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The Mechanism Of Transcript Elongation By Rna Polymerase Ii
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Book Synopsis The Mechanism of Transcript Elongation by RNA Polymerase II by : Michael D. Rudd
Download or read book The Mechanism of Transcript Elongation by RNA Polymerase II written by Michael D. Rudd and published by . This book was released on 1997 with total page 422 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Molecular Mechanisms of Factors that Control RNA Polymerase II Transcription Elongation Dynamics by : Manchuta Dangkulwanich
Download or read book Molecular Mechanisms of Factors that Control RNA Polymerase II Transcription Elongation Dynamics written by Manchuta Dangkulwanich and published by . This book was released on 2015 with total page 137 pages. Available in PDF, EPUB and Kindle. Book excerpt: The expression of a gene begins by transcribing a target region on the DNA to form a molecule of messenger RNA. As transcription is the first step of gene expression, it is there- fore highly regulated. The regulation of transcription is essential in fundamental biological processes, such as cell growth, development and differentiation. The process is carried out by an enzyme, RNA polymerase, which catalyzes the addition of a nucleotide complementary to the template and moves along the DNA one base pair at a time. To complete its tasks, the enzyme functions as a complex molecular machine, possessing various evolutionarily designed parts. In eukaryotes, RNA polymerase has to transcribe through DNA wrapped around histone proteins forming nucleosomes. These structures represent physical barriers to the transcribing enzyme. In chapter 2, we investigated how each nucleosomal component--the histone tails, the specific histone-DNA contacts, and the DNA sequence--contributes to the strength of the barrier. Removal of the tails favors progression of RNA polymerase II into the entry region of the nucleosome by locally increasing the wrapping-unwrapping rates of the DNA around histones. In contrast, point mutations that affect histone-DNA contacts at the dyad abolish the barrier to transcription in the central region by decreasing the local wrapping rate. Moreover, we showed that the nucleosome amplifies sequence-dependent transcriptional pausing, an effect mediated through the structure of the nascent RNA. Each of these nucleosomal elements controls transcription elongation by distinctly affecting the density and duration of polymerase pauses, thus providing multiple and alternative mechanisms for control of gene expression by additional factors. During transcription elongation, RNA polymerase has been assumed to attain equilibrium between pre- and post-translocated states rapidly relative to the subsequent catalysis. Under this assumption, a branched Brownian ratchet mechanism that necessitates a putative secondary nucleotide binding site on the enzyme was proposed. In chapter 3, we challenged individual yeast RNA polymerase II (Pol II) with a nucleosome as a "road block", and separately measured the forward and reverse translocation rates with our single-molecule transcription elongation assay. Surprisingly, we found that the forward translocation rate is comparable to the catalysis rate. This finding reveals a linear, non-branched ratchet mech-anism for the nucleotide addition cycle in which translocation is one of the rate-limiting steps. We further determined all the major on- and off-pathway kinetic parameters in the elongation cycle. This kinetic model provides a framework to study the influence of various factors on transcription dynamics. To further dissect the operation of Pol II, we focused on the trigger loop, a mobile element near the active site of the enzyme. Biochemical and structural studies have demonstrated that the trigger loop makes direct contacts with substrates and promotes nucleotide incorporation. It is also an important regulatory element for transcription fidelity. In chapter 4, we characterized the dynamics of a trigger loop mutant RNA polymerase to elucidate the roles of this element in transcription regulation, and applied the above kinetic framework to quantify the effects of the mutation. In comparison to the wild-type enzyme, we found that the mutant is more sensitive to force, faster at substrate sequestration, and more efficient to return from a pause to active transcription. This work highlighted important roles of regulatory elements in controlling transcription dynamics and fidelity. Moreover, RNA polymerase interacts with various additional factors, which add layers of regulation on transcription. Transcription factors IIS (TFIIS) and IIF (TFIIF) are known to interact with elongating RNA polymerase directly and stimulate transcription. In chapter 5, we studied the effects of these factors on elongation dynamics using our single molecule assay. We found that both TFIIS and TFIIF enhance the overall transcription elongation by reducing the lifetime of transcriptional pauses and that TFIIF also decreases the probability of pause entry. Furthermore, we observed that both factors enhance the efficiency of nucleosomal transcription. Our findings helped elucidate the molecular mechanisms of gene expression modulation by transcription factors. In summary, we have dissected the mechanisms by which the nucleosomal elements regulate transcription, and derived a quantitative kinetic model of transcription elongation in a linear Brownian ratchet scheme with the slow translocation of the enzyme. The corresponding translocation energy landscape shows that the off-pathway states are favored thermodynamically but not kinetically over the on-pathway states. This observation confers the enzyme its high propensity to pause, thus allowing additional regulatory mechanisms during pausing. TFIIS and TFIIF, for example, regulate transcription dynamics by shortening the lifetime of Pol II pauses. On the other hand, the trigger loop of Pol II regulates both the active elongation and pausing. These examples illustrate molecular mechanisms of cis- and trans-acting factors regulate the dynamics of transcription elongation.
