rna polymerase ii

Summary

Summary: A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure and transcribes DNA into RNA. It has different requirements for cations and salt than RNA polymerase I and is strongly inhibited by alpha-amanitin. EC 2.7.7.6.

Top Publications

  1. pmc MicroRNA genes are transcribed by RNA polymerase II
    Yoontae Lee
    Institute of Molecular Biology and Genetics and School of Biological Science, Seoul National University, Seoul, Korea
    EMBO J 23:4051-60. 2004
  2. ncbi High-resolution profiling of histone methylations in the human genome
    Artem Barski
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
    Cell 129:823-37. 2007
  3. ncbi CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
    Sanjeev Shukla
    Center for Cancer Research, Mouse Cancer Genetics Program, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA
    Nature 479:74-9. 2011
  4. pmc Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
    Leighton J Core
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Science 322:1845-8. 2008
  5. pmc Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans
    Karen Adelman
    Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
    Nat Rev Genet 13:720-31. 2012
  6. pmc PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
    Joel Rozowsky
    Molecular Biophysics and Biochemistry Dept, Yale University, PO Box 208114, New Haven, Connecticut 06520 8114, USA
    Nat Biotechnol 27:66-75. 2009
  7. pmc c-Myc regulates transcriptional pause release
    Peter B Rahl
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Cell 141:432-45. 2010
  8. ncbi RNA polymerase II elongation control
    Qiang Zhou
    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
    Annu Rev Biochem 81:119-43. 2012
  9. pmc The RNA polymerase II CTD coordinates transcription and RNA processing
    Jing Ping Hsin
    Department of Biological Sciences, Columbia University, New York, New York 10027, USA
    Genes Dev 26:2119-37. 2012
  10. ncbi Widespread bidirectional promoters are the major source of cryptic transcripts in yeast
    Helen Neil
    Institut Pasteur, Unité de Génétique des Interactions Macromoléculaires, CNRS, URA2171, 75015 Paris, France
    Nature 457:1038-42. 2009

Detail Information

Publications339 found, 100 shown here

  1. pmc MicroRNA genes are transcribed by RNA polymerase II
    Yoontae Lee
    Institute of Molecular Biology and Genetics and School of Biological Science, Seoul National University, Seoul, Korea
    EMBO J 23:4051-60. 2004
    ..Here we present the first direct evidence that miRNA genes are transcribed by RNA polymerase II (pol II)...
  2. ncbi High-resolution profiling of histone methylations in the human genome
    Artem Barski
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
    Cell 129:823-37. 2007
    ..Z, RNA polymerase II, and the insulator binding protein CTCF across the human genome using the Solexa 1G sequencing technology...
  3. ncbi CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
    Sanjeev Shukla
    Center for Cancer Research, Mouse Cancer Genetics Program, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA
    Nature 479:74-9. 2011
    ..protein, CCCTC-binding factor (CTCF), can promote inclusion of weak upstream exons by mediating local RNA polymerase II pausing both in a mammalian model system for alternative splicing, CD45, and genome-wide...
  4. pmc Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
    Leighton J Core
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Science 322:1845-8. 2008
    ..These results imply that the interplay between polymerases and regulators over broad promoter regions dictates the orientation and efficiency of productive transcription...
  5. pmc Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans
    Karen Adelman
    Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
    Nat Rev Genet 13:720-31. 2012
    ..of transcription regulation: whereas traditional models focused solely on the events that brought RNA polymerase II (Pol II) to a gene promoter to initiate RNA synthesis, emerging evidence points to the pausing of Pol II ..
  6. pmc PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
    Joel Rozowsky
    Molecular Biophysics and Biochemistry Dept, Yale University, PO Box 208114, New Haven, Connecticut 06520 8114, USA
    Nat Biotechnol 27:66-75. 2009
    ..Using two deeply sequenced data sets for human RNA polymerase II and STAT1, each with matching input-DNA controls, we describe a general scoring approach to address unique ..
  7. pmc c-Myc regulates transcriptional pause release
    Peter B Rahl
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Cell 141:432-45. 2010
    Recruitment of the RNA polymerase II (Pol II) transcription initiation apparatus to promoters by specific DNA-binding transcription factors is well recognized as a key regulatory step in gene expression...
