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RNA Polymerase II

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https://www.readbyqxmd.com/read/29352065/a-role-for-miniyo-and-quatre-quart-2-in-the-assembly-of-rna-polymerases-ii-iv-and-v-in-arabidopsis
#1
Yaoxi Li, Yuxiang Yuan, Xiaofeng Fang, Xiuli Lu, Bi Lian, Gaozhan Zhao, Yijun Qi
RNA polymerases IV and V (Pol IV and Pol V) are required for the generation of noncoding RNAs in RNA-directed DNA methylation (RdDM). Their subunit compositions resemble that of Pol II. The mechanism and accessory factors involved in their assembly remain largely unknown. In this study, we identified mutant alleles of MINIYO (IYO), QUATRE-QUART 2 (QQT2) and NUCLEAR RNA POLYMERASE B11/D11/E11 (NRPB/D/E11) that cause defects in RdDM in Arabidopsis. We found that Pol IV-dependent small interfering RNAs (siRNAs) and Pol V-dependent transcripts were greatly reduced in the mutants...
January 18, 2018: Plant Cell
https://www.readbyqxmd.com/read/29351914/high-resolution-transcription-maps-reveal-the-widespread-impact-of-roadblock-termination-in-yeast
#2
Tito Candelli, Drice Challal, Jean-Baptiste Briand, Jocelyne Boulay, Odil Porrua, Jessie Colin, Domenico Libri
Transcription termination delimits transcription units but also plays important roles in limiting pervasive transcription. We have previously shown that transcription termination occurs when elongating RNA polymerase II (RNAPII) collides with the DNA-bound general transcription factor Reb1. We demonstrate here that many different DNA-binding proteins can induce termination by a similar roadblock (RB) mechanism. We generated high-resolution transcription maps by the direct detection of RNAPII upon nuclear depletion of two essential RB factors or when the canonical termination pathways for coding and non-coding RNAs are defective...
January 19, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29346759/nf-%C3%AE%C2%BAb-chromatin-interactions-drive-diverse-phenotypes-by-modulating-transcriptional-noise
#3
Victor C Wong, Victor L Bass, M Elise Bullock, Arvind K Chavali, Robin E C Lee, Walther Mothes, Suzanne Gaudet, Kathryn Miller-Jensen
Noisy gene expression generates diverse phenotypes, but little is known about mechanisms that modulate noise. Combining experiments and modeling, we studied how tumor necrosis factor (TNF) initiates noisy expression of latent HIV via the transcription factor nuclear factor κB (NF-κB) and how the HIV genomic integration site modulates noise to generate divergent (low-versus-high) phenotypes of viral activation. We show that TNF-induced transcriptional noise varies more than mean transcript number and that amplification of this noise explains low-versus-high viral activation...
January 16, 2018: Cell Reports
https://www.readbyqxmd.com/read/29345638/molecular-mechanism-of-promoter-opening-by-rna-polymerase-iii
#4
Matthias K Vorländer, Heena Khatter, Rene Wetzel, Wim J H Hagen, Christoph W Müller
RNA polymerase III (Pol III) and transcription factor IIIB (TFIIIB) assemble together on different promoter types to initiate the transcription of small, structured RNAs. Here we present structures of Pol III preinitiation complexes, comprising the 17-subunit Pol III and the heterotrimeric transcription factor TFIIIB, bound to a natural promoter in different functional states. Electron cryo-microscopy reconstructions, varying from 3.7 Å to 5.5 Å resolution, include two early intermediates in which the DNA duplex is closed, an open DNA complex, and an initially transcribing complex with RNA in the active site...
January 17, 2018: Nature
https://www.readbyqxmd.com/read/29345637/structural-basis-of-rna-polymerase-iii-transcription-initiation
#5
Guillermo Abascal-Palacios, Ewan Phillip Ramsay, Fabienne Beuron, Edward Morris, Alessandro Vannini
RNA polymerase (Pol) III transcribes essential non-coding RNAs, including the entire pool of transfer RNAs, the 5S ribosomal RNA and the U6 spliceosomal RNA, and is often deregulated in cancer cells. The initiation of gene transcription by Pol III requires the activity of the transcription factor TFIIIB to form a transcriptionally active Pol III preinitiation complex (PIC). Here we present electron microscopy reconstructions of Pol III PICs at 3.4-4.0 Å and a reconstruction of unbound apo-Pol III at 3.1 Å...
