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Biochemical And Genetic Investigations Of Transcript Initiation And Elongation In Saccharomyces Cerevisiae
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Book Synopsis Biochemical and Genetic Investigations of Transcript Initiation and Elongation in Saccharomyces Cerevisiae by : Rachel Naomi Fish
Download or read book Biochemical and Genetic Investigations of Transcript Initiation and Elongation in Saccharomyces Cerevisiae written by Rachel Naomi Fish and published by . This book was released on 2002 with total page 622 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Biochemical and Genetic Characterization of the Transcription Elongation Factor TFIIS from the Yeast Saccharomyces Cerevisiae by : Karen Renee Christie
Download or read book Biochemical and Genetic Characterization of the Transcription Elongation Factor TFIIS from the Yeast Saccharomyces Cerevisiae written by Karen Renee Christie and published by . This book was released on 1995 with total page 600 pages. Available in PDF, EPUB and Kindle. Book excerpt: Regulation of the process of transcriptional elongation is an important control mechanism in the expression of some genes. To fully understand this form of regulation will require better understanding of the functions of transcription elongation factors. The goal of this work was to characterize the transcription elongation factor TFIIS from Saccharomyces cerevisiae, originally called P37. I demonstrated that, like the mammalian TFIIS proteins, the yeast protein stimulates RNA polymerase II to cleave the nascent RNA transcript and to read-through an intrinsic block to elongation. Investigation of the protein-protein contacts between TFIIS and RNA polymerase II indicated that the carboxyl-terminal domain of the largest subunit, subunit four, and subunit seven of the polymerase are not required for TFIIS to promote cleavage and read-through by the polymerase. In addition the carboxyl-terminal half of the yeast TFIIS protein is sufficient for both of these in vitro activities. This result is consistent with the previous results demonstrating the carboxyl-terminus of mouse TFIIS was sufficient to activate RNA polymerase in vitro.
Book Synopsis Investigation of Transcription Initiation from Cryptic Promoter Sites in Saccharomyces Cerevisiae by : Vanessa Cheung
Download or read book Investigation of Transcription Initiation from Cryptic Promoter Sites in Saccharomyces Cerevisiae written by Vanessa Cheung and published by . This book was released on 2008 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Previous studies in Saccharomyces cerevisiae have shown that mutations in SPT6, SPT16, SET2, and other genes encoding particular chromatin and transcription factors cause the activation of cryptic promoters within coding regions, resulting in the expression of short RNA transcripts. In this work, we examine cryptic initiation in S. cerevisiae on a genome-wide scale to identify all factors required for repressing cryptic promoters and to determine the extent and possible role of cryptic initiation. Using large-scale mutant selections and synthetic genetic array analysis, we have identified mutants affecting histone gene regulators, chromatin remodeling factors, and histories as allowing cryptic initiation. Through microarray analysis, we show that approximately 1,000 genes, or almost one-sixth of the S. cerevisiae genome, express short transcripts in spt6 or spt16 mutants. A significant number of these genes are shown to be conserved with respect to synonymous substitution rates in the transcribed regions corresponding to the short transcripts. Furthermore, we show that short transcripts are capable of being translated into corresponding short proteins. Finally, we show that cryptic initiation can occur in wild-type cells following a nutritional shift from rich to minimal media. Our results demonstrate that maintenance of chromatin structure and modifications is important for repressing a large number of cryptic promoters distributed throughout the genome and suggest that cryptic initiation has the potential to play a physiological role in expressing alternate genetic information in response to environmental changes.
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 Biochemical Analyses of Transcription Initiation in Saccharomyces Cerevisiae by : Paul Wade
Download or read book Biochemical Analyses of Transcription Initiation in Saccharomyces Cerevisiae written by Paul Wade and published by . This book was released on 1993 with total page 324 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 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 The Molecular Biology of the Yeast Saccharomyces, Life Cycle and Inheritance by : Jeffrey N. Strathern
Download or read book The Molecular Biology of the Yeast Saccharomyces, Life Cycle and Inheritance written by Jeffrey N. Strathern and published by . This book was released on 1981 with total page 776 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Genetic and Genomic Analyses of the Saccharomyces Cerevisiae Transcript Elongation Factor, TFIIS by : Caren Jody Stark
Download or read book Genetic and Genomic Analyses of the Saccharomyces Cerevisiae Transcript Elongation Factor, TFIIS written by Caren Jody Stark and published by . This book was released on 2003 with total page 538 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 Yeast Genetics by : Jeffrey S. Smith
Download or read book Yeast Genetics written by Jeffrey S. Smith and published by Humana. This book was released on 2016-09-17 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Yeast Genetics: Methods and Protocols is a collection of methods to best study and manipulate Saccharomyces cerevisiae, a truly genetic powerhouse. The simple nature of a single cell eukaryotic organism, the relative ease of manipulating its genome and the ability to interchangeably exist in both haploid and diploid states have always made it an attractive model organism. Genes can be deleted, mutated, engineered and tagged at will. Saccharomyces cerevisiae has played a major role in the elucidation of multiple conserved cellular processes including MAP kinase signaling, splicing, transcription and many others. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Yeast Genetics: Methods and Protocols will provide a balanced blend of classic and more modern genetic methods relevant to a wide range of research areas and should be widely used as a reference in yeast labs.
