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RNA Polymerase II

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https://www.readbyqxmd.com/read/27932553/normalization-matters-tracking-the-best-strategy-for-sperm-mirna-quantification
#1
Celia Corral-Vazquez, Joan Blanco, Albert Salas-Huetos, Francesca Vidal, Ester Anton
STUDY QUESTION: What is the most reliable normalization strategy for sperm microRNA (miRNA) quantitative Reverse Transcription Polymerase Chain Reactions (qRT-PCR) using singleplex assays? SUMMARY ANSWER: The use of the average expression of hsa-miR-100-5p and hsa-miR-30a-5p as sperm miRNA qRT-PCR data normalizer is suggested as an optimal strategy. WHAT IS KNOWN ALREADY: Mean-centering methods are the most reliable normalization strategies for miRNA high-throughput expression analyses...
December 8, 2016: Molecular Human Reproduction
https://www.readbyqxmd.com/read/27926822/proteomic-and-phylogenetic-coevolution-analyses-of-pm79-and-pm92-identify-interactions-with-rnapii-and-delineate-the-mcmv-late-transcription-complex
#2
Travis J Chapa, Dong Yu, Anthony R French
The regulation of the late viral gene expression in betaherpesviruses is largely undefined. We have previously shown that the murine cytomegalovirus proteins pM79 and pM92 are required for late gene transcription. Here, we provide insight into the mechanism of pM79 and pM92 activity by determining their interaction partners during infection. Co-immunoprecipitation-coupled mass spectrometry studies demonstrate that pM79 and pM92 interact with an array of cellular and viral proteins involved in transcription...
December 7, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27924005/sub1-contacts-the-rna-polymerase-ii-stalk-to-modulate-mrna-synthesis
#3
Miguel Garavís, Noelia González-Polo, Paula Allepuz-Fuster, Jaime Alegrio Louro, Carlos Fernández-Tornero, Olga Calvo
Biogenesis of messenger RNA is critically influenced by the phosphorylation state of the carboxy-terminal domain (CTD) in the largest RNA polymerase II (RNAPII) subunit. Several kinases and phosphatases are required to maintain proper CTD phosphorylation levels and, additionally, several other proteins modulate them, including Rpb4/7 and Sub1. The Rpb4/7 heterodimer, constituting the RNAPII stalk, promote phosphatase functions and Sub1 globally influences CTD phosphorylation, though its mechanism remains mostly unknown...
December 6, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923713/when-transcription-goes-on-holliday-double-holliday-junctions-block-rna-polymerase-ii-transcription-in-vitro
#4
Anne Pipathsouk, Boris P Belotserkovskii, Philip C Hanawalt
Non-canonical DNA structures can obstruct transcription. This transcription blockage could have various biological consequences, including genomic instability and gratuitous transcription-coupled repair. Among potential structures causing transcription blockage are Holliday junctions (HJ), which can be generated as intermediates in homologous recombination or during processing of stalled replication forks. Of particular interest is the double Holliday junction (DHJ), which contains two HJs. Topological considerations impose the constraint that the total number of helical turns in the DNA duplexes between the junctions cannot be altered as long as the flanking DNA duplexes are intact...
December 3, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27920344/smad3-4-binding-to-promoter-ii-of-p450arom-so-as-to-regulate-aromatase-expression-in-endometriosis
#5
Juan Qu, Yuanyuan Zhu, Xiadi Wu, Juan Zheng, Zhen Hou, Yugui Cui, Yundong Mao, Jiayin Liu
Activin A can stimulate aromatase P450 (P450arom) expression in eutopic endometrial stromal cells (ESCs) of endometriosis by activin type I receptor-Smad pathway. In order to identify Smad3/4 binding to P450arom promoter II that mediates activin A response in ESCs, polymerase chain reaction (PCR) products of a serial truncated deletion of the P450arom promoter II region between -904 and +87 bp were inserted into the pGL3-basic vector to generate the promoter reporter plasmids. Luciferase reporter plasmids were cotransfected into cells with or without activin A (25 ng/mL)...
