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RNA Polymerase II

Chao-Jun Hu, Jian-Bo Pan, Guang Song, Xiao-Ting Wen, Zi-Yan Wu, Si Chen, Wen-Xiu Mo, Feng-Chun Zhang, Jiang Qian, Heng Zhu, Yong-Zhe Li
Behcet disease (BD) is a chronic systemic vasculitis and considered as an autoimmune disease. Although rare, BD can be fatal due to ruptured vascular aneurysms or severe neurological complications. To date, no known biomarker has been reported for this disease, making it difficult to diagnosis in the clinics. To undertake this challenge, we employed the HuProt arrays, each comprised of~20,000 unique human proteins, to identify BD-specific autoantibodies using a Two-Phase strategy established previously. In Phase I, we profiled the autoimmunity on the HuProt arrays with 75 serum samples collected from 40 BD patients, 15 diagnosed autoimmune patients who suffer from Takayasu arteritis (TA; N=5)), ANCA associated vasculitis(AAV; N=5), and Sjogren's syndrome(SS; N=5), and 20 healthy subjects, and identified 20 candidate autoantigens that were significantly associated with BD...
October 24, 2016: Molecular & Cellular Proteomics: MCP
Leonid A Serebryannyy, Michaela Yuen, Megan Parilla, Sandra T Cooper, Primal de Lanerolle
Actin plays a crucial role in regulating multiple processes within the nucleus, including transcription and chromatin organization. However, the polymerization state of nuclear actin remains controversial, and there is no evidence for persistent actin filaments in a normal interphase nucleus. Further, several disease pathologies are characterized by polymerization of nuclear actin into stable filaments or rods. These include filaments that stain with phalloidin, resulting from point mutations in skeletal α-actin, detected in the human skeletal disease intranuclear rod myopathy, and cofilin/actin rods that form in response to cellular stressors like heatshock...
2016: Frontiers in Physiology
Célia Jeronimo, Marie-France Langelier, Alain R Bataille, John M Pascal, B Franklin Pugh, François Robert
Mediator is a highly conserved transcriptional coactivator organized into four modules, namely Tail, Middle, Head, and Kinase (CKM). Previous work suggests regulatory roles for Tail and CKM, but an integrated model for these activities is lacking. Here, we analyzed the genome-wide distribution of Mediator subunits in wild-type and mutant yeast cells in which RNA polymerase II promoter escape is blocked, allowing detection of transient Mediator forms. We found that although all modules are recruited to upstream activated regions (UAS), assembly of Mediator within the pre-initiation complex is accompanied by the release of CKM...
October 18, 2016: Molecular Cell
Natalia Petrenko, Yi Jin, Koon Ho Wong, Kevin Struhl
Mediator is a transcriptional co-activator recruited to enhancers by DNA-binding activators, and it also interacts with RNA polymerase (Pol) II as part of the preinitiation complex (PIC). We demonstrate that a single Mediator complex associates with the enhancer and core promoter in vivo, indicating that it can physically bridge these transcriptional elements. However, the Mediator kinase module associates strongly with the enhancer, but not with the core promoter, and it dissociates from the enhancer upon depletion of the TFIIH kinase...
October 19, 2016: Molecular Cell
Thejal Srikumar, Jaya Padmanabhan
This chapter describes the potential use of flavopiridol, a CDK inhibitor with anti-inflammatory and anti-proliferative activities, in the treatment of various chronic diseases. Flavopiridol arrests cell cycle progression in the G1 or G2 phase by inhibiting the kinase activities of CDK1, CDK2, CDK4/6, and CDK7. Additionally, it binds tightly to CDK9, a component of the P-TEFb complex (CDK9/cyclin T), and interferes with RNA polymerase II activation and associated transcription. This in turn inhibits expression of several pro-survival and anti-apoptotic genes, and enhances cytotoxicity in transformed cells or differentiation in growth-arrested cells...
2016: Advances in Experimental Medicine and Biology
Akhi Akhter, Emanuel Rosonina
The Saccharomyces cerevisiae transcription factor Gcn4 is expressed during amino acid starvation and its abundance is controlled by ubiquitin-mediated proteolysis. Cdk8, a kinase component of the RNA polymerase II Mediator complex, phosphorylates Gcn4 which triggers its ubiquitination/proteolysis and is thought to link Gcn4 degradation with transcription of target genes. In addition to phosphorylation and ubiquitination, we previously showed that Gcn4 becomes sumoylated in a DNA-binding dependent manner, while a non-sumoylatable form of Gcn4 showed increased chromatin occupancy, but only if Cdk8 was present...
October 21, 2016: Genetics
Xianghua Wang, Seppo Huhtinen, Karen Hansen
Species limits in the small genus Geopyxis are debatable because of problems with interpreting the few phenotypic features and poor documentation of types. To clarify species boundaries and diversity, we studied the morphology of 74 specimens of Geopyxis from the Northern Hemisphere, including five types, and sequenced four loci for 57 representatives: the nuc rDNA ITS1-5.8S-ITS2 (ITS), D1-D2 domains of nuc 28S rDNA (28S), translation elongation factor (tef1), and (or) part of the second largest subunit of the RNA polymerase II (rpb2) (5-7 region)...
