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RNA Polymerase II

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https://www.readbyqxmd.com/read/28934222/endogenous-rgs14-is-a-cytoplasmic-nuclear-shuttling-protein-that-localizes-to-juxtanuclear-membranes-and-chromatin-rich-regions-of-the-nucleus
#1
Mary Rose Branch, John R Hepler
Regulator of G protein signaling 14 (RGS14) is a multifunctional scaffolding protein that integrates G protein and H-Ras/MAPkinase signaling pathways to regulate synaptic plasticity important for hippocampal learning and memory. However, to date, little is known about the subcellular distribution and roles of endogenous RGS14 in a neuronal cell line. Most of what is known about RGS14 cellular behavior is based on studies of tagged, recombinant RGS14 ectopically overexpressed in unnatural host cells. Here, we report for the first time a comprehensive assessment of the subcellular distribution and dynamic localization of endogenous RGS14 in rat B35 neuroblastoma cells...
2017: PloS One
https://www.readbyqxmd.com/read/28933854/epigenetic-dna-modification-n6-methyladenine-causes-site-specific-rna-polymerase-ii-transcriptional-pausing
#2
Wei Wang, Liang Xu, Lulu Hu, Jenny Chong, Chuan He, Dong Wang
N6-methyladenine (N6-mA or 6mA) is an epigenetic DNA modification in eukaryotic genomes. In contrast to the well-established roles of 5-methylcytosine for epigenetic regulation of gene expression, the functional roles of N6-mA remain elusive. In particular, the impact of N6-mA modification at DNA template on RNA polymerase II (pol II) transcription elongation is not known. In this work, using the Saccharomyces cerevisiae pol II transcriptional elongation system as a model, we investigated the molecular mechanism of pol II recognition and processing of N6-mA sites via both biochemical and structural approaches...
September 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28933322/heitmania-gen-nov-a-new-yeast-genus-in-microbotryomycetes-and-description-of-three-novel-species-heitmania-litseae-sp-nov-heitmania-castanopsis-sp-nov-and-heitmania-elacocarpi-sp-nov
#3
Xin-Zhan Liu, Marizeth Groenewald, Teun Boekhout, Feng-Yan Bai
Nine anamorphic yeast strains isolated from various plant leaves collected in southern China were phylogenetically characterized based on sequences of the internal transcribed spacer (ITS) region, the D1/D2 domains of the large subunit (LSU) rRNA gene, the small subunit (SSU) rRNA gene, the two subunits of the RNA polymerase II gene (RPB1 and RPB2) and the translation elongation factor 1-α (TEF1). Phylogenetic analysis of the combined sequences of the six genes showed that the new strains formed a distinct clade in the class Microbotryomycetes but could not be assigned to any of the existing genera, families or orders of the class...
September 21, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28931603/the-pyhin-protein-p205-regulates-the-inflammasome-by-controlling-asc-expression
#4
Sreya Ghosh, Christina Wallerath, Sergio Covarrubias, Veit Hornung, Susan Carpenter, Katherine A Fitzgerald
Members of the IFN-inducible PYHIN protein family, such as absent in melanoma-2 and IFN-γ-inducible protein (IFI)16, bind dsDNA and form caspase-1-activating inflammasomes that are important in immunity to cytosolic bacteria, DNA viruses, or HIV. IFI16 has also been shown to regulate transcription of type I IFNs during HSV infection. The role of other members of the PYHIN protein family in the regulation of immune responses is much less clear. In this study, we identified an immune-regulatory function for a member of the murine PYHIN protein family, p205 (also called Ifi205)...
September 20, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28928797/role-of-mir-128-in-hypertension-induced-myocardial-injury
#5
Jie Yin, Hongyan Liu, Lei Huan, Suping Song, Liying Han, Faxin Ren, Zengtang Zhang, Zhiqiang Zang, Junye Zhang, Shu Wang
The present study aimed to investigate the role and mechanism of micro RNA (miR)-128 in hypertension-induced myocardial injury. The peripheral blood of patients with hypertension was collected and the expression of miR-128 was detected using fluorescence reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Primary myocardial cells isolated from rat in vitro were cultured under conditions of hypoxia and glucose deprivation, and miR-128 expression was measured by RT-qPCR. The expression of c-Met protein was measured using western blot analysis and the apoptosis of transfected cells was measured by flow cytometry in rat myocardial cells following transfection with miR-128 mimics or c-Met siRNA...