  8. ncbi RNA polymerase II elongation control
    Qiang Zhou
    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
    Annu Rev Biochem 81:119-43. 2012
    Regulation of the elongation phase of transcription by RNA polymerase II (Pol II) is utilized extensively to generate the pattern of mRNAs needed to specify cell types and to respond to environmental changes...
  9. pmc The RNA polymerase II CTD coordinates transcription and RNA processing
    Jing Ping Hsin
    Department of Biological Sciences, Columbia University, New York, New York 10027, USA
    Genes Dev 26:2119-37. 2012
    The C-terminal domain (CTD) of the RNA polymerase II largest subunit consists of multiple heptad repeats (consensus Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7), varying in number from 26 in yeast to 52 in vertebrates...
  10. ncbi Widespread bidirectional promoters are the major source of cryptic transcripts in yeast
    Helen Neil
    Institut Pasteur, Unité de Génétique des Interactions Macromoléculaires, CNRS, URA2171, 75015 Paris, France
    Nature 457:1038-42. 2009
    ..Cryptic unstable transcripts (CUTs) were recently described as a principal class of RNA polymerase II transcripts in Saccharomyces cerevisiae...
  11. pmc Progression through the RNA polymerase II CTD cycle
    Stephen Buratowski
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
    Mol Cell 36:541-6. 2009
    The C-terminal domain of RNA polymerase II's largest subunit undergoes dynamic phosphorylation during transcription, and the different phosphorylation patterns that predominate at each stage of transcription recruit the appropriate set ..
  12. pmc A large fraction of extragenic RNA pol II transcription sites overlap enhancers
    Francesca De Santa
    Department of Experimental Oncology, European Institute of Oncology Campus IFOM IEO, Milan, Italy
    PLoS Biol 8:e1000384. 2010
    ..Discrimination between lncRNAs generated by canonical RNA genes and products of transcribed enhancers will provide a framework for experimental approaches to lncRNAs and help complete the annotation of mammalian genomes...
  13. pmc Genome-wide structure and organization of eukaryotic pre-initiation complexes
    Ho Sung Rhee
    Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Nature 483:295-301. 2012
    ..PICs, including RNA polymerase II and protein complexes TFIIA, TFIIB, TFIID (or TBP), TFIIE, TFIIF, TFIIH and TFIIK were positioned within ..
  14. pmc ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands
    Willem Jan Welboren
    Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
    EMBO J 28:1418-28. 2009
    We used ChIP-Seq to map ERalpha-binding sites and to profile changes in RNA polymerase II (RNAPII) occupancy in MCF-7 cells in response to estradiol (E2), tamoxifen or fulvestrant...
  15. pmc Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation
    Sergei Nechaev
    Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Biochim Biophys Acta 1809:34-45. 2011
    ..key developmental and stimulus-responsive genes, is regulated after the initiation step, by pausing of RNA polymerase II during elongation through the promoter-proximal region...
  16. ncbi RNA exosome depletion reveals transcription upstream of active human promoters
    Pascal Preker
    Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology, C F Møllers Alle, Building 1130, Aarhus University, Denmark
    Science 322:1851-4. 2008
    ..We propose that PROMPT transcription is a common characteristic of RNA polymerase II (RNAPII) transcribed genes with a possible regulatory potential.
  17. ncbi Uniform transitions of the general RNA polymerase II transcription complex
    Andreas Mayer
    Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science, Ludwig Maximilians Universitat Munchen, Munich, Germany
    Nat Struct Mol Biol 17:1272-8. 2010
    ..Transitions are uniform and independent of gene length, type and expression...
  18. pmc mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription
    Kris Brannan
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
    Mol Cell 46:311-24. 2012
    We report a function of human mRNA decapping factors in control of transcription by RNA polymerase II. Decapping proteins Edc3, Dcp1a, and Dcp2 and the termination factor TTF2 coimmunoprecipitate with Xrn2, the nuclear 5'-3' exonuclease "..
  19. ncbi A universal RNA polymerase II CTD cycle is orchestrated by complex interplays between kinase, phosphatase, and isomerase enzymes along genes
    Alain R Bataille
    Institut de Recherches Cliniques de Montreal, Montreal, QC H2W 1R7, Canada
    Mol Cell 45:158-70. 2012
    Transcription by RNA polymerase II (RNAPII) is coupled to mRNA processing and chromatin modifications via the C-terminal domain (CTD) of its largest subunit, consisting of multiple repeats of the heptapeptide YSPTSPS...
