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Sigma 70 Dependent Rna Polymerase Promoter Proximal Pausing In Escherichia Coli And Its Implications For Pause Mediated Transcription Regulation
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Book Synopsis Sigma 70-dependent RNA Polymerase Promoter-proximal Pausing in Escherichia Coli and Its Implications for Pause-mediated Transcription Regulation by : Asma Issam Hatoum
Download or read book Sigma 70-dependent RNA Polymerase Promoter-proximal Pausing in Escherichia Coli and Its Implications for Pause-mediated Transcription Regulation written by Asma Issam Hatoum and published by . This book was released on 2007 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Roles for the Nontranscribed DNA Strand and Sigma-70 Initiation Factor in E. Coli RNA Polymerase Pausing by : Brian Z. Ring
Download or read book Roles for the Nontranscribed DNA Strand and Sigma-70 Initiation Factor in E. Coli RNA Polymerase Pausing written by Brian Z. Ring and published by . This book was released on 1995 with total page 292 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Factors Controlling Promoter-proximal Pausing by RNA Polymerase II by : Nicholas James Fuda
Download or read book Factors Controlling Promoter-proximal Pausing by RNA Polymerase II written by Nicholas James Fuda and published by . This book was released on 2012 with total page 202 pages. Available in PDF, EPUB and Kindle. Book excerpt: Most gene expression is regulated at the level of transcription, and the transition from initiation to productive elongation is a key point of regulation. This transition is accompanied by pausing of transcriptionally engaged polymerase in the promoter-proximal region of several heat shock genes. Although this mechanism of regulation was long thought to be limited to a few genes, recent evidence has indicated that pausing is wide-spread in higher eukaryotes. Therefore, it is increasingly important to understand the mechanisms controlling the paused polymerase. I have investigated how the site of pausing on Hsp70 is specified using highresolution mapping of polymerase on reporter genes with shifted pausing site sequences. The results indicate that the downstream sequence dictates pause position and the overall level of pausing. I have also used RNAi knock-down in Drosophila cell culture to study the roles of several factors in establishing, maintaining, and releasing the paused polymerase. These experiments have shown GAGA factor is required for pausing on many of its target genes, and the knock-down effects indicate it is involved in establishing the pause. In contrast, Spt5, a protein previously shown to enhance pausing in vitro, reduces pausing genome-wide by increasing levels of elongating polymerase. Two kinases, P-TEFb and CDK12, function in productive elongation. Previously our lab showed that P-TEFb inhibition prevented the transition into elongation, limiting the polymerase to the 5' end of the heat shock-induced Hsp70 gene. I mapped these polymerases in high resolution to show they occupied sites further downstream than the normal pause sites, suggesting P-TEFb activity may not solely release the paused polymerase. I also determined the localization of CDK12 on active genes. Its localization downstream of P-TEFb suggests that these kinases may have distinct functions. Finally, I have examined the role of Fcp1 in Hsp70 transcription. Our lab previously showed the CTD phosphatase Fcp1 was required for optimum expression of Hsp70 mRNA. Fcp1 knock-down reduced the heat shock levels of Pol II and increased phosphorylation of nonchromatin bound Pol II, indicating that Fcp1 recycling of RNA polymerase II to an initiationcompetent form is required for optimal Hsp70 heat shock transcription.
