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Rna Polymerase Ii Carboxy Terminal Domain Phosphatase Microform
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Author :Michael S. (Michael Steffen) Kobor Publisher :National Library of Canada = Bibliothèque nationale du Canada ISBN 13 :9780612590236 Total Pages :712 pages Book Rating :4.5/5 (92 download)
Book Synopsis RNA Polymerase II Carboxy-terminal Domain Phosphatase [microform] by : Michael S. (Michael Steffen) Kobor
Download or read book RNA Polymerase II Carboxy-terminal Domain Phosphatase [microform] written by Michael S. (Michael Steffen) Kobor and published by National Library of Canada = Bibliothèque nationale du Canada. This book was released on 2001 with total page 712 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis RNA Polymerase II Carboxy-terminal Domain Phosphatase by :
Download or read book RNA Polymerase II Carboxy-terminal Domain Phosphatase written by and published by . This book was released on 2001 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis RNA Polymerase II Carboxy-terminal Domain Phosphatase by : Michael S. Kobor
Download or read book RNA Polymerase II Carboxy-terminal Domain Phosphatase written by Michael S. Kobor and published by . This book was released on 2001 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The form of RNA polymerase II (RNAPII) that binds preferentially to promoters is not extensively phosphorylated on the carboxy-terminal heptapeptide repeat domain (CTD) of its largest subunit. The CTD becomes phosphorylated during or shortly after initiation and elongating RNAPII generally has a phosphorylated CTD. Prior to or following transcriptional termination, dephosphorylation of the CTD presumably must occur to regenerate the hypophosphorylated form of RNAPII that is capable of reinitiating transcription. This thesis examines the function of the CTD phosphatase Fcp1p in the yeast 'Saccharomyces cerevisiae'. In chapter 2, it is shown that Fcp1 is an unusual eukaryotic protein phosphatase that is required for dephosphorylation of the CTD 'in vivo ' and for transcription by RNAPII 'in vivo'. These results suggest that Fcp1p is the founding member of a new class of protein phosphatases and acts as a general transcription factor 'in vivo'. In chapter 3, affinity chromatography is used to study the binding of Fcp1p to TFIIB and the RAP74 subunit of TFIIF. Fcp1p binds in a similar way to both of these factors. RAP74 and TFIIB have a short region of homology and amino acid changes in this region affect the binding to Fcp1p. The genes encoding RAP74 and Fcp1p interact 'in vivo'. Fcp1p can activate transcription when artificially tethered to a promoter and this effect is largely dependent on binding to RAP74. In chapter 4, it is shown that yeast strains with mutations in ' fcp1' grow much worse when the gene encoding the major CTD kinase Kin28p is also mutated. In contrast, inactivation of another CTD kinase encoded by the 'SRB10' gene suppresses the temperature-sensitivity and the sensitivity to certain cell cycle checkpoint inducing drugs of ' fcp1' mutant strains. These results therefore suggest that Fcp1p and Srb10p have opposing roles 'in vivo'. In chapter 5, analysis of the phosphorylation state of the CTD reveals that reduced Fcp1p activity results in a increased amount of the largest subunit of RNAPII but this subunit is not incorporated into functional enzyme and is largely degraded at a higher temperature.