January 17, 2018: Nature
https://www.readbyqxmd.com/read/29343442/the-transcription-factor-stat6-mediates-direct-repression-of-inflammatory-enhancers-and-limits-activation-of-alternatively-polarized-macrophages
#6
Zsolt Czimmerer, Bence Daniel, Attila Horvath, Dominik Rückerl, Gergely Nagy, Mate Kiss, Matthew Peloquin, Marietta M Budai, Ixchelt Cuaranta-Monroy, Zoltan Simandi, Laszlo Steiner, Bela Nagy, Szilard Poliska, Csaba Banko, Zsolt Bacso, Ira G Schulman, Sascha Sauer, Jean-Francois Deleuze, Judith E Allen, Szilvia Benko, Laszlo Nagy
The molecular basis of signal-dependent transcriptional activation has been extensively studied in macrophage polarization, but our understanding remains limited regarding the molecular determinants of repression. Here we show that IL-4-activated STAT6 transcription factor is required for the direct transcriptional repression of a large number of genes during in vitro and in vivo alternative macrophage polarization. Repression results in decreased lineage-determining transcription factor, p300, and RNA polymerase II binding followed by reduced enhancer RNA expression, H3K27 acetylation, and chromatin accessibility...
January 16, 2018: Immunity
https://www.readbyqxmd.com/read/29342370/fgf8-signaling-alters-the-osteogenic-cell-fate-in-the-hard-palate
#7
J Xu, Z Huang, W Wang, X Tan, H Li, Y Zhang, W Tian, T Hu, Y P Chen
Fibroblast growth factor (FGF) signaling has been implicated in the regulation of osteogenesis in both intramembranous and endochondral ossifications. In the developing palate, the anterior bony palate forms by direct differentiation of cranial neural crest (CNC)-derived mesenchymal cells, but the signals that regulate the osteogenic cell fate in the developing palate remain unclear. In the present study, we investigated the potential role of FGF signaling in osteogenic fate determination of the palatal mesenchymal cells...
January 1, 2018: Journal of Dental Research
https://www.readbyqxmd.com/read/29340213/non-coding-rnas-as-transcriptional-regulators-in-eukaryotes
#8
O Y Burenina, T S Oretskaya, E A Kubareva
Non-coding RNAs up to 1,000 nucleotides in length are widespread in eukaryotes and fulfil various regulatory functions, in particular during chromatin remodeling and cell proliferation. These RNAs are not translated into proteins: thus, they are non-coding RNAs (ncRNAs). The present review describes the eukaryotic ncRNAs involved in transcription regulation, first and foremost, targeting RNA polymerase II (RNAP II) and/or its major proteinaceous transcription factors. The current state of knowledge concerning the regulatory functions of SRA and TAR RNA, 7SK and U1 snRNA, GAS5 and DHFR RNA is summarized herein...
October 2017: Acta Naturae
https://www.readbyqxmd.com/read/29338026/flow-cytometric-analysis-identifies-changes-in-s-and-m-phases-as-novel-cell-cycle-alterations-induced-by-the-splicing-inhibitor-isoginkgetin
#9
Erin J Vanzyl, Kayleigh R C Rick, Alex B Blackmore, Erin M MacFarlane, Bruce C McKay
The spliceosome is a large ribonucleoprotein complex that catalyzes the removal of introns from RNA polymerase II-transcribed RNAs. Spliceosome assembly occurs in a stepwise manner through specific intermediates referred to as pre-spliceosome complexes E, A, B, B* and C. It has been reported that small molecule inhibitors of the spliceosome that target the SF3B1 protein component of complex A lead to the accumulation of cells in the G1 and G2/M phases of the cell cycle. Here we performed a comprehensive flow cytometry analysis of the effects of isoginkgetin (IGG), a natural compound that interferes with spliceosome assembly at a later step, complex B formation...
2018: PloS One
https://www.readbyqxmd.com/read/29336686/phylogeny-and-taxonomy-of-favolus-basidiomycota
#10
Jun-Liang Zhou, Bao-Kai Cui
Favolus is a natural genus that is closely related to Polyporus. A taxonomic study of Favolus was carried out based on morphological characteristics and phylogenetic analysis of the internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2 = ITS) and 18S and 28S genes of the nuc rDNA, translation elongation factor 1-α gene (TEF1-α), the mt 16S rDNA gene (mt rrnS), β-tubulin gene (TBB1), and the RNA polymerase II largest subunit (RPB1) and second largest subunit (RPB2) genes. Fourteen specimens collected from subtropical to tropical regions in China were shown to be different from existing Favolus species...
November 30, 2017: Mycologia
https://www.readbyqxmd.com/read/29332189/the-arabidopsis-histone-chaperone-fact-is-required-for-stress-induced-expression-of-anthocyanin-biosynthetic-genes
#11
Alexander Pfab, Matthias Breindl, Klaus D Grasser
The histone chaperone FACT is involved in the expression of genes encoding anthocyanin biosynthetic enzymes also upon induction by moderate high-light and therefore contributes to the stress-induced plant pigmentation. The histone chaperone FACT consists of the SSRP1 and SPT16 proteins and associates with transcribing RNAPII (RNAPII) along the transcribed region of genes. FACT can promote transcriptional elongation by destabilising nucleosomes in the path of RNA polymerase II, thereby facilitating efficient transcription of chromatin templates...
