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RNA Polymerase II

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https://www.readbyqxmd.com/read/29163825/maternal-histone-acetyltransferase-kat8-is-required-for-porcine-preimplantation-embryo-development
#1
Zubing Cao, Ronghua Wu, Di Gao, Tengteng Xu, Lei Luo, Yunsheng Li, Jianyong Han, Yunhai Zhang
K (lysine) acetyltransferase 8 (KAT8), an acetyltransferase that specifically catalyzes histone H4 lysine 16 acetylation, is critical for key biological processes including cell proliferation and maintenance of genome stability. However, the role of KAT8 during preimplantation development in pigs remains unclear. Results herein showed that KAT8 mRNA is maternally derived and it is required for successful development of early embryos. An abundance of KAT8 transcripts are expressed in oocytes and its abundance continuously decreases throughout meiotic maturation and preimplantation development...
October 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/29159556/effects-of-arsenic-trioxide-on-inf-gamma-gene-expression-in-mrl-lpr-mice-and-human-lupus
#2
Hongye Hu, Enjiu Chen, Yongji Li, Xiaochun Zhu, Ting Zhang, Xiaofang Zhu
Arsenic trioxide (As2O3; ATO), a traditional Chinese medicine, is used to treat patients with acute promye-locytic leukemia, while its application for treatment of systemic lupus erythematosus (SLE) is still under evaluation. The high expression of INF-gamma (INF-γ) is a primary pathogenic factor in SLE. It is found that ATO can reduce INF-γ expression levels in lupus-prone mice, whereas it is not clear whether ATO has the same effect on SLE patients. Therefore, this study was to investigate the underlying mechanism of the effects of ATO on the expression of INF-γ in splenocytes of MRL/lpr mice and PBMCs of human lupus...
November 20, 2017: Biological Trace Element Research
https://www.readbyqxmd.com/read/29158611/phylogeny-of-xerophilic-aspergilli-subgenus-aspergillus-and-taxonomic-revision-of-section-restricti
#3
F Sklenář, Ž Jurjević, P Zalar, J C Frisvad, C M Visagie, M Kolařík, J Houbraken, A J Chen, N Yilmaz, K A Seifert, M Coton, F Déniel, N Gunde-Cimerman, R A Samson, S W Peterson, V Hubka
Aspergillus section Restricti together with sister section Aspergillus (formerly Eurotium) comprises xerophilic species, that are able to grow on substrates with low water activity and in extreme environments. We adressed the monophyly of both sections within subgenus Aspergillus and applied a multidisciplinary approach for definition of species boundaries in sect. Restricti. The monophyly of sections Aspergillus and Restricti was tested on a set of 102 isolates comprising all currently accepted species and was strongly supported by Maximum likelihood (ML) and Bayesian inferrence (BI) analysis based on β-tubulin (benA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) loci...
September 2017: Studies in Mycology
https://www.readbyqxmd.com/read/29158440/cohesin-facilitates-zygotic-genome-activation-in-zebrafish
#4
Michael Meier, Jenny Grant, Amy Dowdle, Amarni Thomas, Jennifer Gerton, Philippe Collas, Justin M O'Sullivan, Julia A Horsfield
At zygotic genome activation (ZGA), changes in chromatin structure are associated with new transcription immediately following the maternal-to-zygotic transition (MZT). The nuclear architectural proteins, cohesin and CCCTC-binding factor (CTCF), contribute to chromatin structure and gene regulation. We show here that normal cohesin function is important for ZGA in zebrafish. Depletion of cohesin subunit Rad21 delays ZGA without affecting cell cycle progression. In contrast, CTCF depletion has little effect on ZGA whereas complete abrogation is lethal...
November 20, 2017: Development
https://www.readbyqxmd.com/read/29158240/novel-genes-and-regulators-that-influence-production-of-cell-surface-exopolysaccharides-in-sinorhizobium-meliloti
#5
Melanie J Barnett, Sharon R Long
Sinorhizobium meliloti is a soil-dwelling α-proteobacterium that engages in a nitrogen-fixing root nodule symbiosis with leguminous plants. Cell surface polysaccharides are important for both adapting to stresses in the soil and development of an effective symbiotic interaction. Among the polysaccharides characterized to date, the acidic exopolysaccharides EPS-I (succinoglycan) and EPS-II (galactoglucan) are particularly important for protection from abiotic stresses, biofilm formation, root colonization, and infection of plant roots...