Book Synopsis Regulation of RNA Polymerase II CTD Phosphatase in S. Cerevisiae by : Susanne Jutta Hoheisel
Download or read book Regulation of RNA Polymerase II CTD Phosphatase in S. Cerevisiae written by Susanne Jutta Hoheisel and published by . This book was released on 2005 with total page 328 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 Structural Basis of RNA Polymerase II C-terminal Domain Kinase and Phosphatase Specificity and Their Impact on Transcriptional Regulation by : Nathaniel Tate Burkholder
Download or read book Structural Basis of RNA Polymerase II C-terminal Domain Kinase and Phosphatase Specificity and Their Impact on Transcriptional Regulation written by Nathaniel Tate Burkholder and published by . This book was released on 2019 with total page 292 pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcription from a most basic perspective is the process of generating strands of RNA from DNA templates. However, in order to control when, where, and how much of specific RNAs are made, cells have evolved vast arrays of transcriptional regulatory mechanisms that allow for extensive differentiation and formation of complex traits. One of the unique and most important mechanisms of transcriptional regulation in eukaryotic cells is the reversible phosphorylation of the RNA polymerase II C-terminal domain (RNAPII CTD). The CTD contains heptad repeats composed of the consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 and all of the non-proline sites are phosphorylated in cells. The human CTD contains 52 repeats where the first 26 proximal heptads are mostly consensus sequence whereas the last 26 distal heptads contain several variations primarily at the Ser7 position. In Chapter 2, I describe how these variations and their modifications alter the phosphorylation of Tyr1 sites by using a combination of biochemical assays and mass spectrometry. Data presented in this chapter reveal how a conserved positively charged pocket in tyrosine kinases likely mediates the interaction residues in the Ser7 position and can potentially affect in vivo Tyr1 phospho-patterning. Futhermore, in Chapter 3 I describe the methodology behind synthesis and testing of cis/trans-locked Ser-Pro CTD peptides for understanding the role of prolyl isomerization on CTD regulation. We used these tools to determine the specificity of several CTD phosphatases, which revealed how the Ser5 phosphatase SSU72 structurally prefers the cis- over the trans-configuration of the phosphorylated Ser5-Pro6 motif. Among the phosphatases discovered to dephosphorylate the CTD, the family of SCP phosphatases seem to be more involved in regulating transcription through dephosphorylation of a different protein called the RE-1 silencing transcription factor (REST). REST is a major silencer of neuronal gene expression in non-neuronal cells which helps prevent development of improper neuronal phenotypes. Abnormally high protein levels of REST have been found in subsets of glioblastoma isolates which likely contributes to their oncogenesis and resistance of chemotherapeutics. SCP1 upregulates REST protein levels through dephosphorylating two degron sites that normally promote rapid turnover of REST, making it a potential drug target for glioblastomas in future studies. In Chapter 4, we show structurally how SCP1 recognizes these REST phosphorylation sites through complex x-ray crystallography. Data presented in this chapter reveal SCP1 specificity for each REST site and how SCP1 activity towards both of them promote REST gene silencing function
Book Synopsis Dynamic Changes in Phosphorylation of RNA Polymerase II Carboxy-terminal Domain During Transcription Cycle by : E. J. Cho
Download or read book Dynamic Changes in Phosphorylation of RNA Polymerase II Carboxy-terminal Domain During Transcription Cycle written by E. J. Cho and published by . This book was released on 2002 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis The Functional Significance of the Carboxyl-terminal Domain of RNA Polymerase IIa/o by : Paul James Laybourn
Download or read book The Functional Significance of the Carboxyl-terminal Domain of RNA Polymerase IIa/o written by Paul James Laybourn and published by . This book was released on 1989 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Phosphorylation of the Carboxyl-terminal Domain of the RNA Polymerase II Largest Subunit by : Jie Zhang
Download or read book Phosphorylation of the Carboxyl-terminal Domain of the RNA Polymerase II Largest Subunit written by Jie Zhang and published by . This book was released on 1991 with total page 98 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Recognition of RNA Polymerase II Carboxy-terminal Domain by 3'-RNA Processing Factors by : Anton Meinhart
Download or read book Recognition of RNA Polymerase II Carboxy-terminal Domain by 3'-RNA Processing Factors written by Anton Meinhart and published by . This book was released on 2004 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis The RNA Polymerase II C-terminal Domain by :
Download or read book The RNA Polymerase II C-terminal Domain written by and published by . This book was released on 2006 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis RNA Polymerase II Controls Transcription Dynamics by :