Book Synopsis Characterization of Novel DNA Elements Necessary for Sigma-dependent Promoter Proximal Transcriptional Pausing by : Jeremy Gilbert Bird
Download or read book Characterization of Novel DNA Elements Necessary for Sigma-dependent Promoter Proximal Transcriptional Pausing written by Jeremy Gilbert Bird and published by . This book was released on 2013 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcription is not necessarily uniform in rate, but instead consists of multiple periods of continuous elongation by RNA polymerase (RNAP) interrupted by occasional pausing events. These pauses have several determined origins, including the interaction of protein co-factors, the influence of transcribed RNA secondary structure, and a direct effect of the sequence composition of the DNA being transcribed. Promoter proximal pauses, in which RNAP pauses tens of nucleotides downstream of the transcription start site, have been observed in systems ranging from bacteria to more complex eukaryotes such as D. melanogaster and humans, and play important regulatory roles in organisms of all levels. In E. coli, [sigma]70-dependent promoter proximal pauses are of particular interest because lambdoid phage late gene promoters require these pauses for the loading of the anti-terminator Q protein, which is necessary for transcription of the phage late genes during lytic growth. The primary interaction that induces [sigma]70-dependent pauses is between the non-template strand of the -10-like sequence and [sigma]70 region 2. However, recent evidence identifies other important sequences including several nucleotides around the pause site itself that are required for pausing (Perdue and Roberts 2010). Mutational studies of lambdoid phage 82 promoter pR' show that a 3-bp GC-rich sequence primarily promotes pausing through the template DNA strand, but also acts through a non-template DNA strand interaction with [sigma]70. I show that this template strand sequence determines where the pause occurs. It is likely that in [sigma]-dependent promoterproximal pausing, the [sigma]70/DNA interaction anchors the elongation complex upstream of the pause site, requiring it to "scrunch" (by analogy to scrunching during initial transcription (Kapanidis et al. 2006)) and to create an enlarged DNA bubble as the active center reaches the pause site. "Scrunched" complexes are energetically strained, but stable at the pause site; my data suggest that the G/C-rich template sequence is a critical element in stabilizing the paused, scrunched structure. Mutational studies of the A/T-rich region demonstrate that the terminal nucleotide of the pause site plays an important role in pause formation, and that the base composition of the A/T-rich sequence determines the likelihood that a transcription complex escapes the pause. My data also suggest that a [sigma]70-dependent paused transcription complex enters the paused state through a pretranslocated state of the enzyme. Through these studies, I have expanded the current understanding of the protein/nucleotide and nucleotide/nucleotide interactions that constitute the [sigma]70dependent promoter proximal paused complex.
Download or read book Index Medicus written by and published by . This book was released on 2004 with total page 2388 pages. Available in PDF, EPUB and Kindle. Book excerpt: Vols. for 1963- include as pt. 2 of the Jan. issue: Medical subject headings.
Book Synopsis Structural Biology of Bacterial Pathogenesis by : Gabriel Waksman
Download or read book Structural Biology of Bacterial Pathogenesis written by Gabriel Waksman and published by Amer Society for Microbiology. This book was released on 2005 with total page 273 pages. Available in PDF, EPUB and Kindle. Book excerpt: Structural Biology of Bacterial Pathogenesis explores recent developments in the understanding of the molecular basis of bacterial infectious diseases, from structures involved in adhesion and host recognition to those describing elements of bacterial secretion systems Compiles engaging, convenient reviews of current research Presents high–quality illustrations of key importance to structural biology Reviews comprehensively the molecular basis of bacterial pathogenesis Provides a link between pathology and its underlying molecular mechanisms Contributors are leading scientists in the fields of structural biology and bacterial infectious diseases
Book Synopsis Fnctional Evolution of Promoter-proximal Pausing Factors in the Regulation of RNA Polymerase II Transcription by : Gregory T. Booth
Download or read book Fnctional Evolution of Promoter-proximal Pausing Factors in the Regulation of RNA Polymerase II Transcription written by Gregory T. Booth and published by . This book was released on 2018 with total page 404 pages. Available in PDF, EPUB and Kindle. Book excerpt: Promoter-proximal pausing of RNA Polymerase II (Pol II) is now recognized as a ubiquitous mechanism for regulating gene expression in metazoans. By capturing engaged Pol II shortly after transcription initiation, genes are primed for activation of RNA synthesis, enabling cells to rapidly alter global transcription programs. However, despite conservation of many factors involved in establishing this regulatory platform, many eukaryotes do not control gene expression through this process. Here, the examination of the global transcriptional landscape in two distantly related yeast revealed unprecedented divergence in Pol II distributions across genes. Previously undescribed pause-like profiles were identified within promoter-proximal regions of the fission yeast, Schizosaccharomyces pombe, that are sensitive to loss of the conserved elongation factor, Spt4. Thus, fission yeast might employ a variant of the system of regulation found in higher eukaryotes In flies and mammals, Pol II arrested within the promoter proximal region of a gene can only be released through the activity of a positive-transcription elongation factor (P-TEFb), composed of kinase (Cdk9) and cyclin (CycT1/2) subunits. Investigating the functional impact of Cdk9 on transcription in fission yeast revealed that, unlike most metazoan systems, Pol II in S. pombe is capable of overcoming the early elongation barrier after kinase inhibition, although not without consequence. However, fission yeast lack the metazoan-specific negative elongation factor complex (NELF) involved in pausing, perhaps limiting their ability to control the release of Pol II through phosphorylation of the elongation complex. Ultimately, by depleting pausing factors from cell lines derived from Drosophila melanogaster, it was tested whether NELF is required for P-TEFb-regulated pause escape. While global transcription is largely unaffected by the loss of NELF, upon inhibition of Cdk9, a significant amount of Pol II is aberrantly released from the pause, suggesting reduced control of this regulation. These findings suggest that NELF may have evolutionarily refined an ancestral promoter-proximal architecture of the transcription elongation complex, giving rise to a novel mechanism for gene regulation.