  20. ncbi Controlling the elongation phase of transcription with P-TEFb
    B Matija Peterlin
    Department of Medicine, Microbiology and Immunology, Rosalind Russell Medical Research Center, University of California, San Francisco, San Francisco, California 94143, USA
    Mol Cell 23:297-305. 2006
    ..factor b (P-TEFb) is a cyclin-dependent kinase that controls the elongation phase of transcription by RNA polymerase II (RNAPII)...
  21. pmc RNA polymerase is poised for activation across the genome
    Ginger W Muse
    Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
    Nat Genet 39:1507-11. 2007
    ..In many cases, recruitment of RNA polymerase II (Pol II) to a promoter is necessary and sufficient for activation of genes...
  22. ncbi RNA degradation by the exosome is promoted by a nuclear polyadenylation complex
    John LaCava
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
    Cell 121:713-24. 2005
    ..We speculate that this function was maintained in eukaryotic nuclei, while cytoplasmic mRNA poly(A) tails acquired different roles in translation...
  23. ncbi Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase
    Françoise Wyers
    Equipe labelisée La Ligue, Avenue de la Terrasse, 91190 Gif sur Yvette, Paris, France
    Cell 121:725-37. 2005
    ..cerevisiae are actually transcribed by RNA polymerase II, suggesting that the expressed fraction of the genome is higher than anticipated...
  24. pmc Transcription regulation through promoter-proximal pausing of RNA polymerase II
    Leighton J Core
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Science 319:1791-2. 2008
    Recent work has shown that the RNA polymerase II enzyme pauses at a promoter-proximal site of many genes in Drosophila and mammals. This rate-limiting step occurs after recruitment and initiation of RNA polymerase II at a gene promoter...
  25. ncbi CTD tyrosine phosphorylation impairs termination factor recruitment to RNA polymerase II
    Andreas Mayer
    Gene Center and Department of Biochemistry, Center for Integrated Protein Science Munich, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Science 336:1723-5. 2012
    ..These results show that CTD modifications trigger and block factor recruitment and lead to an extended CTD code that explains transcription cycle coordination on the basis of differential phosphorylation of Tyr(1), Ser(2), and Ser(5)...
  26. pmc BRD4 is an atypical kinase that phosphorylates serine2 of the RNA polymerase II carboxy-terminal domain
    Ballachanda N Devaiah
    Experimental Immunology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 109:6927-32. 2012
    ..We report that BRD4 is an atypical kinase that binds to the carboxyl-terminal domain (CTD) of RNA polymerase II and directly phosphorylates its serine 2 (Ser2) sites both in vitro and in vivo under conditions where other ..
  27. pmc Fast transcription rates of RNA polymerase II in human cells
    Paolo Maiuri
    Laboratory of Molecular Virology, International Centre for Genetic Engineering and Biotechnology ICGEB, Padriciano 99, Trieste 34149, Italy
    EMBO Rep 12:1280-5. 2011
    Averaged estimates of RNA polymerase II (RNAPII) elongation rates in mammalian cells have been shown to range between 1.3 and 4.3 kb min(-1)...
  28. ncbi Dynamics of replication-independent histone turnover in budding yeast
    Michael F Dion
    Faculty of Arts and Sciences, Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
    Science 315:1405-8. 2007
    ..In addition, rapid histone turnover is found at known chromatin boundary elements. These results suggest that rapid histone turnover serves to functionally separate chromatin domains and prevent spread of histone states...
  29. ncbi Dissecting the regulatory circuitry of a eukaryotic genome
    F C Holstege
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Cell 95:717-28. 1998
    ..Components of the RNA polymerase II holoenzyme, the general transcription factor TFIID, and the SAGA chromatin modification complex were found ..
  30. ncbi Recruitment of P-TEFb for stimulation of transcriptional elongation by the bromodomain protein Brd4
    Zhiyuan Yang
    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
    Mol Cell 19:535-45. 2005
    ..that constitutes core P-TEFb is generally presumed to be the transcriptionally active form for stimulating RNA polymerase II elongation...
