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RNA Polymerase II

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https://www.readbyqxmd.com/read/28441405/mediator18-and-mediator20-confer-susceptibility-to-fusarium-oxysporum-in-arabidopsis-thaliana
#1
Thorya Fallath, Brendan N Kidd, Jiri Stiller, Celine Davoine, Stefan Björklund, John M Manners, Kemal Kazan, Peer M Schenk
The conserved protein complex known as Mediator conveys transcriptional signals by acting as an intermediary between transcription factors and RNA polymerase II. As a result, Mediator subunits play multiple roles in regulating developmental as well as abiotic and biotic stress pathways. In this report we identify the head domain subunits MEDIATOR18 and MEDIATOR20 as important susceptibility factors for Fusarium oxysporum infection in Arabidopsis thaliana. Mutants of MED18 and MED20 display down-regulation of genes associated with jasmonate signaling and biosynthesis while up-regulation of salicylic acid associated pathogenesis related genes and reactive oxygen producing and scavenging genes...
2017: PloS One
https://www.readbyqxmd.com/read/28440894/chromatin-sumoylation-in-heat-stress-to-protect-pause-and-organise-sumo-stress-response-on-chromatin
#2
REVIEW
Einari A Niskanen, Jorma J Palvimo
Post-translational modifications, e.g. SUMO modifications (SUMOylation), provide a mechanism for swiftly changing a protein's activity. Various stress conditions trigger a SUMO stress response (SSR) - a stress-induced rapid change in the conjugation of SUMO to multiple proteins, which predominantly targets nuclear proteins. The SSR has been postulated to protect stressed cells by preserving the functionality of crucial proteins. However, it is unclear how it exerts its protective functions. Interestingly, heat stress (HS) increases SUMOylation of proteins at active promoters and enhancers...
April 25, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28437704/conserved-rna-polymerase-ii-initiation-complex-structure
#3
REVIEW
Merle Hantsche, Patrick Cramer
Recent cryo-electron microscopic studies have arrived at atomic models of the core transcription initiation complex comprising RNA polymerase (Pol) II and the basal transcription factors TBP, TFIIA, TFIIB, TFIIE, and TFIIF. A detailed comparison of two independently derived yeast and human core initiation complex structures reveals that they are virtually identical, demonstrating the conservation of the basic transcription machinery amongst eukaryotes. The additional factors TFIID, TFIIH, and Mediator have been located on the periphery of the core initiation complex, providing the topology of the entire initiation assembly, which comprises approximately 70 polypeptides with a molecular weight of ∼4 Megadalton...
April 21, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28436950/mre11-stability-is-regulated-by-ck2-dependent-interaction-with-r2tp-complex
#4
P von Morgen, K Burdova, T G Flower, N J O'Reilly, S J Boulton, S J Smerdon, L Macurek, Z Hořejší
The MRN (MRE11-RAD50-NBS1) complex is essential for repair of DNA double-strand breaks and stalled replication forks. Mutations of the MRN complex subunit MRE11 cause the hereditary cancer-susceptibility disease ataxia-telangiectasia-like disorder (ATLD). Here we show that MRE11 directly interacts with PIH1D1, a subunit of heat-shock protein 90 cochaperone R2TP complex, which is required for the assembly of large protein complexes, such as RNA polymerase II, small nucleolar ribonucleoproteins and mammalian target of rapamycin complex 1...
April 24, 2017: Oncogene
https://www.readbyqxmd.com/read/28435892/dramatic-improvement-of-crispr-cas9-editing-in-candida-albicans-by-increased-single-guide-rna-expression
#5
Henry Ng, Neta Dean
The clustered regularly interspaced short palindromic repeat system with CRISPR-associated protein 9 nuclease (CRISPR/Cas9) has emerged as a versatile tool for genome editing in Candida albicans. Mounting evidence from other model systems suggests that the intracellular levels of single guide RNA (sgRNA) limit the efficiency of Cas9-dependent DNA cleavage. Here, we tested this idea and describe a new means of sgRNA delivery that improves previously described methods by ~10-fold. The efficiency of Cas9/sgRNA-dependent cleavage and repair of a single-copy yeast enhanced monomeric red fluorescent protein (RFP) gene was measured as a function of various parameters that are hypothesized to affect sgRNA accumulation, including transcriptional and posttranscriptional processing...