December 5, 2016: Reproductive Sciences
https://www.readbyqxmd.com/read/27920087/structural-visualization-of-the-p53-rna-polymerase-ii-assembly
#6
Sameer K Singh, Zhen Qiao, Lihua Song, Vijay Jani, William Rice, Edward Eng, Robert A Coleman, Wei-Li Liu
The master tumor suppressor p53 activates transcription in response to various cellular stresses in part by facilitating recruitment of the transcription machinery to DNA. Recent studies have documented a direct yet poorly characterized interaction between p53 and RNA polymerase II (Pol II). Therefore, we dissected the human p53/Pol II interaction via single-particle cryo-electron microscopy, structural docking, and biochemical analyses. This study reveals that p53 binds Pol II via the Rpb1 and Rpb2 subunits, bridging the DNA-binding cleft of Pol II proximal to the upstream DNA entry site...
December 5, 2016: Genes & Development
https://www.readbyqxmd.com/read/27918433/protein-phosphatase-1-regulates-expression-of-neuregulin-1
#7
Tatiana Ammosova, Kareem Washington, Jamie Rotimi, Namita Kumari, Kahli A Smith, Xiaomei Niu, Marina Jerebtsova, Sergei Nekhai
Protein phosphatase 1 (PP1), a cellular serine/threonine phosphatase, is targeted to cellular promoters by its major regulatory subunits, PP1 nuclear targeting subunit, nuclear inhibitor of PP1 (NIPP1) and RepoMan. PP1 is also targeted to RNA polymerase II (RNAPII) by NIPP1 where it can dephosphorylate RNAPII and cycle-dependent kinase 9 (CDK9). Here, we show that treatment of cells with a small molecule activator of PP1 increases the abundance of a neuregulin-1 (NRG-1)-derived peptide. NRG-1 mRNA and protein levels were increased in the cells stably or transiently expressing mutant NIPP1 (mNIPP1) that does not bind PP1, but not in the cells expressing NIPP1...
December 2, 2016: Biology
https://www.readbyqxmd.com/read/27916598/pic-activation-through-functional-interplay-between-mediator-and-tfiih
#8
Sohail Malik, Henrik Molina, Zhu Xue
The multiprotein Mediator coactivator complex functions in large part by controlling formation and function of the promoter-bound preinitiation complex (PIC), which consists of RNA polymerase II (Pol II) and general transcription factors. However, precisely how Mediator impacts the PIC, especially post-recruitment, has remained unclear. Here, we have studied Mediator effects on basal transcription in an in vitro transcription system reconstituted from purified components. Our results reveal a close functional interplay between Mediator and TFIIH in the early stages of PIC development...
December 1, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27912133/fate-of-tetracycline-resistance-in-synthetic-livestock-carcass-leachate-for-two-years
#9
Dennis Espineli Salcedo, Sungpyo Kim
To simulate the fate of antibiotic resistance in leachate from anaerobic carcass landfill site, anaerobic reactors were set-up and their antibiotic resistance activities were monitored for 2 years. Initially, Escherichia coli DH5α with tetracycline resistance pB10 plasmid was inoculated in nutrient rich anaerobic reactors. The fate of tetracycline resistant bacteria (TRB) was tracked by analysis using culture-based method, EC50 (half maximal effective concentration), and quantitative polymerase chain reaction (qPCR)...
November 29, 2016: Journal of Environmental Management
https://www.readbyqxmd.com/read/27911794/activation-of-mutant-tert-promoter-by-ras-erk-signaling-is-a-key-step-in-malignant-progression-of-braf-mutant-human-melanomas
#10
Yinghui Li, Hui Shan Cheng, Wee Joo Chng, Vinay Tergaonkar
Although activating BRAF/NRAS mutations are frequently seen in melanomas, they are not sufficient to drive malignant transformation and require additional events. Frequent co-occurrence of mutations in the promoter for telomerase reverse transcriptase (TERT), along with BRAF alterations, has recently been noted and correlated with poorer prognosis, implicating a functional link between BRAF signaling and telomerase reactivation in melanomas. Here, we report that RAS-ERK signaling in BRAF mutant melanomas is critical for regulating active chromatin state and recruitment of RNA polymerase II at mutant TERT promoters...