November 20, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/29157917/the-mediator-complex-in-genomic-and-non-genomic-signaling-in-cancer
#6
Hannah Weber, Michael J Garabedian
Mediator is a conserved, multi-subunit macromolecular machine divided structurally into head, middle, and tail modules, along with a transiently associating kinase module. Mediator functions as an integrator of transcriptional regulatory activity by interacting with DNA-bound transcription factors and with RNA polymerase II (Pol II) to both activate and repress gene expression. Mediator has been shown to affect multiple steps in transcription, including chromatin looping between enhancers and promoters, pre-initiation complex formation, transcriptional elongation, and mRNA splicing...
November 17, 2017: Steroids
https://www.readbyqxmd.com/read/29155810/regulation-of-transcription-elongation-in-response-to-osmostress
#7
Andrea Silva, Santiago Cavero, Victoria Sarah, Carme Solé, René Böttcher, Sebastián Chávez, Francesc Posas, Eulàlia de Nadal
Cells trigger massive changes in gene expression upon environmental fluctuations. The Hog1 stress-activated protein kinase (SAPK) is an important regulator of the transcriptional activation program that maximizes cell fitness when yeast cells are exposed to osmostress. Besides being associated with transcription factors bound at target promoters to stimulate transcriptional initiation, activated Hog1 behaves as a transcriptional elongation factor that is selective for stress-responsive genes. Here, we provide insights into how this signaling kinase functions in transcription elongation...
November 20, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29155791/improved-protocol-for-chromatin-immunoprecipitation-from-mouse-skeletal-muscle
#8
Shilpy Joshi, Vanessa Ueberschlag-Pitiot, Daniel Metzger, Irwin Davidson
We describe an efficient and reproducible protocol for the preparation of chromatin from adult mouse skeletal muscle, a physically resistant tissue with a high content of structural proteins. Dissected limb muscles from adult mice are physically disrupted by mechanical homogenisation, or a combination of mincing and douncing, in a hypotonic buffer before formaldehyde fixation of the cell lysate. The fixed nuclei are purified by further cycles of mechanical homogenisation or douncing and sequential filtrations to remove cell debris...
November 6, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29153392/polycomb-repressive-complex-2-methylates-elongin-a-to-regulate-transcription
#9
M Behfar Ardehali, Anthony Anselmo, Jesse C Cochrane, Sharmistha Kundu, Ruslan I Sadreyev, Robert E Kingston
Polycomb repressive complex 2 (PRC2-EZH2) methylates histone H3 at lysine 27 (H3K27) and is required to maintain gene repression during development. Misregulation of PRC2 is linked to a range of neoplastic malignancies, which is believed to involve methylation of H3K27. However, the full spectrum of non-histone substrates of PRC2 that might also contribute to PRC2 function is not known. We characterized the target recognition specificity of the PRC2 active site and used the resultant data to screen for uncharacterized potential targets...
November 15, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29153391/structure-of-a-thermostable-group-ii-intron-reverse-transcriptase-with-template-primer-and-its-functional-and-evolutionary-implications
#10
Jennifer L Stamos, Alfred M Lentzsch, Alan M Lambowitz
Bacterial group II intron reverse transcriptases (RTs) function in both intron mobility and RNA splicing and are evolutionary predecessors of retrotransposon, telomerase, and retroviral RTs as well as the spliceosomal protein Prp8 in eukaryotes. Here we determined a crystal structure of a full-length thermostable group II intron RT in complex with an RNA template-DNA primer duplex and incoming deoxynucleotide triphosphate (dNTP) at 3.0-Å resolution. We find that the binding of template-primer and key aspects of the RT active site are surprisingly different from retroviral RTs but remarkably similar to viral RNA-dependent RNA polymerases...