Book Synopsis The Mechanics of Transcription by RNA Polymerase by : Elio Aaron Abbondanzieri
Download or read book The Mechanics of Transcription by RNA Polymerase written by Elio Aaron Abbondanzieri and published by . This book was released on 2005 with total page 164 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Mechanisms of Transcription Elongation and the Nuclease Activity of RNA Polymerase II by : Eric Eugene Sheagley
Download or read book Mechanisms of Transcription Elongation and the Nuclease Activity of RNA Polymerase II written by Eric Eugene Sheagley and published by . This book was released on 2003 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Transcription and Splicing by : B. D. Hames
Download or read book Transcription and Splicing written by B. D. Hames and published by Oxford University Press, USA. This book was released on 1988 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book gives a co-ordinated review of our present knowledge of eukaryotic RNA synthesis.
Book Synopsis Dissection of the Precise Mechanisms of RNA Polymerase II Pausing and Elongation Using Nascent Transcript Analysis by : Hojoong Kwak
Download or read book Dissection of the Precise Mechanisms of RNA Polymerase II Pausing and Elongation Using Nascent Transcript Analysis written by Hojoong Kwak and published by . This book was released on 2013 with total page 183 pages. Available in PDF, EPUB and Kindle. Book excerpt: Limiting RNA polymerase II (Pol II) at various stages of the transcription cycle is critical for gene regulation, which often occurs during the elongation stage at promoter proximal pause sites and in gene bodies. To determine the distribution of Pol II along genes, I used nascent transcript analysis as a general method. First, I identified the precise positions of Pol II pausing near promoters using a genome-wide nuclear run-on, called Precision Run-On sequencing (PRO-seq) in Drosophila embryonic cells. Using this, I revealed how the position of pausing is associated with initiation and promoter DNA elements. To further dissect the precise dynamics of paused Pol II, I probed the stability of paused Pol II and its termination by analyzing steady-state turn-over of the nascent transcript associated with Drosophila Hsp70 promoter. This shows that paused Pol II on Hsp70 is stable for around 5 min and can either terminate or elongate into the gene body, which is consistent with optical measurements of paused Pol II. I also examined how Pol II elongates during the time course of rapid and robust inhibition of pause escape in mouse embryonic stem cells. The analysis of the elongation rates in nearly 1,000 genes showed tight interplay between promoter proximal pausing, early elongation rates, and co-transcriptional splicing at the beginning of the genes. Finally, I demonstrate that the nascent transcriptome analysis methods can be directly extended into mammalian tissues, and show possibility of linking the study of the fundamental mechanism of Pol II into biomedical applications.
Book Synopsis Mechanism and Regulation of Yeast RNA Polymerase II Transcription Initiation and Termination by : Jason Nicholas Kuehner
Download or read book Mechanism and Regulation of Yeast RNA Polymerase II Transcription Initiation and Termination written by Jason Nicholas Kuehner and published by . This book was released on 2008 with total page 188 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Mechanisms of Transcription Elongation and Proofreading by Human RNA Polymerase II by : Matthew Joseph Thomas
Download or read book Mechanisms of Transcription Elongation and Proofreading by Human RNA Polymerase II written by Matthew Joseph Thomas and published by . This book was released on 1997 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Structural Basis of Initiation and Elongation by RNA Polymerase II by : Kenneth Dale Westover
Download or read book Structural Basis of Initiation and Elongation by RNA Polymerase II written by Kenneth Dale Westover and published by . This book was released on 2005 with total page 222 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Mechanisms of Transcription by : Kirill Konovalov
Download or read book Mechanisms of Transcription written by Kirill Konovalov and published by . This book was released on 2021 with total page 96 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Mechanisms of RNA Polymerase II Transcription Initiation by : Catherine Patricia George
Download or read book Mechanisms of RNA Polymerase II Transcription Initiation written by Catherine Patricia George and published by . This book was released on 1996 with total page 232 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis RNA Polymerase II During Transcript Elongation by : Stephanie Ellen Kong
Download or read book RNA Polymerase II During Transcript Elongation written by Stephanie Ellen Kong and published by . This book was released on 2001 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis The Regulation of Transcription Initiation and Elongation by RNA Polymerase II. by : Michael Justin Blau
Download or read book The Regulation of Transcription Initiation and Elongation by RNA Polymerase II. written by Michael Justin Blau and published by . This book was released on 1996 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis RNA as Molecular Motors 2E by : Robert Landick
Download or read book RNA as Molecular Motors 2E written by Robert Landick and published by Royal Society of Chemistry. This book was released on 2021-12-15 with total page 295 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book, written by expert scientists in the field, analyses how these diverse fields of research interact on a specific example - RNA polymerase.
Book Synopsis Cell Biology by the Numbers by : Ron Milo
Download or read book Cell Biology by the Numbers written by Ron Milo and published by Garland Science. This book was released on 2015-12-07 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: A Top 25 CHOICE 2016 Title, and recipient of the CHOICE Outstanding Academic Title (OAT) Award. How much energy is released in ATP hydrolysis? How many mRNAs are in a cell? How genetically similar are two random people? What is faster, transcription or translation?Cell Biology by the Numbers explores these questions and dozens of others provid
Book Synopsis RNA Polymerase II Collision & Its Role in Transcript Elongation by : David James Hobson
Download or read book RNA Polymerase II Collision & Its Role in Transcript Elongation written by David James Hobson and published by . This book was released on 2012 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Elongation by RNA Polymerase II by : Hongliang Guo
Download or read book Elongation by RNA Polymerase II written by Hongliang Guo and published by . This book was released on 1993 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: