biochemical Studies of Transcription by RNA Polymerase II by : Mark E. Samuels
Download or read book Biochemical Studies of Transcription by RNA Polymerase II written by Mark E. Samuels and published by . This book was released on 1985 with total page 424 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis A Biochemical Analysis of Transcription Initiation by RNA Polymerase II by : Sharon Lynn Wampler
Download or read book A Biochemical Analysis of Transcription Initiation by RNA Polymerase II written by Sharon Lynn Wampler and published by . This book was released on 1993 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Protein Phosphorylation in Human Health by : Cai Huang
Download or read book Protein Phosphorylation in Human Health written by Cai Huang and published by BoD – Books on Demand. This book was released on 2012-09-06 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: 15 chapters on protein phosphorylation and human health written by expert scientists. Covers most important research hot points, such as Akt, AMPK and mTOR. Bridges the basic protein phosphorylation pathways with human health and diseases. Detailed and comprehensive text with excellent figure illustration.
Book Synopsis Structural and Biochemical Studies of the Transcription Termination Machinery by : Peter Hsu
Download or read book Structural and Biochemical Studies of the Transcription Termination Machinery written by Peter Hsu and published by . This book was released on 2013 with total page 118 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA Polymerase II (PolII) dependent transcription of mRNAs is central to gene expression throughout eukaryotes. Transcription is a highly regulated process, with a defined initiation, elongation, and termination phase, all of which are controlled by multiple trans-acting protein factors and cis-acting elements on the template DNA and transcribed RNA. Extensive work has shown that the phosphorylation state of the C- terminal domain (CTD) of PolII plays a central role in the recruitment of trans-acting factors during all phases of transcription. Aberrant phosphorylation can result in a lethal phenotype in yeasts, therefore implying that correct control of phosphorylation by kinases and phosphatases specific for the CTD is critical for life. In addition to the polymerase, conserved cis-acting sequence elements near the 3'-end on pre-mRNAs help to define and recruit various RNA processing machines to the transcription elongation complex in order to properly process and package the pre-mRNA for export to the cytoplasm for translation. In this thesis, I first review current knowledge regarding PolII CTD phosphorylation and its effects on the transcription elongation complex. Additionally, in this first chapter, I will also provide an overview of the 3'-end mRNA processing/transcription termination machinery. In the second part of my thesis, I will describe my doctoral work on the structural and biochemical characterization of Rtr1, a unique PolII CTD phosphatase that represents a novel new member of this class of enzymes. In my studies, I show that Rtr1 is a bona fide phosphatase of unique sequence and structure that is allosterically regulated by its own C-terminus. Additionally, I show that Rtr1 is a dual specificity phosphatase, with activities against both serine and tyrosine residues on the CTD. In chapter 3 of this thesis, I describe my work on the in vitro reconstitution of the Cleavage Stimulation Factor (CstF) responsible for the recognition of sequences downstream of the polyadenylation site on pre-mRNAs that help to define the 3'-end processing reaction that occur at the end of genes. Using highly purified proteins, I show for the first time that CstF is a dimer of trimers, with two copies of each subunit in the entire assembly. In addition, I show that CstF, as a complex, can bind to G/U rich RNAs with nanomolar affinities, in stark contrast with previous studies showing that singly purified proteins from the complex binding with much weaker affinities.
