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The Functional Significance Of The Carboxyl Terminal Domain Of Rna Polymerase Iia O
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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 Role of O-GlcNAc on the RNA Polymerase II Carboxyl-terminal Domain by : Frank Irvin Comer
Download or read book Role of O-GlcNAc on the RNA Polymerase II Carboxyl-terminal Domain written by Frank Irvin Comer and published by . This book was released on 2000 with total page 254 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 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 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 Functions of Mediator and the RNA Polymerase II C-terminal Domain in Transcription Initiation by : Stefan Böing
Download or read book Functions of Mediator and the RNA Polymerase II C-terminal Domain in Transcription Initiation written by Stefan Böing and published by . This book was released on 2008 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 Mutational Analysis of the Carboxyl-terminal Domain of the RNA Polymerase II Largest Subunit by : Marilyn A. L. West
Download or read book A Mutational Analysis of the Carboxyl-terminal Domain of the RNA Polymerase II Largest Subunit written by Marilyn A. L. West and published by . This book was released on 1992 with total page 214 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Role of the RNA Polymerase II C-terminal Domain in Transcription Termination and Function of Spt5 in 3' RNA-processing Factor Recruitment by : Amelie Erna Schreieck
Download or read book Role of the RNA Polymerase II C-terminal Domain in Transcription Termination and Function of Spt5 in 3' RNA-processing Factor Recruitment written by Amelie Erna Schreieck and published by . This book was released on 2013 with total page 196 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 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 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 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 Post-translational Modification of the C-terminal Domain of RNA Polymerase II by : Joshua Edward Mayfield
Download or read book Post-translational Modification of the C-terminal Domain of RNA Polymerase II written by Joshua Edward Mayfield and published by . This book was released on 2017 with total page 336 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA polymerase II is a highly regulated protein complex that transcribes all protein coding mRNA and many non-coding RNAs. A key mechanism that facilitates its activity is post-translational modification of the carboxyl-terminal domain of RNA polymerase II (CTD). This unstructured domain is conserved throughout eukaryotes and composed of repeats of the consensus amino acid heptad Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. This domain acts as a platform for the recruitment of transcriptional regulators that specifically recognize post-translational modification states of the CTD. The majority of our understanding of CTD modification comes from the use of phospho-specific antibodies, which provide identity and abundance information but give only low-resolution information for how these marks co-exist and interact at the molecular level. During my graduate work I sought to utilize the tools of chemical biology to investigate CTD modification in high resolution. Using a combination of chemical tools, analytical chemistry, and molecular biology I studied CTD modification in extremely high resolution. This work reveals the existence of interactions between CTD modifications, the influence of CTD sequence divergence on modification events, and presents initial data to support a role for previously encoded modifications to direct subsequent modification events
Book Synopsis Functional Analysis of the RNA Polymerase II C-terminal Domain Kinase Ctk1 in the Yeast Saccharomyces Cerevisiae by : Susanne Röther
Download or read book Functional Analysis of the RNA Polymerase II C-terminal Domain Kinase Ctk1 in the Yeast Saccharomyces Cerevisiae written by Susanne Röther and published by . This book was released on 2007 with total page 204 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 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