January 13, 2018: Plant Molecular Biology
https://www.readbyqxmd.com/read/29330702/ptac10-an-s1-domain-containing-component-of-the-transcriptionally-active-chromosome-complex-is-essential-for-plastid-gene-expression-in-arabidopsis-thaliana-and-is-phosphorylated-by-chloroplast-targeted-casein-kinase-ii
#12
Qing-Bo Yu, Tuan-Tuan Zhao, Lin-Shan Ye, Ling Cheng, Ying-Qian Wu, Chao Huang, Zhong-Nan Yang
In higher plant chloroplasts, the plastid-encoded RNA polymerase (PEP) consists of four catalytic subunits and numerous nuclear-encoded accessory proteins, including pTAC10, an S1-domain-containing protein. In this study, pTAC10 knockout lines were characterized. Two ptac10 mutants had an albino phenotype and severely impaired chloroplast development. The pTAC10 genomic sequence fused to a four-tandem MYC tag driven by its own promoter functionally complemented the ptac10-1 mutant phenotype. pTAC10 was present in both the chloroplast stroma and thylakoids...
January 12, 2018: Photosynthesis Research
https://www.readbyqxmd.com/read/29329291/ovule-identity-mediated-by-pre-mrna-processing-in-arabidopsis
#13
Encarnación Rodríguez-Cazorla, Samanta Ortuño-Miquel, Héctor Candela, Lindsay J Bailey-Steinitz, Martin F Yanofsky, Antonio Martínez-Laborda, Juan-José Ripoll, Antonio Vera
Ovules are fundamental for plant reproduction and crop yield as they are the precursors of seeds. Therefore, ovule specification is a critical developmental program. In Arabidopsis thaliana, ovule identity is redundantly conferred by the homeotic D-class genes SHATTERPROOF1 (SHP1), SHP2 and SEEDSTICK (STK), phylogenetically related to the MADS-domain regulatory gene AGAMOUS (AG), essential in floral organ specification. Previous studies have shown that the HUA-PEP activity, comprised of a suite of RNA-binding protein (RBP) encoding genes, regulates AG pre-mRNA processing and thus flower patterning and organ identity...
January 12, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29326042/keratin-13-gene-is-epigenetically-suppressed-during-transforming-growth-factor-%C3%AE-1-induced-epithelial-mesenchymal-transition-in-a-human-keratinocyte-cell-line
#14
Mitsutoki Hatta, Yuki Miyake, Kunitoshi Uchida, Jun Yamazaki
Epithelial-mesenchymal transition (EMT) is a biological event in which epithelial cells lose their polarity and cell-cell adhesions and concomitantly acquire mesenchymal traits, and is thought to play an important role in pathological processes such as wound healing and cancer progression. In this study, we evaluated transforming growth factor (TGF)-β1-treated human keratinocyte HaCaT cells as an in vitro model of EMT. HaCaT cells were changed into an elongated fibroblast-like morphology, which is indicative of EMT in response to TGF-β1...
January 8, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29322784/bioinformatic-analysis-of-changes-in-rna-polymerase-ii-transcription-stimulated-by-estradiol-in-mcf7-cells
#15
J Wu, Y Cai, G Zhao
Estradiol (E2) is the most potent estrogen and RNA polymerase II (Pol II) regulates a great mass of gene expression. This study was designed to illustrate the mechanisms of estrogen-dependent human breast cancer (BC) through Pol II. ChIP-seq data, DNase-seq data and other sequencing data of human BC MCF-7 cells were downloaded from Gene Expression Omnibus database. Each of these datasets included one control and one E2 treated sample. Sequence alignment was performed and Pol II factor binding signal was determined...
2018: Neoplasma
https://www.readbyqxmd.com/read/29322219/sirt6-mediated-transcriptional-suppression-of-txnip-is-critical-for-pancreatic-beta-cell-function-and-survival-in-mice
#16
Kunhua Qin, Ning Zhang, Zhao Zhang, Michael Nipper, Zhenxin Zhu, Jake Leighton, Kexin Xu, Nicolas Musi, Pei Wang
AIMS/HYPOTHESIS: Better understanding of how genetic and epigenetic components control beta cell differentiation and function is key to the discovery of novel therapeutic approaches to prevent beta cell dysfunction and failure in the progression of type 2 diabetes. Our goal was to elucidate the role of histone deacetylase sirtuin 6 (SIRT6) in beta cell development and homeostasis. METHODS: Sirt6 endocrine progenitor cell conditional knockout and beta cell-specific knockout mice were generated using the Cre-loxP system...