Book Synopsis RNA Polymerase and Associated Factors, Part A by : Sankar Adhya
Download or read book RNA Polymerase and Associated Factors, Part A written by Sankar Adhya and published by Academic Press. This book was released on 1996-09-16 with total page 416 pages. Available in PDF, EPUB and Kindle. Book excerpt: The critically acclaimed laboratory standard for more than forty years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. More than 270 volumes have been published (all of them still in print) and much of the material is relevant even today--truly an essential publication for researchers in all fields of life sciences. Key Features * Promoter elements and RNA polymerase components * RNA polymerase and its subunits in prokaryotes * Biochemical assays of transcription initiation * RNA polymerase and associated factors from eukaryotes * Genetic analysis of transcription and its regulation
Book Synopsis Transcription by : Ronald C. Conaway
Download or read book Transcription written by Ronald C. Conaway and published by Raven Press (ID). This book was released on 1994 with total page 600 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presents a coherent account of many productive lines of investigation, organized as a series of mini-reviews that focus on major research areas including studies on the structure and mechanisms of action of bacterial, viral, and eukaryotic RNA polymerases, and the transcription factors that control their activities. Each review provides a brief but up-to-date account of the progress of research in a particular area, a discussion of the major issues and questions driving that research, and a brief description of the evolving approaches and technologies used to address those questions. Annotation copyright by Book News, Inc., Portland, OR
Book Synopsis Structural Heterogeneity in the RNA Polymerase II C-Terminal Domain by : Bede Portz
Download or read book Structural Heterogeneity in the RNA Polymerase II C-Terminal Domain written by Bede Portz and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA polymerase II contains a repetitive and intrinsically disordered C-Terminal Domain (CTD) composed of heptad repeats of the consensus sequence YSPTSPS. The CTD can be heavily phosphorylated and serves as a scaffold, interacting with factors involved in transcription initiation, elongation, termination, RNA processing and chromatin modification. Despite its role as a nexus of eukaryotic gene regulation, the structure of the CTD and the structural implications of CTD phosphorylation, are poorly understood. Additionally, there is an increasing awareness of the importance of intrinsically disordered proteins (IDPs) that function without adopting a stably folded structure. Here I present a biophysical and biochemical interrogation of the structure of the full-length CTD of D. melanogaster, which I conclude is a compact random coil. I find that the repetitive CTD is structurally heterogeneous as evidenced by a discontinuous pattern of cutting in limited proteolysis assays. Small Angle X-Ray scattering (SAXS) is a method ideally suited for the structural interrogation of large IDPs and can be employed to measure the size of a protein and to monitor structural changes in response to post-translational modification. Using SAXS I determined that phosphorylation by the kinase P-TEFb caused an increase in CTD radius and stiffness. Limited proteolysis of the phosphorylated CTD showed these gross structural changes are accompanied by increased protease accessibility and an alteration in relative protease accessibility across the length of the CTD.Additionally, we show that the human CTD is also structurally heterogeneous and able to substitute for the Drosophila melanogaster CTD in supporting the development of flies to adulthood. These finding implicate conserved structural organization, not a precise array of heptad motifs, as important to CTD function.The CTD is attached to the catalytic core of Pol II via a linker. I show that this linker is more compact than the CTD repeats and serves as an independent structural unit. The phosphorylated linker-CTD remains flexible relative to the phosphorylated CTD alone. Together, these results support a mechanism by which phosphorylation reduces the conformational entropy of the CTD, generating a more binding competent dock for CTD:protein interactions, with the linker region maintaining the ability of CTD bound factors to sample the 3-dimensional space which may be required for RNA processing and histone modification.The data described herein represent the most thorough structural characterization to date of the full length CTD on the global and local scales, examining both the overall size and local structural organization of the CTD. These studies establish the Drosophila CTD as an attractive model for the biophysical, biochemical and genetic interrogation of the structure and function of the CTD from a developmentally complex organism.
Book Synopsis Functions of Transcription Factor IIF in Initiation and Elongation by RNA Polymerase II by : Chun-hsiang Chang
Download or read book Functions of Transcription Factor IIF in Initiation and Elongation by RNA Polymerase II written by Chun-hsiang Chang and published by . This book was released on 1995 with total page 336 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis The Functions of the RNA Polymerase II CTD in Transcription and RNA Processing by :
Download or read book The Functions of the RNA Polymerase II CTD in Transcription and RNA Processing written by and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Finally, Chapter 4 describes what we have found the functions of CTD Tyr 1. Using the DT40-Rpb1 cells, I created stable cell lines expressing an Rpb1 with all Tyr residues mutated to phenylalanine (Phe). We found these cells were inviable, and the mutant Rpb1-Y1F was degraded to a CTD-less protein. Interestingly, the instability of Rpb1-Y1F was restored by reintroduction of one Tyr residue at the last heptad repeat. Further analysis provided evidence showing the involvement of Tyr phosphorylation in preventing Rpb1 from degradation by the 20S proteasome. Next, using ChIP assay, we showed Tyr phosphorylation was detected mostly at promoters, indicating a function of Tyr phosphorylation in transcription initiation. Indeed, transcription initiation defects were uncovered by assessing the recruitment of general transcription factors in cells with Y1F mutation. Extending this, we found an accumulation of upstream antisense RNAs in about one hundred reference genes by RNA-Seq analysis.