October 19, 2016: Mycologia
Wei-Lin Wang, David Shechter
Chromatin, primarily a complex of DNA and histone proteins, is the physiological form of the genome. Chromatin is generally repressive for transcription and other information transactions that occur on DNA. A wealth of post-translational modifications on canonical histones and histone variants encode regulatory information to recruit or repel effector proteins on chromatin, promoting and further repressing transcription and thereby form the basis of epigenetic information. During metazoan oogenesis, large quantities of histone proteins are synthesized and stored in preparation for the rapid early cell cycles of development and to elicit maternal control of chromatin assembly pathways...
2016: International Journal of Developmental Biology
Olivia Lombardi, Dhaval Varshney, Nicola M Phillips, Victoria H Cowling
c-Myc is a potent driver of many human cancers. Since strategies for directly targeting c-Myc protein have had limited success, upstream regulators and downstream effectors of c-Myc are being investigated as alternatives for therapeutic intervention. c-Myc regulates transcription and formation of the mRNA cap, which is important for transcript maturation and translation. However, the direct mechanism by which c-Myc upregulates mRNA capping is unclear. mRNA cap formation initiates with the linkage of inverted guanosine via a triphosphate bridge to the first transcribed nucleotide, catalysed by mRNA capping enzyme (CE/RNGTT)...
October 16, 2016: Oncotarget
Vasily M Studitsky, Ekaterina V Nizovtseva, Alexey K Shaytan, Donal S Luse
Packaging of DNA into chromatin affects all processes on DNA. Nucleosomes present a strong barrier to transcription, raising important questions about the nature and the mechanisms of overcoming the barrier. Recently it was shown that DNA sequence, DNA-histone interactions and backtracking by RNA polymerase II (Pol II) all contribute to formation of the barrier. After partial uncoiling of nucleosomal DNA from histone octamer by Pol II and backtracking of the enzyme, nucleosomal DNA recoils on the octamer, locking Pol II in the arrested state...
2016: Biochemistry & Molecular Biology Journal
Alexandros Strikoudis, Charalampos Lazaris, Thomas Trimarchi, Antonio L Galvao Neto, Yan Yang, Panagiotis Ntziachristos, Scott Rothbart, Shannon Buckley, Igor Dolgalev, Matthias Stadtfeld, Brian D Strahl, Brian D Dynlacht, Aristotelis Tsirigos, Iannis Aifantis
Pluripotent embryonic stem cells (ESCs) self-renew or differentiate into all tissues of the developing embryo and cell-specification factors are necessary to balance gene expression. Here we delineate the function of the PHD-finger protein 5a (Phf5a) in ESC self-renewal and ascribe its role in regulating pluripotency, cellular reprogramming and myoblast specification. We demonstrate that Phf5a is essential for maintaining pluripotency, since depleted ESCs exhibit hallmarks of differentiation. Mechanistically, we attribute Phf5a function to the stabilization of the Paf1 transcriptional complex and control of RNA polymerase II elongation on pluripotency loci...
October 17, 2016: Nature Cell Biology
Larissa Becirovic, Ian R Brown
Heat shock proteins (Hsps) are a set of highly conserved proteins involved in cellular repair and protective mechanisms. The intracellular localization of inducible members of the HSPA (HSP70) family can be used as an index to identify stress-sensitive sites in differentiated human neuronal cells. Following thermal stress, the little studied HSPA6 (HSP70B') was targeted to the periphery of nuclear speckles (perispeckles) that are sites of transcription factories. Triptolide, a fast-acting transcription inhibitor, knocked down levels of the large subunit of RNA polymerase II, RPB1, during the time-frame when HSPA6 associated with perispeckles...
October 14, 2016: Neurochemical Research
Naotaka Nakazawa, Aneesh R Sathe, G V Shivashankar, Michael P Sheetz
Substrate rigidity affects many physiological processes through mechanochemical signals from focal adhesion (FA) complexes that subsequently modulate gene expression. We find that shuttling of the LIM domain (domain discovered in the proteins, Lin11, Isl-1, and Mec-3) protein four-and-a-half LIM domains 2 (FHL2) between FAs and the nucleus depends on matrix mechanics. In particular, on soft surfaces or after the loss of force, FHL2 moves from FAs into the nucleus and concentrates at RNA polymerase (Pol) II sites, where it acts as a transcriptional cofactor, causing an increase in p21 gene expression that will inhibit growth on soft surfaces...
October 14, 2016: Proceedings of the National Academy of Sciences of the United States of America
João Paulo Zen Siqueira, Deanna A Sutton, Dania García, Josepa Gené, Pamela Thomson, Nathan Wiederhold, Josep Guarro
Aspergillus section Versicolores includes species of clinical relevance and many others that have been poorly studied but are occasionally found in clinical samples. The aim of this study was to investigate, using a multilocus phylogenetic approach, the spectrum of species of the section Versicolores and to determine their in vitro antifungal susceptibility. The study was based on a set of 77 clinical isolates from different USA medical centres, which had been previously identified as belonging to this section...