November 23, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27911772/c-terminal-domain-ctd-phosphatase-links-rho-gtpase-signaling-to-pol-ii-ctd-phosphorylation-in-arabidopsis-and-yeast
#11
Bo Zhang, Guohua Yang, Yu Chen, Yihong Zhao, Peng Gao, Bo Liu, Haiyang Wang, Zhi-Liang Zheng
Rho GTPases, including the Rho, Cdc42, Rac, and ROP subfamilies, act as pivotal signaling switches in various growth and developmental processes. Compared with the well-defined role of cytoskeletal organization in Rho signaling, much less is known regarding transcriptional regulation. In a mutant screen for phenotypic enhancers of transgenic Arabidopsis plants expressing a constitutively active form of ROP2 (designated CA1-1), we identified RNA polymerase II (Pol II) C-terminal domain (CTD) phosphatase-like 1 (CPL1) as a transcriptional regulator of ROP2 signaling...
November 28, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27902763/temperature-shift-alters-dna-methylation-and-histone-modification-patterns-in-gonadal-aromatase-cyp19a1-gene-in-species-with-temperature-dependent-sex-determination
#12
Yuiko Matsumoto, Brette Hannigan, David Crews
The environment surrounding the embryos has a profound impact on the developmental process and phenotypic outcomes of the organism. In species with temperature-dependent sex determination, gonadal sex is determined by the incubation temperature of the eggs. A mechanistic link between temperature and transcriptional regulation of developmental genes, however, remains elusive. In this study, we examine the changes in DNA methylation and histone modification patterns of the aromatase (cyp19a1) gene in embryonic gonads of red-eared slider turtles (Trachemys scripta) subjected to a temperature shift during development...
2016: PloS One
https://www.readbyqxmd.com/read/27900476/antarctomyces-pellizariae-sp-nov-a-new-endemic-blue-snow-resident-psychrophilic-ascomycete-fungus-from-antarctica
#13
Graciéle C A de Menezes, Valéria M Godinho, Bárbara A Porto, Vívian N Gonçalves, Luiz H Rosa
In the present study, we have identified and characterised a new snow resident ascomycete blue stain fungus from Antarctica named Antarctomyces pellizariae sp. nov. Menezes, Godinho, Porto, Gonçalves and Rosa, using polyphasic taxonomy techniques. This fungal species was recovered from the seasonal snow of the Antarctic Peninsula. Antarctomyces pellizariae displayed different macro- and micromorphology when compared with A. psychrotrophicus Stchigel and Guarro, the only other Antarctomyces species reported until date...
November 30, 2016: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/27899598/kinetics-of-transcription-initiation-directed-by-multiple-cis-regulatory-elements-on-the-glnap2-promoter
#14
Yaolai Wang, Feng Liu, Wei Wang
Transcription initiation is orchestrated by dynamic molecular interactions, with kinetic steps difficult to detect. Utilizing a hybrid method, we aim to unravel essential kinetic steps of transcriptional regulation on the glnAp2 promoter, whose regulatory region includes two enhancers (sites I and II) and three low-affinity sequences (sites III-V), to which the transcriptional activator NtrC binds. By structure reconstruction, we analyze all possible organization architectures of the transcription apparatus (TA)...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899590/different%C3%A2-enhancer-classes-in-drosophila-bind-distinct-architectural-proteins-and-mediate-unique-chromatin-interactions-and-3d-architecture
#15
Caelin Cubeñas-Potts, M Jordan Rowley, Xiaowen Lyu, Ge Li, Elissa P Lei, Victor G Corces
Eukaryotic gene expression is regulated by enhancer-promoter interactions but the molecular mechanisms that govern specificity have remained elusive. Genome-wide studies utilizing STARR-seq identified two enhancer classes in Drosophila that interact with different core promoters: housekeeping enhancers (hkCP) and developmental enhancers (dCP). We hypothesized that the two enhancer classes are occupied by distinct architectural proteins, affecting their enhancer-promoter contacts. By evaluating ChIP-seq occupancy of architectural proteins, typical enhancer-associated proteins, and histone modifications, we determine that both enhancer classes are enriched for RNA Polymerase II, CBP, and architectural proteins but there are also distinctions...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899423/myc-mediates-mrna-cap-methylation-of-canonical-wnt-beta-catenin-signaling-transcripts-by-recruiting-cdk7-and-rna-methyltransferase
#16
Valeriya Posternak, Matthew H Ung, Chao Cheng, Michael D Cole
: MYC is a pleiotropic transcription factor that activates and represses a wide range of target genes and is frequently deregulated in human tumors. While much is known about the role of MYC in transcriptional activation and repression, MYC can also regulate mRNA cap methylation through a mechanism that has remained poorly understood. Here it is reported that MYC enhances mRNA cap methylation of transcripts globally, specifically increasing mRNA cap methylation of genes involved in Wnt/beta-catenin signaling...