Book Synopsis MECHANISTIC STUDIES OF RNA POLYMERASE II SPECIES-SPECIFIC TRANSCRIPTION INITIATION PATTERNS by : Chen Yang
Download or read book MECHANISTIC STUDIES OF RNA POLYMERASE II SPECIES-SPECIFIC TRANSCRIPTION INITIATION PATTERNS written by Chen Yang and published by . This book was released on 2010 with total page 213 pages. Available in PDF, EPUB and Kindle. Book excerpt: The basal eukaryotic transcription machinery for protein coding genes is highly conserved from yeast to high eukaryotes. However, while human cells usually initiate at a single transcription start site approximately 30 bp downstream of a TATA element, Schizosaccharomyces pombe typically initiates at multiple sites 30-70 bp, and Saccharomyces cerevisiae 40 to 200 bp downstream of the TATA. The determinant factor(s) for the species specific initiation and the underlying mechanisms for the multiple far downstream start site utilization in yeast are not well understood. By swapping the highly purified transcription factors between S. pombe and S. cerevisiae reconstituted transcription systems, we confirmed previous observations that RNA polymerase II and/or the general transcription factor TFIIB determine the species-specific start site utilization patterns. Further genetic and biochemical assays of TFIIB chimeras indicated that RNAPII, but not TFIIB as previously proposed, determines the distinct initiation patterns not only between the two yeast systems but also between human and yeast systems. Bubble template initiation assays showed that there is an inverse correlation between the amount of negative charge in the TFIIB B-fingertip and the efficiency of the first phosphodiester bond formation. Moreover, biochemical studies indicate that multiple initiation steps, including first phosphodiester bond formation, and RNA:DNA hybrid stability determined initiation-to-elongation transition, could be modulated to regulate the far downstream start sites utilization in S. cerevisiae. A model for multiple far downstream transcription start sites formation in S. cerevisiae is proposed.
Book Synopsis Influence of RNA Polymerase II Catalytic Activity on Transcription Start Site Selection by : Huiyan Jin
Download or read book Influence of RNA Polymerase II Catalytic Activity on Transcription Start Site Selection written by Huiyan Jin and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA Polymerase II (Pol II) is responsible for expression of all protein-coding genes in eukaryotes. To understand gene expression at the molecular level, it is essential to understand the mechanisms of Pol II function. I investigate how Pol II catalytic activity influences the first step of gene expression, transcription initiation, in Saccharomyces cerevisiae. My dissertation focuses on the mechanisms by which Pol II activity defects contribute to transcription start site (TSS) selection/utilization and promoter output. I utilize mutants with substitutions in the Pol II active site that have different elongation rates in vitro and show varied growth phenotypes in vivo that correlate with the observed alterations in elongation rates. I employ genetic and biochemical approaches to investigate the relationships between the TSS phenotypes of Pol II activity/General Transcription Factor (GTF) mutants and conditional and general growth phenotypes. I show that while some conditional growth phenotypes correlate closely with TSS defects, TSS defects are not likely the main determinant for general growth defects. I further explore growth phenotypes and TSS defects between Pol II genetic interactors and GTF mutants combined with Pol II activity mutants and present different models for the relationships discovered so far. I discover a novel function of Sub1, which is suggested to play positive roles in transcription as an initiation factor, altering TSS utilization on its own and modifying TSS defects conferred by Pol II activity mutants. I take a genome wide approach to map TSSs, general transcription factor occupancies, and nucleosome positions to investigate the mechanism of Pol II activity control over initiation, and determine how promoter architecture influences TSS selection/utilization and nucleosome positioning. I show that promoter architecture is a critical parameter in determination of various initiation properties including transcription output (gene expression) levels. The electronic version of this dissertation is accessible from http://hdl.handle.net/1969.1/155628
Book Synopsis Proteins in Eukaryotic Transcription by :
Download or read book Proteins in Eukaryotic Transcription written by and published by Elsevier. This book was released on 2004-03-19 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein Transcription is a key element of cellular and organ regulation. Proteins in Eukaryotic Transcription covers structure and function of all major elements associated with transcription. Mechanism of RNA polymerase I Transcription Structure and function of RNA Polymerase II Structure and function of the TFIID complex Functional properties of Chromatin Remodeling Enzymes Posttranslational modification