  31. pmc Control of inducible gene expression by signal-dependent transcriptional elongation
    Diana C Hargreaves
    Howard Hughes Medical Institute and Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
    Cell 138:129-45. 2009
    ..Here we show that many PRGs, in contrast to SRGs, have preassembled RNA polymerase II (Pol II) and positive histone modifications at their promoters in the basal state...
  32. ncbi Chromatin organization marks exon-intron structure
    Schraga Schwartz
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
    Nat Struct Mol Biol 16:990-5. 2009
    ..Our results suggest an RNA polymerase II-mediated cross-talk between chromatin structure and exon-intron architecture, implying that exon selection ..
  33. pmc "Cotranscriptionality": the transcription elongation complex as a nexus for nuclear transactions
    Roberto Perales
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, UCHSC, MS8101, P O Box 6511, Aurora CO, 80045, USA
    Mol Cell 36:178-91. 2009
    ..From this perspective, TECs can be viewed as potent "community organizers" within the nucleus...
  34. pmc Gene-specific RNA polymerase II phosphorylation and the CTD code
    Hyunmin Kim
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
    Nat Struct Mol Biol 17:1279-86. 2010
    ..Nrd1 and Pcf11 frequently colocalize, suggesting functional overlap. Unexpectedly, Pcf11 is enriched at centromeres and Pol III-transcribed genes...
  35. pmc Genome-wide profiling of PPARgamma:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis
    Ronni Nielsen
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
    Genes Dev 22:2953-67. 2008
    ..deep sequencing to generate genome-wide maps of PPARgamma and retinoid X receptor (RXR)-binding sites, and RNA polymerase II (RNAPII) occupancy at very high resolution throughout adipocyte differentiation of 3T3-L1 cells...
  36. ncbi Dynamic phosphorylation patterns of RNA polymerase II CTD during transcription
    Martin Heidemann
    Department of Molecular Epigenetics, Center for Integrated Protein Science Munich, Munich, Germany
    Biochim Biophys Acta 1829:55-62. 2013
    The eukaryotic RNA polymerase II (RNAPII) catalyzes the transcription of all protein encoding genes and is also responsible for the generation of small regulatory RNAs...
  37. pmc RNA polymerase II collision interrupts convergent transcription
    David J Hobson
    Mechanisms of Transcription Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, South Mimms, London EN6 3LD, UK
    Mol Cell 48:365-74. 2012
    ..The existence of such transcription units raises the question of what happens when RNA polymerase II (RNAPII) molecules collide head-to-head...
  38. ncbi Updating the RNA polymerase CTD code: adding gene-specific layers
    Sylvain Egloff
    Universite de Toulouse, UPS, Laboratoire de Biologie Moleculaire Eucaryote, F 31000 Toulouse, France
    Trends Genet 28:333-41. 2012
    ..As modification of the CTD has a major impact on gene expression, a better understanding of the CTD code is integral to the understanding of how gene expression is regulated...
  39. pmc Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation
    Daniel A Gilchrist
    Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Cell 143:540-51. 2010
    ..either coordinated recruitment of transcription machinery to the gene promoter or regulated pausing of RNA polymerase II (Pol II) in early elongation...
  40. pmc Defining mechanisms that regulate RNA polymerase II transcription in vivo
    Nicholas J Fuda
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 461:186-92. 2009
    ..genome, the thousands of genes that encode messenger RNA are transcribed by a molecular machine called RNA polymerase II. Analysing the distribution and status of RNA polymerase II across a genome has provided crucial insights ..
  41. ncbi Cracking the RNA polymerase II CTD code
    Sylvain Egloff
    Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
    Trends Genet 24:280-8. 2008
    The carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II comprises multiple tandem conserved heptapeptide repeats, unique to this eukaryotic RNA polymerase...
  42. ncbi The bromodomain protein Brd4 is a positive regulatory component of P-TEFb and stimulates RNA polymerase II-dependent transcription
    Moon Kyoo Jang
    Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
    Mol Cell 19:523-34. 2005
    ..An increase in Brd4 expression led to increased P-TEFb-dependent phosphorylation of RNA polymerase II (RNAPII) CTD and stimulation of transcription from promoters in vivo...