October 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28928151/comparative-analysis-reveals-genomic-features-of-stress-induced-transcriptional-readthrough
#6
Anna Vilborg, Niv Sabath, Yuval Wiesel, Jenny Nathans, Flonia Levy-Adam, Therese A Yario, Joan A Steitz, Reut Shalgi
Transcription is a highly regulated process, and stress-induced changes in gene transcription have been shown to play a major role in stress responses and adaptation. Genome-wide studies reveal prevalent transcription beyond known protein-coding gene loci, generating a variety of RNA classes, most of unknown function. One such class, termed downstream of gene-containing transcripts (DoGs), was reported to result from transcriptional readthrough upon osmotic stress in human cells. However, how widespread the readthrough phenomenon is, and what its causes and consequences are, remain elusive...
September 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28927412/analysis-of-microrna-mirna-expression-profiles-reveals-11-key-biomarkers-associated-with-non-small-cell-lung-cancer
#7
Ke Wang, Mingwei Chen, Wei Wu
BACKGROUND: Non-small cell lung cancer (NSCLC) accounts for more than 85% of lung cancer cases which cause most of cancer-related deaths globally. However, the results vary largely in different studies due to different platforms and sample sizes. Here, we aim to identify the key miRNAs in the carcinogenesis of NSCLC that might be potential biomarkers for this cancer. METHODS: Meta-analysis was performed on miRNA profile using seven datasets of NSCLC studies. Furthermore, we predicted and investigated the functions of genes regulated by key miRNAs...
September 19, 2017: World Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28925811/it-s-fun-to-transcribe-with-fun30-a-model-for-nucleosome-dynamics-during-rna-polymerase-ii-mediated-elongation
#8
Junwoo Lee, Eun Shik Choi, Daeyoup Lee
The ability of elongating RNA polymerase II (RNAPII) to regulate the nucleosome barrier is poorly understood because we do not know enough about the involved factors and we lack a conceptual framework to model this process. Our group recently identified the conserved Fun30/SMARCAD1 family chromatin-remodeling factor, Fun30(Fft3), as being critical for relieving the nucleosome barrier during RNAPII-mediated elongation, and proposed a model illustrating how Fun30(Fft3) may contribute to nucleosome disassembly during RNAPII-mediated elongation...
September 19, 2017: Transcription
https://www.readbyqxmd.com/read/28918903/saga-is-a-general-cofactor-for-rna-polymerase-ii-transcription
#9
Tiago Baptista, Sebastian Grünberg, Nadège Minoungou, Maria J E Koster, H T Marc Timmers, Steve Hahn, Didier Devys, László Tora
Prior studies suggested that SAGA and TFIID are alternative factors that promote RNA polymerase II transcription, with about 10% of genes in S. cerevisiae dependent on SAGA. We reassessed the role of SAGA by mapping its genome-wide location and role in global transcription in budding yeast. We find that SAGA maps to the UAS elements of most genes, overlapping with Mediator binding and irrespective of previous designations of SAGA- or TFIID-dominated genes. Disruption of SAGA through mutation or rapid subunit depletion reduces transcription from nearly all genes, measured by newly synthesized RNA...
September 11, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28918900/transcription-of-nearly-all-yeast-rna-polymerase-ii-transcribed-genes-is-dependent-on-transcription-factor-tfiid
#10
Linda Warfield, Srinivas Ramachandran, Tiago Baptista, Didier Devys, Laszlo Tora, Steven Hahn
Previous studies suggested that expression of most yeast mRNAs is dominated by either transcription factor TFIID or SAGA. We re-examined the role of TFIID by rapid depletion of S. cerevisiae TFIID subunits and measurement of changes in nascent transcription. We find that transcription of nearly all mRNAs is strongly dependent on TFIID function. Degron-dependent depletion of Taf1, Taf2, Taf7, Taf11, and Taf13 showed similar transcription decreases for genes in the Taf1-depleted, Taf1-enriched, TATA-containing, and TATA-less gene classes...