Book Synopsis Study of RNA Polymerase II Transcription Complex During Transcription Initiation by : Haini Cai
Download or read book Study of RNA Polymerase II Transcription Complex During Transcription Initiation written by Haini Cai and published by . This book was released on 1987 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Mechanisms of Yeast RNA Polymerase II Transcription and the Role of Transcription Factor IIF by :
Download or read book Mechanisms of Yeast RNA Polymerase II Transcription and the Role of Transcription Factor IIF written by and published by . This book was released on 2006 with total page 204 pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcription of protein-coding genes by eukaryotic RNA polymerase II (RNAPII) is a multistep process that involves the concerted action of RNAPII and accessory proteins including the general transcription factors (GTFs); TFIID, TFIIB, TFIIF, TFIIE and TFIIH. The GTFs are being intensely studied to determine their function during the different stages of the transcription cycle. Numerous investigations have reported functions for the general transcription factor IIF (TFIIF) of higher eukaryotes in multiple stages of the transcription cycle, although few studies have examined the TFIIF homolog in the yeast Saccharomyces cerevisiae. The objective of this dissertation is to better understand the mechanism of action of S. cerevisiae TFIIF during the different stages of the RNAPII transcription cycle. Although the basal transcription factors are highly homologous in eukaryotes, the mechanism of transcription start site utilization on TATA-dependent promoters in S. cerevisiae is fundamentally different from that in higher eukaryotes, where the PIC assembles on the promoter and transcription initiates at a discrete site 25-30 base pairs downstream of the TATA element with the architecture of the PIC determining the initiation site. In contrast, the S. cerevisiae RNAPII machinery typically initiates at multiple sites in a window from 45 to 120 base pairs downstream of the TATA element. Results in this thesis support a transcription initiation mechanism that involves transcription-independent translocation of the yeast RNAPII to the far downstream start sites. Previous work in our laboratory identified mutations in the yeast TFIIF subunits Tfg1 and Tfg2 that confer upstream shifts in start site utilization. In vivo and in vitro studies demonstrate that TFIIF modulates the utilization of transcription start site sequences through its interaction with RNAPII. In the second and third part of this dissertation, genetic and biochemical approaches were utilized to better define TFIIF functions at post-initiation steps in the S. cerevisiae transcription cycle, and support a role for TFIIF in both promoter escape and early elongation. Combined results of this work support a model for TFIIF function where the TFIIF, through its interaction with RNAPII, affects the DNA recognition properties of the polymerase during start site utilization, promoter escape, and early elongation.
Book Synopsis Mechanisms of Transcription Factor IIF Function During the RNA Polymerase II Transcription Cycle by :
Download or read book Mechanisms of Transcription Factor IIF Function During the RNA Polymerase II Transcription Cycle written by and published by . This book was released on 2008 with total page 176 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the yeast Saccharomyces cerevisiae, transcription frequently initiates at multiple sites ranging from 45 to 120 base pairs or greater downstream of the site of preinitiation complex assembly. Previous studies in our laboratory and others have established that RNA polymerase II (RNAPII) and the general transcription factors IIB (TFIIB) and IIF (TFIIF) play important roles in determining the positions of the mRNA 5' ends in S. cerevisiae. In this dissertation, I report the results from biochemical studies analyzing the functional alterations conferred by mutations in RNAPII and TFIIF that cause changes in transcription start site utilization. I report that the downstream shifts in start site utilization conferred by the Rpb1-R344A mutation are associated with increased abortive transcription and inability to efficiently stabilize a short RNA/DNA hybrid in the RNAPII active center. In contrast, the upstream shifts conferred by the Tfg1-E346A substitution in TFIIF are associated with both enhanced efficiency of early phosphodiester bond formation and processive elongation in vitro. These data are discussed within a proposed model for the mechanism of yeast transcription initiation in which TFIIF interaction with RNAPII modulates both early bond formation during start site utilization and conversion of RNAPII to a more processive elongating form.