  43. ncbi Transcribing RNA polymerase II is phosphorylated at CTD residue serine-7
    Rob D Chapman
    Institute of Clinical Molecular Biology and Tumour Genetics, GSF Research Center of Environment and Health, Munich Center for Integrated Protein Science CIPSM, Marchioninistrasse 25, 81377 Munich, Germany
    Science 318:1780-2. 2007
    b>RNA polymerase II is distinguished by its large carboxyl-terminal repeat domain (CTD), composed of repeats of the consensus heptapeptide Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7...
  44. pmc The nuclear RNA polymerase II surveillance system targets polymerase III transcripts
    Wiebke Wlotzka
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
    EMBO J 30:1790-803. 2011
    ..Surveillance targets were enriched for non-encoded A-rich tails. These were generally very short (1–5 nt), potentially explaining why adenylation destabilizes these RNAs while stabilizing mRNAs with long poly(A) tails...
  45. ncbi Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells
    Julie K Stock
    Nuclear Organisation, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
    Nat Cell Biol 9:1428-35. 2007
    Changes in phosphorylation of the carboxy-terminal domain (CTD) of RNA polymerase II (RNAP) are associated with transcription initiation, elongation and termination...
  46. pmc Precise maps of RNA polymerase reveal how promoters direct initiation and pausing
    Hojoong Kwak
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Science 339:950-3. 2013
    Transcription regulation occurs frequently through promoter-associated pausing of RNA polymerase II (Pol II)...
  47. pmc Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells
    Charles G Danko
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Mol Cell 50:212-22. 2013
    b>RNA polymerase II (Pol II) transcribes hundreds of kilobases of DNA, limiting the production of mRNAs and lncRNAs. We used global run-on sequencing (GRO-seq) to measure the rates of transcription by Pol II following gene activation...
  48. pmc Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome
    Ryan A Flynn
    David H Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
    Proc Natl Acad Sci U S A 108:10460-5. 2011
    Divergent transcription occurs at the majority of RNA polymerase II (RNAPII) promoters in mouse embryonic stem cells (mESCs), and this activity correlates with CpG islands...
  49. pmc Real-time observation of transcription initiation and elongation on an endogenous yeast gene
    Daniel R Larson
    Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Science 332:475-8. 2011
    ..By measuring the abundance and intranuclear mobility of an upstream transcription factor, we observe that the gene firing rate is directly determined by trans-activating factor search times...
  50. ncbi NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation
    Y Yamaguchi
    Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
    Cell 97:41-51. 1999
    DRB is a classic inhibitor of transcription elongation by RNA polymerase II (pol II). Since DRB generally affects class II genes, factors involved in this process must play fundamental roles in pol II elongation...
  51. pmc Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles
    Gwendal Le Martelot
    Department of Molecular Biology, University of Geneva, Geneva, Switzerland
    PLoS Biol 10:e1001442. 2012
    ..basis of diurnal rhythms in mouse liver genome-wide, we generated temporal DNA occupancy profiles by RNA polymerase II (Pol II) as well as profiles of the histone modifications H3K4me3 and H3K36me3...
  52. ncbi The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II
    Minkyu Kim
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
    Nature 432:517-22. 2004
    The carboxy-terminal domain (CTD) of the RNA polymerase II (RNApII) largest subunit consists of multiple heptapeptide repeats with the consensus sequence YSPTSPS...
  53. pmc The role of Mediator in small and long noncoding RNA production in Arabidopsis thaliana
    Yun Ju Kim
    Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
    EMBO J 30:814-22. 2011
    Mediator is a conserved multi-subunit complex known to promote the transcription of protein-coding genes by RNA polymerase II (Pol II) in eukaryotes...
  54. ncbi Polycomb protein Ezh1 promotes RNA polymerase II elongation
    Kambiz Mousavi
    Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20852, USA
    Mol Cell 45:255-62. 2012
    ..Here, we provide evidence for genome-wide association of Ezh1 complex with active epigenetic mark (H3K4me3), RNA polymerase II (Pol II), and mRNA production...
  55. ncbi 7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T complexes
    V T Nguyen
    Genetique Moleculaire, UMR 8541 CNRS, Ecole Normale Superieure, 46 rue d Ulm, 75230 Paris Cedex 05, France
    Nature 414:322-5. 2001
    ..The transcription-dependent interaction of P-TEFb with 7SK may therefore contribute to an important feedback loop modulating the activity of RNA Pol II...