Download or read book RNA Polymerase II Controls Transcription Dynamics written by and published by . This book was released on 2013 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The C-terminal domain (CTD) of RNA polymerase II (Pol II) consists of conserved heptapeptide repeats that are subject to sequential waves of posttranslational modifications during specific stages of the transcription cycle. These patterned modifications have led to the postulation of the CTD code hypothesis, where stage-specific patterns define a spatiotemporal code that is recognized by the appropriate interacting partners. This thesis summarizes our efforts to define the CTD code, identify the writers and erasers, and explore the function of the code during transcription. We examined the genome-wide distributions of the phospho-serine modifications. We found unique profile clusters for the "early" serine 5 phosphorylation (Ser5-P), the "mid" serine 7 phosphorylation (Ser7-P), and the "late" serine 2 phosphorylation (Ser2-P). We also identified gene class-specific patterns and find widespread co-occurrence of the CTD marks. These phosphorylation marks are placed by an array of phospho-serine kinases. We identified Kin28 (CDK7) as a Ser7-P kinase, and specific inhibition of Kin28 caused a significant decrease in Ser7-P levels at promoters. However, the promoter-distal Ser7-P marks are not remnants of early phosphorylation by Kin28. Instead, we find that Bur1 (CDK9) is positioned to phosphorylate Ser7 within the coding regions. Next, we investigated the phosphatases that erase the CTD code. The importance of these enzymes is emphasized by our observation that an inability to remove Ser7-P marks is lethal. We identified Ssu72 as a Ser7-P phosphatase, and inactivation of Ssu72 triggers a drastic remodeling of Ser7-P distributions across protein-coding and non-coding genes. Furthermore, we report that removal of all phospho-CTD marks during transcription termination is mechanistically coupled. An inability to remove these marks prevents Pol II from terminating efficiently at both gene classes and also impedes proper transcription initiation. Interestingly, Ssu72 seems to be enriched within introns, peaking at the 3' splice site. Interestingly, we do not find polymerase pausing at the 3' splice site or at the terminal exons, as has been previously reported. Instead, we believe Ssu72 may be involved in facilitating the cotranscriptional recruitment of splicing factors by establishing a chromatin state accommodating to splicing.
Book Synopsis Phosphatases and Prolyl-isomerase in the Regulation of the C-terminal Domain of Eukaryotic RNA Polymerase II by : Mengmeng Zhang
Download or read book Phosphatases and Prolyl-isomerase in the Regulation of the C-terminal Domain of Eukaryotic RNA Polymerase II written by Mengmeng Zhang and published by . This book was released on 2012 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: In eukaryotes, the first step of interpreting the genetic information is the transcription of DNA into RNA. For protein-coding genes, such transcription is carried out by RNA polymerase II. A special domain of RNA polymerase II, called the C-terminal domain (CTD), functions as a master controller for the transcription process by providing a platform to recruit regulatory proteins to nascent mRNA (Chapter 1-2). The modifications and conformational states of the CTD, termed the 'CTD code', represent a critical regulatory checkpoint for transcription. The CTD, found only in eukaryotes, consists of 26--52 tandem heptapeptide repeats with the consensus sequence, Tyr1Ser2Pro3Thr4Ser5Pro6Ser--. Phosphorylation of the serines and prolyl isomerization of the prolines represent two major regulatory mechanisms of the CTD. Interestingly, the phosphorylation sites are typically close to prolines, thus the conformation of the adjacent proline could impact the specificity of the corresponding kinases and phosphatases. Understanding how those modifying enzymes recognize and regulate the CTD is important for expanding our knowledge on the transcription regulation and deciphering the 'CTD code'. During my PhD study, I studied the function of CTD phosphatases and prolyl isomerase in the CTD regulation using Scp1, Ssu72 and Pin1 as model regulators. Scp1 and Ssu72 are both Ser5 phosphatases. However, Ssu72 is an essential protein and regulates the global transcription while Scp1 epigenetically silences the expression of specific neuronal genes. Pin1 is a highly conserved phosphorylation-specific prolyl isomerase that recognizes the phospho-Ser/Thr-Pro motif within the CTD as one of its primary substrates in vivo. Among these enzymes, Scp1 is the focal point of this dissertation, as it was studied from different angles, such as enzymatic mechanism (Chapter 3 describes the capture of phospho-aspartyl intermediate of Scp1 as a direct evidence for the proposed two-step mechanism), specific inhibition (Chapter 4 describes the identification and characterization of the first specific inhibitor of Scp1), and its non-active-site contact with the CTD (Chapter 5 describes the structural basis of this contact). These studies are of great importance towards understanding the molecular mechanism of the dephosphorylation process of the CTD by Scp1.