March 2017: MSphere
https://www.readbyqxmd.com/read/28434999/smfret-experiments-of-the-rna-polymerase-ii-transcription-initiation-complex
#6
REVIEW
Nicole Malkusch, Thilo Dörfler, Julia Nagy, Tobias Eilert, Jens Michaelis
Single-molecule fluorescence and in particular single-molecule Förster Resonance Energy Transfer (smFRET(1)) is a powerful tool to provide real-time information on the dynamic architecture of large macromolecular structures such as eukaryotic transcription initiation complexes. In contrast to other structural biology methods, not only structural details, but dynamics transitions are revealed thus closing in on the underlying molecular mechanisms. Here, we describe a comprehensive quantitative biophysical toolbox which can be used for rigorous analysis of dynamic protein-nucleic acid complexes and is applied to the study of eukaryotic transcription initiation...
April 18, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28434903/measuring-transcription-dynamics-in-living-cells-using-a-photobleaching-approach
#7
REVIEW
Hodaya Hochberg, Yehuda Brody, Yaron Shav-Tal
The transcriptional kinetics of RNA polymerase II, the enzyme responsible for mRNA transcription in the nucleoplasm, can be modulated by a variety of factors. It is therefore important to establish experimental systems that will enable the readout of transcription kinetics of specific genes as they occur in real time within individual cells. This can be performed by implementing fluorescent tagging of the mRNA under live-cell conditions. This chapter describes how to generate fluorescently tagged genes and mRNA, and how a photobleaching approach can produce information on mRNA transcription kinetics...
April 20, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28431135/reconstitution-of-a-functional-7sk-snrnp
#8
John E Brogie, David H Price
The 7SK small nuclear ribonucleoprotein (snRNP) plays a central role in RNA polymerase II elongation control by regulating the availability of active P-TEFb. We optimized conditions for analyzing 7SK RNA by SHAPE and demonstrated a hysteretic effect of magnesium on 7SK folding dynamics including a 7SK GAUC motif switch. We also found evidence that the 5΄ end pairs alternatively with two different regions of 7SK giving rise to open and closed forms that dictate the state of the 7SK motif. We then used recombinant P-TEFb, HEXIM1, LARP7 and MEPCE to reconstruct a functional 7SK snRNP in vitro...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28426094/sirt7-dependent-deacetylation-of-cdk9-activates-rna-polymerase-ii-transcription
#9
Maximilian F Blank, Sifan Chen, Fabian Poetz, Martina Schnölzer, Renate Voit, Ingrid Grummt
SIRT7 is an NAD+-dependent protein deacetylase that regulates cell growth and proliferation. Previous studies have shown that SIRT7 is required for RNA polymerase I (Pol I) transcription and pre-rRNA processing. Here, we took a proteomic approach to identify novel molecular targets and characterize the role of SIRT7 in non-nucleolar processes. We show that SIRT7 interacts with numerous proteins involved in transcriptional regulation and RNA metabolism, the majority of interactions requiring ongoing transcription...
March 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28425504/suv39h1-reduction-is-implicated-in-abnormal-inflammation-in-copd
#10
Tzu-Tao Chen, Sheng-Ming Wu, Shu-Chuan Ho, Hsiao-Chi Chuang, Chien-Ying Liu, Yao-Fei Chan, Lu-Wei Kuo, Po-Hao Feng, Wen-Te Liu, Kuan-Yuan Chen, Ta-Chih Hsiao, Jer-Nan Juang, Kang-Yun Lee
Chronic obstructive pulmonary disease(COPD) is characterized by enhanced chronic inflammation in the airways, lung parenchyma, and circulation. We investigated whether SUV39H1, a histone methyltransferase, is causatively implicated in the abnormal inflammation observed in COPD. The SUV39H1 and H3K9me3 levels were reduced in peripheral blood mononuclear cells(PBMCs), primary human small airway epithelial cells(HSAEpCs) and lung tissues from COPD patients, which were correlated with poor lung function and the serum IL-8 and IL-6 levels...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28424048/phylogeny-divergence-time-and-historical-biogeography-of-laetiporus-basidiomycota-polyporales
#11
Jie Song, Bao-Kai Cui
BACKGROUND: The aim of this study was to characterize the molecular relationship, origin and historical biogeography of the species in important brown rot fungal genus Laetiporus from East Asia, Europe, Pan-America, Hawaii and South Africa. We used six genetic markers to estimate a genus-level phylogeny including (1) the internal transcribed spacer (ITS), (2) nuclear large subunit rDNA (nrLSU), (3) nuclear small subunit rDNA (nrSSU), (4) translation elongation factor 1-α (EF-1α), (5) DNA-directed RNA polymerase II subunit 2 (RPB2), and (6) mitochondrial small subunit rDNA (mtSSU)...