Download or read book Cumulated Index Medicus written by and published by . This book was released on 1991 with total page 1460 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis RNA Exosome by : Torben Heick Jensen
Download or read book RNA Exosome written by Torben Heick Jensen and published by Springer Science & Business Media. This book was released on 2011-06-29 with total page 161 pages. Available in PDF, EPUB and Kindle. Book excerpt: The diversity of RNAs inside living cells is amazing. We have known of the more “classic” RNA species: mRNA, tRNA, rRNA, snRNA and snoRNA for some time now, but in a steady stream new types of molecules are being described as it is becoming clear that most of the genomic information of cells ends up in RNA. To deal with the enormous load of resulting RNA processing and degradation reactions, cells need adequate and efficient molecular machines. The RNA exosome is arising as a major facilitator to this effect. Structural and functional data gathered over the last decade have illustrated the biochemical importance of this multimeric complex and its many co-factors, revealing its enormous regulatory power. By gathering some of the most prominent researchers in the exosome field, it is the aim of this volume to introduce this fascinating protein complex as well as to give a timely and rich account of its many functions. The exosome was discovered more than a decade ago by Phil Mitchell and David Tollervey by its ability to trim the 3’end of yeast, S. cerevisiae, 5. 8S rRNA. In a historic account they laid out the events surrounding this identification and the subsequent birth of the research field. In the chapter by Kurt Januszyk and Christopher Lima the structural organization of eukaryotic exosomes and their evolutionary counterparts in bacteria and archaea are discussed in large part through presentation of structures.
Book Synopsis Mechanism of Sigma-dependent Pausing in Regulation of the Bacteriophage Lambda Late Gene Operon by : Eric John Strobel
Download or read book Mechanism of Sigma-dependent Pausing in Regulation of the Bacteriophage Lambda Late Gene Operon written by Eric John Strobel and published by . This book was released on 2015 with total page 115 pages. Available in PDF, EPUB and Kindle. Book excerpt: The movement of RNA polymerase (RNAP) along a DNA template is punctuated by frequent pauses during which the elongation complex persists at a single position for an extended period of time. Such pausing events have been shown to function in the regulation of gene expression at the level of transcription. A prototypical example of regulatory pausing is provided by the lambdoid phage late gene operon, in which a DNA-encoded [sigma]70-dependent pause element halts transcription to facilitate incorporation of the antiterminator Q into the paused elongation complex. Upon binding, Q triggers rapid escape of the now terminator-resistant elongation complex from the pause site. The [sigma]70-dependent pause element consists of a hexameric "-10-like sequence", which functions by capturing RNAP through contacts with the [sigma]70 subunit, and a "translocation pause element" (TPE), a pause-inducing element that underlies transcription pausing in E. coli. Here, we show that the TPE contributes to [sigma]70-dependent pausing by limiting the rate at which paused complexes attempt to escape the pause and we identify a novel sub-element that contributes to TPE function. Furthermore, we use a functional analog to show that Q drives escape from the [sigma]70-dependent pause in a process that is mechanistically related to escape from a promoter during transcription initiation.
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 Sequence Insertion 3 of Escherichia Coli RNA Polymerase Regulates Transcriptional Pausing by : Yu Bao (Ph.D.)