Book Synopsis The C-terminal Domain of RNA Polymerase II by : Anton Yuryev
Download or read book The C-terminal Domain of RNA Polymerase II written by Anton Yuryev and published by . This book was released on 1995 with total page 162 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis A Functional Analysis of the RNA Polymerase II Large Subunit Carboxy-terminal Domain by : Rob Chapman
Download or read book A Functional Analysis of the RNA Polymerase II Large Subunit Carboxy-terminal Domain written by Rob Chapman and published by . This book was released on 2002 with total page 122 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis The Role of the CTD Phosphatase Rtr1 and Post-translational Modifications in Regulation of RNA Polymerase II by : Mary L. Cox
Download or read book The Role of the CTD Phosphatase Rtr1 and Post-translational Modifications in Regulation of RNA Polymerase II written by Mary L. Cox and published by . This book was released on 2013 with total page 186 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA polymerase II (RNAPII) is regulated by multiple modifications to the C-terminal domain (CTD) of the largest subunit, Rpb1. This study has focused on the relationship between hyperphosphorylation of the CTD and RNAPII turnover and proteolytic degradation as well as post-translational modifications of the globular core of RNAPII. Following tandem affinity purification, western blot analysis showed that MG132 treated RTR1 ERG6 deletion yeast cells have accumulation of total RNAPII and in particular, the hyperphosphorylated form of the protein complex. In addition, proteomic studies using MuDPIT have revealed increased interaction between proteins of the ubiquitin-proteasome degradation system in the mutant MG132 treated yeast cells as well as potential ubiquitin and phosphorylation sites in RNAPII subunits, Rpb6 and Rpb1, respectively. A novel Rpb1 phosphorylation site, T1471-P, is located in the linker region between the CTD and globular domain of Rpb1 and will be the focus of future studies to determine biological significance of this post-translational modification.
Book Synopsis Mutant Analysis of the RNA Polymerase II Carboxy-terminal Domain by : Lauren McCarl
Download or read book Mutant Analysis of the RNA Polymerase II Carboxy-terminal Domain written by Lauren McCarl and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The carboxy-terminal domain (CTD) of Rpb1, the largest subunit of RNA polymerase II (RNAPII), is a tail-like extension that enables RNAPII to interact with a myriad of factors essential for transcription and co-transcriptional RNA processing. It is characterized by tandem heptad repeats, the consensus sequence of which is YSPTSPS. Different combinations of phosphorylated residues have been found to correlate with different stages of the transcription cycle. To enhance our understanding of the functionally enigmatic nonconsensus heptads, two distinct generations of CTD mutant transgenic fly lines were generated by the Gilmour lab. The first generation expressed both endogenous RNAPII and a CTD mutant version of the polymerase. The second generation, designed to determine rescue ability, co-expressed short hairpin RNA against endogenous Rpb1 mRNA (shRpb1) and a shRpb1-resistant version of CTD mutant RNAPII. In addition to helping construct several plasmids to create these CTD mutants, I also characterized previously generated mutants by beta-galactosidase ([beta]-gal) staining assay and quantitative real-time PCR (qRT-PCR). The [delta]Hep(exp) mutant, characterized by the deletion of a highly conserved, eight-repeat region containing the only two conserved heptads of the Drosophila CTD, was of particular interest because it is lethal in adult flies. My [beta]-gal assays and qRT-PCR analysis showed the [delta]Hep(exp) mutation had largely no effect on hsp70 reporter gene expression or endogenous hsp70 mRNA synthesis, respectively. This suggests the defect associated with [delta]Hep(exp) may involve a gene (or genes) other than hsp70.
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