January 10, 2018: Diabetologia
https://www.readbyqxmd.com/read/29321498/the-ppi-network-analysis-of-mrna-expression-profile-of-uterus-from-primary-dysmenorrheal-rats
#17
Pei Fan, Qiao-Hui Lin, Ying Guo, Lan-Ling Zhao, He Ning, Meng-Ying Liu, Dong-Qing Wei
To elucidate the mechanisms of molecular regulations underlying primary dysmenorrhea (PD), we used our previously published mRNA expression profile of uterus from PD syndrome rats to construct protein-protein interactions (PPI) network via STRING Interactome. Consequently, 34 subnetworks, including a "continent" (Subnetwork 1) and 33 "islands" (Subnetwork 2-34) were generated. The nodes, with relative expression ratios, were visualized in the PPI networks and their connections were identified. Through path and module exploring in the network, the bridges were found from pathways of cellular response to calcium ion, SMAD protein signal transduction, regulation of transcription from RNA polymerase II promoter in response to stress and muscle stretch that were significantly enriched by the up-regulated mRNAs, to the cascades of cAMP metabolic processes and positive regulation of cyclase activities by the down-regulated ones...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29320736/the-rna-polymerase-ii-factor-rpap1-is-critical-for-mediator-driven-transcription-and-cell-identity
#18
Cian J Lynch, Raquel Bernad, Isabel Calvo, Sandrina Nóbrega-Pereira, Sergio Ruiz, Nuria Ibarz, Ana Martinez-Val, Osvaldo Graña-Castro, Gonzalo Gómez-López, Eduardo Andrés-León, Vladimir Espinosa Angarica, Antonio Del Sol, Sagrario Ortega, Oscar Fernandez-Capetillo, Enrique Rojo, Javier Munoz, Manuel Serrano
The RNA polymerase II-associated protein 1 (RPAP1) is conserved across metazoa and required for stem cell differentiation in plants; however, very little is known about its mechanism of action or its role in mammalian cells. Here, we report that RPAP1 is essential for the expression of cell identity genes and for cell viability. Depletion of RPAP1 triggers cell de-differentiation, facilitates reprogramming toward pluripotency, and impairs differentiation. Mechanistically, we show that RPAP1 is essential for the interaction between RNA polymerase II (RNA Pol II) and Mediator, as well as for the recruitment of important regulators, such as the Mediator-specific RNA Pol II factor Gdown1 and the C-terminal domain (CTD) phosphatase RPAP2...
January 9, 2018: Cell Reports
https://www.readbyqxmd.com/read/29317789/aspergillus-subgenus-polypaecilum-from-the-built-environment
#19
J B Tanney, C M Visagie, N Yilmaz, K A Seifert
Xerophilic fungi, especially Aspergillus species, are prevalent in the built environment. In this study, we employed a combined culture-independent (454-pyrosequencing) and culture-dependent (dilution-to-extinction) approach to investigate the mycobiota of indoor dust collected from 93 buildings in 12 countries worldwide. High and low water activity (aw) media were used to capture mesophile and xerophile biodiversity, resulting in the isolation of approximately 9 000 strains. Among these, 340 strains representing seven putative species in Aspergillus subgenus Polypaecilum were isolated, mostly from lowered aw media, and tentatively identified based on colony morphology and internal transcribed spacer rDNA region (ITS) barcodes...
September 2017: Studies in Mycology
https://www.readbyqxmd.com/read/29317594/polymorphism-in-tmem132d-regulates-expression-and-anxiety-related-behavior-through-binding-of-rna-polymerase-ii-complex
#20
Roshan R Naik, Sergey V Sotnikov, Rebekka P Diepold, Stella Iurato, Patrick O Markt, Andrea Bultmann, Nadine Brehm, Tobias Mattheus, Beat Lutz, Angelika Erhardt, Elisabeth B Binder, Ulrike Schmidt, Florian Holsboer, Rainer Landgraf, Ludwig Czibere
TMEM132D is a candidate gene, where risk genotypes have been associated with anxiety severity along with higher mRNA expression in the frontal cortex of panic disorder patients. Concurrently, in a high (HAB) and low (LAB) trait anxiety mouse model, Tmem132d was found to show increased expression in the anterior cingulate cortex (aCC) of HAB as compared to LAB mice. To understand the molecular underpinnings underlying the differential expression, we sequenced the gene and found two single-nucleotide polymorphisms (SNPs) in the promoter differing between both lines which could explain the observed mRNA expression profiles using gene reporter assays...
January 10, 2018: Translational Psychiatry
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