November 9, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29144843/brevicollum-a-new-genus-in-neohendersoniaceae-pleosporales
#11
Kazuaki Tanaka, Akira Hashimoto, Misato Matsumura, Toyozo Sato
A new genus, Brevicollum, is established for two new species, B. hyalosporum on Syzygium samarangense and B. versicolor on Volkameria inermis, in Japan. This genus is characterized by the presence of immersed ascomata with an excentric to central, short cylindrical ostiolar neck, thin ascomatal wall, clavate asci with a shallow ocular chamber, and broadly fusiform, hyaline to pale brown ascospores with a sheath. Molecular phylogenetic analyses based on a combined data set of sequences of 18S and 28S nuc rDNA genes and the second largest subunit of RNA polymerase II (RPB2) revealed that Brevicollum is a member of Neohendersoniaceae (Pleosporales, Dothideomycetes)...
October 5, 2017: Mycologia
https://www.readbyqxmd.com/read/29144457/a-ubiquitin-dependent-signalling-axis-specific-for-alkbh-mediated-dna-dealkylation-repair
#12
Joshua R Brickner, Jennifer M Soll, Patrick M Lombardi, Cathrine B Vågbø, Miranda C Mudge, Clement Oyeniran, Renana Rabe, Jessica Jackson, Meagan E Sullender, Elyse Blazosky, Andrea K Byrum, Yu Zhao, Mark A Corbett, Jozef Gécz, Michael Field, Alessandro Vindigni, Geir Slupphaug, Cynthia Wolberger, Nima Mosammaparast
DNA repair is essential to prevent the cytotoxic or mutagenic effects of various types of DNA lesions, which are sensed by distinct pathways to recruit repair factors specific to the damage type. Although biochemical mechanisms for repairing several forms of genomic insults are well understood, the upstream signalling pathways that trigger repair are established for only certain types of damage, such as double-stranded breaks and interstrand crosslinks. Understanding the upstream signalling events that mediate recognition and repair of DNA alkylation damage is particularly important, since alkylation chemotherapy is one of the most widely used systemic modalities for cancer treatment and because environmental chemicals may trigger DNA alkylation...
November 16, 2017: Nature
https://www.readbyqxmd.com/read/29138860/an-rna%C3%A2-sequencing-study-identifies-candidate-genes-for-angiotensin-ii%C3%A2-induced-cardiac-remodeling
#13
Jin Shu, Zhanwen Liu, Li Jin, Haiya Wang
The present study aimed to reveal the underlying mechanism of angiotensin II (AngII)‑induced cardiac remodeling and to identify potential therapeutic targets for prevention. Rat cardiac fibroblasts (CFs) were cultured with 10 nM AngII for 12 h, and CFs without AngII were used as the control. Following RNA isolation from AngII treated and control CFs, RNA‑sequencing was performed to detect gene expression levels. Differentially‑expressed genes (DEGs) were identified using the linear models for microarray analysis package in R software, and their functions and pathways were examined via enrichment analysis...
November 14, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29134331/optimization-and-application-of-a-dna-launched-infectious-clone-of-equine-arteritis-virus
#14
Ting Qi, Xiaojun Wang
Reverse genetics is one of the most powerful tools in modern virology. Equine arteritis virus (EAV) is the prototype member of the Equartevirus. In this study, a new reverse genetics system for the recovery of equine arteritis virus from a cDNA plasmid, which contains viral cDNA sequence flanked by hammerhead ribozyme (HamRz) and hepatitis delta virus ribozyme (HdvRz) sequences in both terminals of the viral genome, was developed by optimization of the promoter and terminator regions. Cellular RNA polymerase II drove the transcription of the viral genome...
November 13, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29133017/rpb5-modulates-the-rna-polymerase-ii-transition-from-initiation-to-elongation-by-influencing-spt5-association-and-backtracking
#15
Verónica Martínez-Fernández, Ana Isabel Garrido-Godino, María Carmen Mirón-García, Victoria Begley, Antonio Fernández-Pévida, Jesús de la Cruz, Sebastián Chávez, Francisco Navarro
Rpb5 is a subunit shared by the three eukaryotic RNA polymerases although its role in transcription remains unclear. It has been proposed that it makes contact with the promoter DNA and to participate in the coordination of the opening/closing of the RNA polymerase II DNA cleft. Here, we report the specific role of Rpb5 in the function of the yeast RNA polymerase II. The rpb5-P151T mutation specifically impairs transcription elongation by RNA polymerase II but does not influence the functions of RNA polymerases I or III...
