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Author : Melodi Damla Tastemel
Release : 2018
Genre :
Kind : eBook
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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. This book was released on 2018. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Gregory T. Booth
Release : 2018
Genre :
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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. This book was released on 2018. 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.
Author : Torben Heick Jensen
Release : 2011-06-29
Genre : Medical
Kind : eBook
Book Rating : 410/5 ( reviews)
Book Synopsis RNA Exosome by : Torben Heick Jensen
Download or read book RNA Exosome written by Torben Heick Jensen. This book was released on 2011-06-29. 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.
Author : Nicholas James Fuda
Release : 2012
Genre :
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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. This book was released on 2012. 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.
Author : Hojoong Kwak
Release : 2013
Genre :
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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. This book was released on 2013. 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.