Book Synopsis Methods in Yeast Genetics by : David C. Amberg
Download or read book Methods in Yeast Genetics written by David C. Amberg and published by CSHL Press. This book was released on 2005 with total page 250 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Methods in Yeast Genetics" is a course that has been offered annually at Cold Spring Harbor for the last 30 years. This provides a set of teaching experiments along with the protocols and recipes for the standard techniques and reagents used in the study of yeast biology.
Book Synopsis Molecular Biology of The Cell by : Bruce Alberts
Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Chromatin Signaling and Diseases by : Olivier Binda
Download or read book Chromatin Signaling and Diseases written by Olivier Binda and published by Academic Press. This book was released on 2016-08-06 with total page 468 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chromatin Signaling and Diseases covers the molecular mechanisms that regulate gene expression, which govern everything from embryonic development, growth, and human pathologies associated with aging, such as cancer. This book helps researchers learn about or keep up with the quickly expanding field of chromatin signaling. After reading this book, clinicians will be more capable of explaining the mechanisms of gene expression regulation to their patients to reassure them about new drug developments that target chromatin signaling mechanisms. For example, several epigenetic drugs that act on chromatin signaling factors are in clinical trials or even approved for usage in cancer treatments, Alzheimer's, and Huntington's diseases. Other epigenetic drugs are in development to regulate various class of chromatin signaling factors. To keep up with this changing landscape, clinicians and doctors will need to stay familiar with genetic advances that translate to clinical practice, such as chromatin signaling. Although sequencing of the human genome was completed over a decade ago and its structure investigated for nearly half a century, molecular mechanisms that regulate gene expression remain largely misunderstood. An emerging concept called chromatin signaling proposes that small protein domains recognize chemical modifications on the genome scaffolding histone proteins, facilitating the nucleation of enzymatic complexes at specific loci that then open up or shut down the access to genetic information, thereby regulating gene expression. The addition and removal of chemical modifications on histones, as well as the proteins that specifically recognize these, is reviewed in Chromatin Signaling and Diseases. Finally, the impact of gene expression defects associated with malfunctioning chromatin signaling is also explored. Explains molecular mechanisms that regulate gene expression, which governs everything from embryonic development, growth, and human pathologies associated with aging Educates clinicians and researchers about chromatin signaling, a molecular mechanism that is changing our understanding of human pathology Explores the addition and removal of chemical modifications on histones, the proteins that specifically recognize these, and the impact of gene expression defects associated with malfunctioning chromatin signaling Helps researchers learn about the quickly expanding field of chromatin signaling
Author :Errol C. Friedberg Publisher :American Society for Microbiology Press ISBN 13 :1555813194 Total Pages :2587 pages Book Rating :4.5/5 (558 download)
Book Synopsis DNA Repair and Mutagenesis by : Errol C. Friedberg
Download or read book DNA Repair and Mutagenesis written by Errol C. Friedberg and published by American Society for Microbiology Press. This book was released on 2005-11-22 with total page 2587 pages. Available in PDF, EPUB and Kindle. Book excerpt: An essential resource for all scientists researching cellular responses to DNA damage. • Introduces important new material reflective of the major changes and developments that have occurred in the field over the last decade. • Discussed the field within a strong historical framework, and all aspects of biological responses to DNA damage are detailed. • Provides information on covering sources and consequences of DNA damage; correcting altered bases in DNA: DNA repair; DNA damage tolerance and mutagenesis; regulatory responses to DNA damage in eukaryotes; and disease states associated with defective biological responses to DNA damage.
Book Synopsis Stress-Activated Protein Kinases by : Francesc Posas
Download or read book Stress-Activated Protein Kinases written by Francesc Posas and published by Springer Science & Business Media. This book was released on 2008-01-24 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this book leading researchers in the field discuss the state-of-the-art of many aspects of SAPK signaling in various systems from yeast to mammals. These include various chapters on regulatory mechanisms as well as the contribution of the SAPK signaling pathways to processes such as gene expression, metabolism, cell cycle regulation, immune responses and tumorigenesis. Written by international experts, the book will appeal to cell biologists and biochemists.
Download or read book Genes & Signals written by Mark Ptashne and published by CSHL Press. This book was released on 2002 with total page 212 pages. Available in PDF, EPUB and Kindle. Book excerpt: P. 103.