April 20, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28423325/rapid-genome-wide-recruitment-of-rna-polymerase-ii-drives-transcription-splicing-and-translation-events-during-t-cell-responses
#12
Kathrin Davari, Johannes Lichti, Christian Gallus, Franziska Greulich, N Henriette Uhlenhaut, Matthias Heinig, Caroline C Friedel, Elke Glasmacher
Activation of immune cells results in rapid functional changes, but how such fast changes are accomplished remains enigmatic. By combining time courses of 4sU-seq, RNA-seq, ribosome profiling (RP), and RNA polymerase II (RNA Pol II) ChIP-seq during T cell activation, we illustrate genome-wide temporal dynamics for ∼10,000 genes. This approach reveals not only immediate-early and posttranscriptionally regulated genes but also coupled changes in transcription and translation for >90% of genes. Recruitment, rather than release of paused RNA Pol II, primarily mediates transcriptional changes...
April 18, 2017: Cell Reports
https://www.readbyqxmd.com/read/28422315/regulation-of-the-alternative-splicing-and-function-of-cyclin-t1-by-the-serine-arginine-rich-protein-asf-sf2
#13
Jieqiong Zhou, Guozhen Gao, Panpan Hou, Chun-Mei Li, Deyin Guo
Positive transcription elongation factor-b (P-TEFb) is required for the release of RNA polymerase II (RNAPII) from its pause near the gene promoters and thus for efficient proceeding to the transcription elongation. It consists of two core subunits - CDK9 and one of T-typed or K-typed cyclin, of which, cyclin T1/CDK9 is the major and most studied combination. We have previously identified a novel splice variant of cyclin T1, cyclin T1b, which negatively regulates the transcription elongation of HIV-1 genes as well as several host genes...
April 19, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28416772/dna-methylation-of-mettl7a-gene-body-regulates-its-transcriptional-level-in-thyroid-cancer
#14
Shasha Zhou, Yihang Shen, Min Zheng, Linlin Wang, Raymond Che, Wanning Hu, Pin Li
DNA methylation is the best-studied epigenetic mechanism for regulating gene transcription and maintaining genome stability. Current research progress of transcriptional regulation by DNA methylation mostly focuses on promoter region where hypomethylated CpG islands are present transcriptional activity, as hypermethylated CpG islands generally result in gene repression. Recently, the DNA methylation patterns across the gene body (intragenic methylation) have increasingly attracted attention towards their role in transcriptional regulation and efficiency, due to the improvement of numerous genome-wide DNA methylation profiling studies...
March 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28416637/a-kinase-independent-role-for-cdk19-in-p53-response
#15
K Audrey Audetat, Matthew D Galbraith, Aaron T Odell, Thomas Lee, Ahwan Pandey, Joaquin M Espinosa, Robin D Dowell, Dylan J Taatjes
The human Mediator complex regulates RNA Polymerase II transcription genome-wide. A general factor that regulates Mediator function is the four-subunit kinase module, which contains either CDK8 or CDK19. Whereas CDK8 is linked to specific signaling cascades and oncogenesis, the cellular roles of its paralog, CDK19, are poorly studied. We discovered that osteosarcoma cells (SJSA) are naturally depleted of CDK8 protein. Whereas stable CDK19 knockdown was tolerated in SJSA cells, proliferation was reduced. Notably, proliferation defects were rescued upon re-expression of wild-type or kinase-dead CDK19...