  56. pmc Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation
    James A Goodrich
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Colorado 80309, USA
    Nat Rev Genet 11:549-58. 2010
    ..Furthermore, new roles for components of these complexes have been identified beyond development; for example, in mediating interactions with chromatin and in maintaining active gene expression across cell divisions...
  57. pmc A chromatin landmark and transcription initiation at most promoters in human cells
    Matthew G Guenther
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Cell 130:77-88. 2007
    ..We found that nucleosomes with H3K4me3 and H3K9,14Ac modifications, together with RNA polymerase II, occupy the promoters of most protein-coding genes in human embryonic stem cells...
  58. pmc Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II
    Courtney Hodges
    Jason L Choy Laboratory of Single Molecule Biophysics and Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
    Science 325:626-8. 2009
    b>RNA polymerase II (Pol II) must overcome the barriers imposed by nucleosomes during transcription elongation. We have developed an optical tweezers assay to follow individual Pol II complexes as they transcribe nucleosomal DNA...
  59. pmc Paused RNA polymerase II as a developmental checkpoint
    Michael Levine
    Division of Genetics, Genomics, and Development, Department of Molecular and Cell Biology, Center for Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
    Cell 145:502-11. 2011
    The textbook view of gene activation is that the rate-limiting step is the interaction of RNA polymerase II (Pol II) with the gene's promoter...
  60. ncbi Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution
    Brian T Wilhelm
    Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
    Nature 453:1239-43. 2008
    ..Splicing efficiency was largely coordinated with transcript levels, and increased transcription led to increased splicing in test genes. Hundreds of introns showed such regulated splicing during cellular proliferation or differentiation...
  61. ncbi Global analysis of nascent RNA reveals transcriptional pausing in terminal exons
    Fernando Carrillo Oesterreich
    Max Planck Institute of Molecular Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    Mol Cell 40:571-81. 2010
    ..The discovery of terminal exon pausing demonstrates functional coupling of transcription and splicing near gene ends...
  62. pmc Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila
    Sergei Nechaev
    Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Science 327:335-8. 2010
    Emerging evidence indicates that gene expression in higher organisms is regulated by RNA polymerase II stalling during early transcription elongation...
  63. pmc TFIIH-associated Cdk7 kinase functions in phosphorylation of C-terminal domain Ser7 residues, promoter-proximal pausing, and termination by RNA polymerase II
    Kira Glover-Cutter
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, UCHSC, MS 8101, P O Box 6511, Aurora, CO 80045, USA
    Mol Cell Biol 29:5455-64. 2009
    The function of human TFIIH-associated Cdk7 in RNA polymerase II (Pol II) transcription and C-terminal domain (CTD) phosphorylation was investigated in analogue-sensitive Cdk7(as/as) mutant cells where the kinase can be inhibited without ..
  64. pmc Threonine-4 of mammalian RNA polymerase II CTD is targeted by Polo-like kinase 3 and required for transcriptional elongation
    Corinna Hintermair
    Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science, Germany
    EMBO J 31:2784-97. 2012
    Eukaryotic RNA polymerase II (Pol II) has evolved an array of heptad repeats with the consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 at the carboxy-terminal domain (CTD) of the large subunit (Rpb1)...
  65. pmc Regulation of gene expression via the core promoter and the basal transcriptional machinery
    Tamar Juven-Gershon
    Section of Molecular Biology, 0347, University of California, San Diego, La Jolla, CA 92093 0347, USA
    Dev Biol 339:225-9. 2010
    The RNA polymerase II core promoter is a structurally and functionally diverse transcriptional regulatory element. There are two main strategies for transcription initiation - focused and dispersed initiation...
  66. pmc Disengaging polymerase: terminating RNA polymerase II transcription in budding yeast
    Hannah E Mischo
    Cancer Research UK London Research Institute, Blanche Lane South Mimms, Herts, UK
    Biochim Biophys Acta 1829:174-85. 2013
    Termination of transcription by RNA polymerase II requires two distinct processes: The formation of a defined 3' end of the transcribed RNA, as well as the disengagement of RNA polymerase from its DNA template...
  67. pmc Rates of in situ transcription and splicing in large human genes
    Jarnail Singh
    Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
    Nat Struct Mol Biol 16:1128-33. 2009
    ..We found that the rate of RNA polymerase II transcription over long genomic distances is about 3...