November 2016: Fungal Biology
Chen Chen, Gerard J M Verkley, Guangyu Sun, Johannes Z Groenewald, Pedro W Crous
Species in Neofabraea, Pezicula, and related genera have been reported as saprobes, plant pathogens or endophytes from a wide range of hosts. The asexual morphs of Neofabraea and Pezicula had been placed in Cryptosporiopsis, now a synonym of Pezicula, while Neofabraea was also linked to Phlyctema. Based on morphology and molecular data of the partial large subunit nrDNA (LSU), the internal transcribed spacer region with intervening 5.8S nrDNA (ITS), partial β-tubulin region (tub2), and the partial RNA polymerase II second largest subunit region (rpb2), the taxonomy and phylogenetic relationships of these fungi were investigated...
November 2016: Fungal Biology
John-Erich Haight, Gary A Laursen, Jessie A Glaeser, D Lee Taylor
Fungal species with a broad distribution may exhibit considerable genetic variation over their geographic ranges. Variation may develop among populations based on geographic isolation, lack of migration, and genetic drift, though this genetic variation may not always be evident when examining phenotypic characters. Fomitopsis pinicola is an abundant saprotrophic fungus found on decaying logs throughout temperate regions of the Northern Hemisphere. Phylogenetic studies have addressed the relationship of F. pinicola to other wood-rotting fungi, but pan-continental variation within F...
September 2016: Mycologia
B Roche, B Arcangioli, R A Martienssen
Quiescent cells play a predominant role in most organisms. Here, we identify RNA interference (RNAi) as a major requirement for quiescence (G0) in Schizosaccharomyces pombe RNAi mutants lose viability at G0-entry and are unable to maintain long-term quiescence. We obtained dcr1Δ G0 suppressors, which mapped to genes involved in chromosome segregation, RNA polymerase-associated factors, and heterochromatin formation. We propose a model in which RNAi promotes RNA polymerase release in cycling and quiescent cells: (i) RNA pol II release mediates heterochromatin formation at centromeres allowing proper chromosome segregation during mitotic growth and G0-entry, and (ii) RNA pol I release prevents heterochromatin formation at rDNA during quiescence maintenance...
October 13, 2016: Science
Younguk Sun, Huimin Zhang, Majid Kazemian, Joseph M Troy, Christopher Seward, Xiaochen Lu, Lisa Stubbs
Mammalian genomes contain hundreds of genes transcribed by RNA Polymerase III (Pol III), encoding noncoding RNAs and especially the tRNAs specialized to carry specific amino acids to the ribosome for protein synthesis. In addition to this well-known function, tRNAs and their genes (tDNAs) serve a variety of other critical cellular functions. For example, tRNAs and other Pol III transcripts can be cleaved to yield small RNAs with potent regulatory activities. Furthermore, from yeast to mammals, active tDNAs and related "extra-TFIIIC" (ETC) loci provide the DNA scaffolds for the most ancient known mechanism of three-dimensional chromatin architecture...
October 6, 2016: Oncotarget
Leiming Li, Yan Li, Jiansong Zhao, Shuli Fan, Liguo Wang, Xu Li
Osteosarcoma (OS) is the most common primary bone tumor, but molecular mechanisms of the disease have not been well understood, and treatment of metastatic OS remains a challenge. Rapid ribosomal RNA synthesis in cancer is transcribed by RNA polymerase I, which results in unbridled cell growth. The recent discovery of CX-5461, a selective RNA polymerase I inhibitor, exerted its inhibitory effect of ribosomal RNA synthesis and antiproliferative potency. Here, we demonstrate that CX-5461 induces G2 arrest in the cell cycle and expression of microtubule-associated protein 1 light chain 3 II isoform in OS cell lines...
2016: OncoTargets and Therapy
Eitan Lerner, SangYoon Chung, Benjamin L Allen, Shuang Wang, Jookyung Lee, Shijia W Lu, Logan W Grimaud, Antonino Ingargiola, Xavier Michalet, Yazan Alhadid, Sergei Borukhov, Terence R Strick, Dylan J Taatjes, Shimon Weiss
Initiation is a highly regulated, rate-limiting step in transcription. We used a series of approaches to examine the kinetics of RNA polymerase (RNAP) transcription initiation in greater detail. Quenched kinetics assays, in combination with gel-based assays, showed that RNAP exit kinetics from complexes stalled at later stages of initiation (e.g., from a 7-base transcript) were markedly slower than from earlier stages (e.g., from a 2- or 4-base transcript). In addition, the RNAP-GreA endonuclease accelerated transcription kinetics from otherwise delayed initiation states...
October 11, 2016: Proceedings of the National Academy of Sciences of the United States of America
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