Mechanisms of Factor Recruitment at Promoters During RNA Polymerase II Transcription PDF Download
Are you looking for read ebook online? Search for your book and save it on your Kindle device, PC, phones or tablets. Download Mechanisms of Factor Recruitment at Promoters During RNA Polymerase II Transcription PDF full book. Access full book title Mechanisms of Factor Recruitment at Promoters During RNA Polymerase II Transcription by Natalya Yudkovsky. Download full books in PDF and EPUB format.
Author: Natalya Yudkovsky
Publisher:
ISBN:
Category :
Languages : en
Pages : 188
Get Book Here
Book Description
Author: Natalya Yudkovsky
Publisher:
ISBN:
Category :
Languages : en
Pages : 188
Get Book Here
Book Description
Author: Mark Ptashne
Publisher: CSHL Press
ISBN: 9780879696337
Category : Medical
Languages : en
Pages : 212
Get Book Here
Book Description
P. 103.
Author: Marc Böhning
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
Get Book Here
Book Description
Transcription of protein-coding genes by RNA polymerase (Pol) II is a highly coordinated process. In metazoan cells, transcription is regulated both at the initiation step by recruitment of the Pol II machinery as well as during early elongation by promoter-proximal pausing. Prior to transcription initiation, Pol II forms short-lived clusters near active gene promoters, but the underlying molecular basis has remained unknown. Pol II possesses a disordered C-terminal heptad repeat domain (CTD) that is essential for factor recruitment during the transcription cycle. CTD length is organism-spe...
Author: Muyu Xu
Publisher:
ISBN:
Category : Genetic regulation
Languages : en
Pages : 178
Get Book Here
Book Description
Author: Catherine Patricia George
Publisher:
ISBN:
Category :
Languages : en
Pages : 232
Get Book Here
Book Description
Author: Ronald C. Conaway
Publisher: Raven Press (ID)
ISBN:
Category : Science
Languages : en
Pages : 600
Get Book Here
Book Description
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
Author: Manchuta Dangkulwanich
Publisher:
ISBN:
Category :
Languages : en
Pages : 137
Get Book Here
Book Description
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.
Author:
Publisher:
ISBN:
Category :
Languages : en
Pages : 204
Get Book Here
Book Description
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.
Author: Albert J. Courey
Publisher: John Wiley & Sons
ISBN: 1444300458
Category : Science
Languages : en
Pages : 248
Get Book Here
Book Description
Mechanisms in Transcriptional Regulation provides a concisediscussion of the fundamental concepts in transcription and itsregulation. Covers RNA polymerases, transcriptional machinery, mechanismsof transcriptional activation, the histone code hypothesis, theepigenetic control of transcription, and combinatorial control insignaling and development Features over 80 figures available to download online Chapters include comprehensive reading lists, boxeshighlighting theoretical concepts and experimental methods andproblems designed to build and test understanding
Author: Ming Yan
Publisher:
ISBN:
Category :
Languages : en
Pages : 204
Get Book Here
Book Description