November 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29132393/interferon-%C3%AE-inducible-protein-16-ifi16-is-required-for-the-maintenance-of-epstein-barr-virus-latency
#16
Gina Pisano, Arunava Roy, Mairaj Ahmed Ansari, Binod Kumar, Leela Chikoti, Bala Chandran
BACKGROUND: Epstein-Barr virus (EBV) exhibits both lytic and latent (Lat. I, II, and III) phases in an infected individual. It's during the latent phase of EBV that all EBV-associated cancers, including Burkitt's lymphoma, nasopharyngeal carcinoma and lymphoproliferative disease arise. Interferon-γ-inducible protein 16 (IFI16) is a well-established innate immune sensor and viral transcriptional regulator involved in response to invading DNA viruses. During latency, IFI16 remains in the nucleus, in part bound to the EBV genome; however, neither its role in EBV lytic cycle or latency has been established...
November 13, 2017: Virology Journal
https://www.readbyqxmd.com/read/29129639/determinants-of-histone-h3k4-methylation-patterns
#17
Luis M Soares, P Cody He, Yujin Chun, Hyunsuk Suh, TaeSoo Kim, Stephen Buratowski
Various factors differentially recognize trimethylated histone H3 lysine 4 (H3K4me3) near promoters, H3K4me2 just downstream, and promoter-distal H3K4me1 to modulate gene expression. This methylation "gradient" is thought to result from preferential binding of the H3K4 methyltransferase Set1/complex associated with Set1 (COMPASS) to promoter-proximal RNA polymerase II. However, other studies have suggested that location-specific cues allosterically activate Set1. Chromatin immunoprecipitation sequencing (ChIP-seq) experiments show that H3K4 methylation patterns on active genes are not universal or fixed and change in response to both transcription elongation rate and frequency as well as reduced COMPASS activity...
November 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29122615/ultrastructural-and-molecular-characterization-of-vairimorpha-austropotamobii-sp-nov-microsporidia-burenellidae-and-thelohania-contejeani-microsporidia-thelohaniidae-two-parasites-of-the-white-clawed-crayfish-austropotamobius-pallipes-complex-decapoda-astacidae
#18
Tobia Pretto, Francesco Montesi, Daniela Ghia, Valeria Berton, Miriam Abbadi, Michele Gastaldelli, Amedeo Manfrin, Gianluca Fea
The microsporidiosis of the endangered white-clawed crayfish Austropotamobius pallipes complex has generally been attributed to only one species, Thelohania contejeani, the agent of porcelain disease. Species identification was mostly assessed by macroscopic examination or microscopic evaluation of muscle samples rather than by molecular or ultrastructural analyses. A survey conducted on A. pallipes complex populations in Northern Italy highlighted the presence of two different microsporidia causing similar muscular lesions, T...
November 6, 2017: Journal of Invertebrate Pathology
https://www.readbyqxmd.com/read/29122461/histone-marks-in-the-driver-s-seat-functional-roles-in-steering-the-transcription-cycle
#19
REVIEW
Leah A Gates, Charles E Foulds, Bert W O'Malley
Particular chromatin modifications are associated with different states of gene transcription, yet our understanding of which modifications are causal 'drivers' in promoting transcription is incomplete. Here, we discuss new developments describing the ordered, mechanistic role of select histone marks occurring during distinct steps in the RNA polymerase II (Pol II) transcription cycle. In particular, we highlight the interplay between histone marks in specifying the 'next step' of transcription. While many studies have described correlative relationships between histone marks and their occupancy at distinct gene regions, we focus on studies that elucidate clear functional consequences of specific histone marks during different stages of transcription...
November 6, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/29121981/intrinsic-dna-curvature-in-trypanosomes
#20
Pablo Smircich, Najib M El-Sayed, Beatriz Garat
BACKGROUND: Trypanosoma cruzi and Trypanosoma brucei are protozoan parasites causing Chagas disease and African sleeping sickness, displaying unique features of cellular and molecular biology. Remarkably, no canonical signals for RNA polymerase II promoters, which drive protein coding genes transcription, have been identified so far. The secondary structure of DNA has long been recognized as a signal in biological processes and more recently, its involvement in transcription initiation in Leishmania was proposed...
November 9, 2017: BMC Research Notes
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