September 13, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28912275/nmr-reveals-the-intrinsically-disordered-domain-2-of-ns5a-protein-as-an-allosteric-regulator-of-the-hepatitis-c-virus-rna-polymerase-ns5b
#11
Luiza M Bessa, Hélène Launay, Marie Dujardin, François-Xavier Cantrelle, Guy Lippens, Isabelle Landrieu, Robert Schneider, Xavier Hanoulle
Non-structural protein 5B (NS5B) is the RNAdependent RNA polymerase that catalyses replication of the hepatitis C virus (HCV) RNA genome, and so is central for its life cycle. NS5B interacts with the intrinsically disordered domain 2 of NS5A (NS5A-D2), another essential multifunctional HCV protein that is required for RNA replication. As a result, these two proteins represent important targets for anti-HCV chemotherapies. Despite this importance and the existence of NS5B crystal structures, our understanding of the conformational and dynamic behaviour of NS5B in solution and its relationship with NS5A-D2 remain incomplete...
September 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28912271/the-complex-structure-and-function-of-mediator
#12
Thomas M Harper, Dylan J Taatjes
In eukaryotes, RNA polymerase II (pol II) transcribes all protein-coding genes and many non-coding RNAs. Whereas numerous factors contribute to the regulation of pol II activity, the Mediator complex is required for expression of most, if not all, pol II transcripts. Structural characterization of Mediator is challenging due to its large size (~20 subunits in yeast, 26 subunits in humans) and conformational flexibility. However, recent studies have revealed structural details at higher resolution. Here, we summarize recent findings and place in context with previous results, highlighting regions within Mediator that are important for regulating its structure and function...
September 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28904013/integrative-analysis-of-rna-polymerase-ii-and-transcriptional-dynamics-upon-myc-activation
#13
Stefano de Pretis, Theresia R Kress, Marco J Morelli, Arianna Sabò, Chiara Locarno, Alessandro Verrecchia, Mirko Doni, Stefano Campaner, Bruno Amati, Mattia Pelizzola
Overexpression of the MYC transcription factor causes its widespread interaction with regulatory elements in the genome but leads to the up- and down-regulation of discrete sets of genes. The molecular determinants of these selective transcriptional responses remain elusive. Here, we present an integrated time-course analysis of transcription and mRNA dynamics following MYC activation in proliferating mouse fibroblasts, based on chromatin immunoprecipitation, metabolic labeling of newly synthesized RNA, extensive sequencing, and mathematical modeling...
September 13, 2017: Genome Research
https://www.readbyqxmd.com/read/28902838/the-cryo-electron-microscopy-structure-of-human-transcription-factor-iih
#14
Basil J Greber, Thi Hoang Duong Nguyen, Jie Fang, Pavel V Afonine, Paul D Adams, Eva Nogales
Human transcription factor IIH (TFIIH) is part of the general transcriptional machinery required by RNA polymerase II for the initiation of eukaryotic gene transcription. Composed of ten subunits that add up to a molecular mass of about 500 kDa, TFIIH is also essential for nucleotide excision repair. The seven-subunit TFIIH core complex formed by XPB, XPD, p62, p52, p44, p34, and p8 is competent for DNA repair, while the CDK-activating kinase subcomplex, which includes the kinase activity of CDK7 as well as the cyclin H and MAT1 subunits, is additionally required for transcription initiation...
September 13, 2017: Nature
https://www.readbyqxmd.com/read/28894972/gene-regulation-of-mammalian-long-non-coding-rna
#15
REVIEW
Heeyoun Bunch
RNA polymerase II (Pol II) transcribes two classes of RNAs, protein-coding and non-protein-coding (ncRNA) genes. ncRNAs are also synthesized by RNA polymerases I and III (Pol I and III). In humans, the number of ncRNA genes exceeds more than twice that of protein-coding genes. However, the history of studying Pol II-synthesized ncRNA is relatively short. Since early 2000s, important biological and pathological functions of these ncRNA genes have begun to be discovered and intensively studied. And transcription mechanisms of long non-coding RNA (lncRNA) have been recently reported...