November 29, 2016: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/27898685/high-resolution-phenotypic-landscape-of-the-rna-polymerase-ii-trigger-loop
#17
Chenxi Qiu, Olivia C Erinne, Jui M Dave, Ping Cui, Huiyan Jin, Nandhini Muthukrishnan, Leung K Tang, Sabareesh Ganesh Babu, Kenny C Lam, Paul J Vandeventer, Ralf Strohner, Jan Van den Brulle, Sing-Hoi Sze, Craig D Kaplan
The active sites of multisubunit RNA polymerases have a "trigger loop" (TL) that multitasks in substrate selection, catalysis, and translocation. To dissect the Saccharomyces cerevisiae RNA polymerase II TL at individual-residue resolution, we quantitatively phenotyped nearly all TL single variants en masse. Three mutant classes, revealed by phenotypes linked to transcription defects or various stresses, have distinct distributions among TL residues. We find that mutations disrupting an intra-TL hydrophobic pocket, proposed to provide a mechanism for substrate-triggered TL folding through destabilization of a catalytically inactive TL state, confer phenotypes consistent with pocket disruption and increased catalysis...
November 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27895185/correction-for-abrisch-et-al-infection-by-herpes-simplex-virus-1-causes-near-complete-loss-of-rna-polymerase-ii-occupancy-on-the-host-cell-genome
#18
Robert G Abrisch, Tess M Eidem, Petro Yakovchuk, Jennifer F Kugel, James A Goodrich
No abstract text is available yet for this article.
December 15, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27889238/insights-into-nucleosome-organization-in-mouse-embryonic-stem-cells-through-chemical-mapping
#19
Lilien N Voong, Liqun Xi, Amy C Sebeson, Bin Xiong, Ji-Ping Wang, Xiaozhong Wang
Nucleosome organization influences gene activity by controlling DNA accessibility to transcription machinery. Here, we develop a chemical biology approach to determine mammalian nucleosome positions genome-wide. We uncovered surprising features of nucleosome organization in mouse embryonic stem cells. In contrast to the prevailing model, we observe that for nearly all mouse genes, a class of fragile nucleosomes occupies previously designated nucleosome-depleted regions around transcription start sites and transcription termination sites...
December 1, 2016: Cell
https://www.readbyqxmd.com/read/27884105/structural-features-of-dna-that-determine-rna-polymerase-ii-core-promoter
#20
Irina A Il'icheva, Mingian V Khodikov, Maria S Poptsova, Dmitry Yu Nechipurenko, Yury D Nechipurenko, Sergei L Grokhovsky
BACKGROUND: The general structure and action of all eukaryotic and archaeal RNA polymerases machinery have an astonishing similarity despite the diversity of core promoter sequences in different species. The goal of our work is to find common characteristics of DNA region that define it as a promoter for the RNA polymerase II (Pol II). RESULTS: The profiles of a large number of physical and structural characteristics, averaged over representative sets of the Pol II minimal core promoters of the evolutionary divergent species from animals, plants and unicellular fungi were analysed...
November 25, 2016: BMC Genomics
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