April 17, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28414715/transcriptional-regulatory-logic-of-the-diurnal-cycle-in-the-mouse-liver
#16
Jonathan Aryeh Sobel, Irina Krier, Teemu Andersin, Sunil Raghav, Donatella Canella, Federica Gilardi, Alexandra Styliani Kalantzi, Guillaume Rey, Benjamin Weger, Frédéric Gachon, Matteo Dal Peraro, Nouria Hernandez, Ueli Schibler, Bart Deplancke, Felix Naef
Many organisms exhibit temporal rhythms in gene expression that propel diurnal cycles in physiology. In the liver of mammals, these rhythms are controlled by transcription-translation feedback loops of the core circadian clock and by feeding-fasting cycles. To better understand the regulatory interplay between the circadian clock and feeding rhythms, we mapped DNase I hypersensitive sites (DHSs) in the mouse liver during a diurnal cycle. The intensity of DNase I cleavages cycled at a substantial fraction of all DHSs, suggesting that DHSs harbor regulatory elements that control rhythmic transcription...
April 2017: PLoS Biology
https://www.readbyqxmd.com/read/28413462/identification-of-mirna-biomarkers-of-pneumonia-using-rna-sequencing-and-bioinformatics-analysis
#17
Sai Huang, Cong Feng, Yong-Zhi Zhai, Xuan Zhou, Bei Li, Li-Li Wang, Wei Chen, Fa-Qin Lv, Tan-Shi Li
Pneumonia is a lower respiratory tract infection that causes dramatic mortality worldwide. The present study aimed to investigate the pathogenesis of pneumonia and identify microRNA (miRNA) biomarkers as candidates for targeted therapy. RNA from the peripheral blood plasma of participants with pneumonia (severe, n=9; non-severe, n=9) and controls (n=9) was isolated and paired-end sequencing was performed on an Illumina HiSeq4000 system. Following the processing of raw reads, the sequences were aligned against the Genome Reference Consortium human genome assembly 38 reference genome using Bowtie2 software...
April 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28412353/crystal-structure-of-rna-polymerase-ii-from-komagataella-pastoris
#18
Haruhiko Ehara, Takashi Umehara, Shun-Ichi Sekine, Shigeyuki Yokoyama
RNA polymerase II (Pol II) is a 12-subunit protein complex that conducts the transcription of mRNA and some small RNAs. In this work, the crystal structure of Pol II from the methylotropic yeast Komagataella pastoris (Pichia pastoris) was determined. While the structure is highly homologous to that of Pol II from the budding yeast Saccharomyces cerevisiae, the stalk and clamp modules of the K. pastoris Pol II displayed large inward rotations, closing the central cleft to a greater extent than in the known S...
April 12, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28408437/the-myc-mrna-3-utr-couples-rna-polymerase-ii-function-to-glutamine-and-ribonucleotide-levels
#19
Francesca R Dejure, Nadine Royla, Steffi Herold, Jacqueline Kalb, Susanne Walz, Carsten P Ade, Guido Mastrobuoni, Jens T Vanselow, Andreas Schlosser, Elmar Wolf, Stefan Kempa, Martin Eilers
Deregulated expression of MYC enhances glutamine utilization and renders cell survival dependent on glutamine, inducing "glutamine addiction". Surprisingly, colon cancer cells that express high levels of MYC due to WNT pathway mutations are not glutamine-addicted but undergo a reversible cell cycle arrest upon glutamine deprivation. We show here that glutamine deprivation suppresses translation of endogenous MYC via the 3'-UTR of the MYC mRNA, enabling escape from apoptosis. This regulation is mediated by glutamine-dependent changes in adenosine-nucleotide levels...
April 13, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28404924/antitumor-effects-of-cyclin-dependent-kinase-9-inhibition-in-esophageal-adenocarcinoma
#20
Zhimin Tong, Devkumar Chatterjee, Defeng Deng, Omkara Veeranki, Alicia Mejia, Jaffer A Ajani, Wayne Hofstetter, Steven Lin, Sushovan Guha, Scott Kopetz, Sunil Krishnan, Dipen Maru
Role of cyclin dependent kinase 9(CDK9) as a potential target in esophageal adenocarcinoma (EAC) is unknown. We investigated CDK9 protein expression in EAC and Barrett's esophagus and role of CDK9 in oncogenic processes of EAC in vitro and in murine xenografts. The CDK9 expression was significantly higher in EAC as compared to Barrett's esophagus in patient samples. Stable shCDK9 in SKGT4 reduced proliferation by 37% at day 4, increased apoptosis at 48 hours and induced G1 cell cycle arrest at 48 hours (58...
February 23, 2017: Oncotarget
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