September 11, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28893534/solution-structure-of-the-n-terminal-domain-of-mediator-subunit-med26-and-molecular-characterization-of-its-interaction-with-eaf1-and-taf7
#16
Zoé Lens, François-Xavier Cantrelle, Riccardo Peruzzini, Xavier Hanoulle, Frédérique Dewitte, Elisabeth Ferreira, Jean-Luc Baert, Didier Monté, Marc Aumercier, Vincent Villeret, Alexis Verger, Isabelle Landrieu
MED26 is a subunit of Mediator, a large complex central to the regulation of gene transcription by RNA Polymerase II (RNA Pol II). MED26 plays a role in the switch between the initiation and elongation phases of RNA Pol II-mediated transcription process. Regulation of these steps requires successive binding of MED26 N-Terminal domain (NTD) to TBP-associated factor 7 (TAF7) and EAF1 (Eleven-nineteen lysine-rich in leukemia-Associated Factor 1). In order to investigate the mechanism of regulation by MED26, MED26-NTD structure was solved by nuclear magnetic resonance spectroscopy (NMR), revealing a 4-helix bundle...
September 9, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28892040/structure-of-a-transcribing-rna-polymerase-ii-dsif-complex-reveals-a-multidentate-dna-rna-clamp
#17
Carrie Bernecky, Jürgen M Plitzko, Patrick Cramer
During transcription, RNA polymerase II (Pol II) associates with the conserved elongation factor DSIF. DSIF renders the elongation complex stable and functions during Pol II pausing and RNA processing. We combined cryo-EM and X-ray crystallography to determine the structure of the mammalian Pol II-DSIF elongation complex at a nominal resolution of 3.4 Å. Human DSIF has a modular structure with two domains forming a DNA clamp, two domains forming an RNA clamp, and one domain buttressing the RNA clamp. The clamps maintain the transcription bubble, position upstream DNA, and retain the RNA transcript in the exit tunnel...
September 11, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28888101/what-s-new-in-sclc-a-review
#18
REVIEW
Bryan Oronsky, Tony R Reid, Arnold Oronsky, Corey A Carter
A few years ago the answer to the question in the title of this review would have been, "unfortunately not much" or even "nothing", likely eliciting knowing nods of agreement from oncologists. For the last 3 decades, SCLC has been notorious for its lack of progress, as drug after drug, over 60 of them, in fact, including inhibitors of VEGF, IGFR, mTOR, EGFR and HGF has failed and fallen by the wayside due to little or no impact on PFS or OS, while SCLC's cousin, NSCLC, has notched success after success with a spate of targeted treatment and immunotherapy regulatory approvals...
September 6, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28886274/the-plant-rna-polymerase-ii-elongation-complex-a-hub-coordinating-transcript-elongation-and-mrna-processing
#19
Marion Grasser, Klaus D Grasser
Characterisation of the Arabidopsis RNA polymerase II (RNAPII) elongation complex revealed an assembly of a conserved set of transcript elongation factors associated with chromatin remodellers, histone modifiers as well as with various pre-mRNA splicing and polyadenylation factors. Therefore, transcribing RNAPII streamlines the processes of mRNA synthesis and processing in plants.
September 8, 2017: Transcription
https://www.readbyqxmd.com/read/28884116/the-role-of-pontin-and-reptin-in-cellular-physiology-and-cancer-etiology
#20
REVIEW
Yu-Qian Mao, Walid A Houry
Pontin (RUVBL1, TIP49, TIP49a, Rvb1) and Reptin (RUVBL2, TIP48, TIP49b, Rvb2) are highly conserved ATPases of the AAA+ (ATPases Associated with various cellular Activities) superfamily and are involved in various cellular processes that are important for oncogenesis. First identified as being upregulated in hepatocellular carcinoma and colorectal cancer, their overexpression has since been shown in multiple cancer types such as breast, lung, gastric, esophageal, pancreatic, kidney, bladder as well as lymphatic, and leukemic cancers...
2017: Frontiers in Molecular Biosciences
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