Download or read book Sequence Insertion 3 of Escherichia Coli RNA Polymerase Regulates Transcriptional Pausing written by Yu Bao (Ph.D.) and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gene expression in all life forms relies on multi-subunit RNA polymerase (RNAP). In transcription elongation stage, RNAP senses specific DNA signals and enters an offline, pausing state, which has multiple interconverting subtypes and allows versatile regulatory options. This work focuses on understanding the pausing regulatory function of sequence insertion 3 (SI3) in Escherichia coli (E. coli) RNAP. In E. coli, the catalytic trigger loop (TL) is interrupted by surface-exposed, 188-aa sequence insertion 3 (SI3). SI3 occupies different locations in paused transcription complexes, but its dynamics during pausing are undefined. We report design, optimization, and use of a Cys-triplet reporter to measure the positional bias of SI3 in different transcription complexes and to determine the effect of restricting SI3 movement on pausing. RNA hairpin-stabilized pausing biases SI3 toward a swiveled position that inhibits TL folding while the consensus elemental pausing biases SI3 toward a closed position that potentially stabilized a pre-translocated state of RNAP. Our findings establish that SI3 functions by modulating the TL folding to aid transcriptional regulation. To investigate SI3's genomic function in transcriptional pausing, we constructed a viable E. coli strain lacking SI3 enabled by a suppressor TL substitution ([beta]'Ala941-Thr; [delta]SI3*). [delta]SI3* increased transcription rate in vitro relative to [delta]SI3, possibly explaining its viability, but retained both positive and negative effects of [delta]SI3 on pausing. Using NET-seq, we found that [delta]SI3*-enhanced pauses resemble the consensus elemental pause sequence whereas sequences at [delta]SI3*-suppressed pauses, which exhibited greater association with PHs, were more divergent. [delta]SI3*-suppressed pauses also were associated with apparent pausing one nt upstream from the consensus sequence, often generating tandem pause sites. Our results document multiple ways that SI3 modulates pausing in vivo and may explain differences in consensus pause sequences found in some NET-seq studies. In conclusion, our comprehensive studies provide compelling evidence linking the movements of the SI3 domain to the formation and stabilization of diverse transcriptional pause signals. We demonstrate the potential of biochemical crosslink assays in exploring conformational changes within large protein complexes. Additionally, our research emphasizes the necessity for refining current NET-seq protocols to prevent unintended cleavage during library preparation.
Book Synopsis Regulation of Transcription Through RNA Polymerase II Promoter-proximal Pausing by : Melodi Damla Tastemel
Download or read book Regulation of Transcription Through RNA Polymerase II Promoter-proximal Pausing written by Melodi Damla Tastemel and published by . This book was released on 2018 with total page 100 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book RNA Chaperones written by Tilman Heise and published by . This book was released on 2020 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a wide spectrum of methods to study RNA chaperones in vitro, at the single molecule level, and protocols useful for cell-based assays. Beginning with a section on a number of bacterial proteins for study, the volume also explores proteins from eukaryotic cells and how to delve into the complex interactions between RNA chaperones and the folding and unfolding of proteins. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, RNA Chaperones: Methods and Protocols serves as an ideal guide for scientists and students interested in RNA biology and RNA chaperones. Chapter 3 is available Open Access under a CC-BY 4.0 license via link.springer.com.
Book Synopsis RNA Binding to E. Coli DNA Dependent RNA Polymerase by : Curtis R. Altmann
Download or read book RNA Binding to E. Coli DNA Dependent RNA Polymerase written by Curtis R. Altmann and published by . This book was released on 1994 with total page 366 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Transcription by : Ronald C. Conaway
Download or read book Transcription written by Ronald C. Conaway and published by Raven Press (ID). This book was released on 1994 with total page 600 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Download or read book Encyclopedia of Cell Biology written by and published by Academic Press. This book was released on 2015-08-07 with total page 2972 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Encyclopedia of Cell Biology, Four Volume Set offers a broad overview of cell biology, offering reputable, foundational content for researchers and students across the biological and medical sciences. This important work includes 285 articles from domain experts covering every aspect of cell biology, with fully annotated figures, abundant illustrations, videos, and references for further reading. Each entry is built with a layered approach to the content, providing basic information for those new to the area and more detailed material for the more experienced researcher. With authored contributions by experts in the field, the Encyclopedia of Cell Biology provides a fully cross-referenced, one-stop resource for students, researchers, and teaching faculty across the biological and medical sciences. Fully annotated color images and videos for full comprehension of concepts, with layered content for readers from different levels of experience Includes information on cytokinesis, cell biology, cell mechanics, cytoskeleton dynamics, stem cells, prokaryotic cell biology, RNA biology, aging, cell growth, cell Injury, and more In-depth linking to Academic Press/Elsevier content and additional links to outside websites and resources for further reading A one-stop resource for students, researchers, and teaching faculty across the biological and medical sciences