  68. pmc Evasion of the innate immune response: the Old World alphavirus nsP2 protein induces rapid degradation of Rpb1, a catalytic subunit of RNA polymerase II
    Ivan Akhrymuk
    Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
    J Virol 86:7180-91. 2012
    ..This indicates that the nsP2-induced degradation of Rpb1 is a critical mechanism utilized by the Old World alphaviruses to subvert the cellular antiviral response...
  69. pmc Role of Mediator in regulating Pol II elongation and nucleosome displacement in Saccharomyces cerevisiae
    Selena B Kremer
    Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana 71130
    Genetics 191:95-106. 2012
    Mediator is a modular multisubunit complex that functions as a critical coregulator of RNA polymerase II (Pol II) transcription...
  70. pmc The protein interaction network of the human transcription machinery reveals a role for the conserved GTPase RPAP4/GPN1 and microtubule assembly in nuclear import and biogenesis of RNA polymerase II
    Diane Forget
    Institut de Recherches Cliniques de Montreal, Montreal, Québec H2W1R7, Canada
    Mol Cell Proteomics 9:2827-39. 2010
    b>RNA polymerase II (RNAPII), the 12-subunit enzyme that synthesizes all mRNAs and several non-coding RNAs in eukaryotes, plays a central role in cell function...
  71. ncbi Spliceosome assembly is coupled to RNA polymerase II dynamics at the 3' end of human genes
    Sandra Bento Martins
    Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
    Nat Struct Mol Biol 18:1115-23. 2011
    ....
  72. pmc The control of HIV transcription: keeping RNA polymerase II on track
    Melanie Ott
    Gladstone Institutes of Virology and Immunology, University of California, San Francisco, 94158, USA
    Cell Host Microbe 10:426-35. 2011
    ....
  73. pmc SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase
    Xiong Ji
    State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
    Cell 153:855-68. 2013
    ..These findings reveal an unanticipated SR protein function, a role for promoter-proximal nascent RNA in gene activation, and an analogous mechanism to HIV Tat/TAR for activating cellular genes...
  74. pmc Genome-wide control of RNA polymerase II activity by cohesin
    Cheri A Schaaf
    Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
    PLoS Genet 9:e1003382. 2013
    ..To clarify cohesin's roles in transcription, we measured how cohesin controls RNA polymerase II (Pol II) activity by genome-wide chromatin immunoprecipitation and precision global run-on sequencing...
  75. ncbi Unravelling the means to an end: RNA polymerase II transcription termination
    Jason N Kuehner
    Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
    Nat Rev Mol Cell Biol 12:283-94. 2011
    The pervasiveness of RNA synthesis in eukaryotes is largely the result of RNA polymerase II (Pol II)-mediated transcription, and termination of its activity is necessary to partition the genome and maintain the proper expression of ..
  76. pmc Rapid, transcription-independent loss of nucleosomes over a large chromatin domain at Hsp70 loci
    Steven J Petesch
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Cell 134:74-84. 2008
    To efficiently transcribe genes, RNA Polymerase II (Pol II) must overcome barriers imposed by nucleosomes and higher-order chromatin structure...
  77. pmc Activation-induced cytidine deaminase targets DNA at sites of RNA polymerase II stalling by interaction with Spt5
    Rushad Pavri
    Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10065, USA
    Cell 143:122-33. 2010
    ..We found that Spt5, a factor associated with stalled RNA polymerase II (Pol II) and single stranded DNA (ssDNA), is required for CSR...
  78. ncbi RNA-binding protein Nrd1 directs poly(A)-independent 3'-end formation of RNA polymerase II transcripts
    E J Steinmetz
    Department of Biomolecular Chemistry, University of Wisconsin Medical School, Madison, Wisconsin 53706 1532, USA
    Nature 413:327-31. 2001
    ..The same proteins are required for maintaining normal levels of Nrd1 mRNA, indicating that these proteins may control elongation of a subset of mRNA transcripts...
  79. pmc Small regulatory RNAs inhibit RNA polymerase II during the elongation phase of transcription
    Shouhong Guang
    Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA
    Nature 465:1097-101. 2010
    ..In addition, these results establish a novel mode of RNAP II regulation: siRNA-directed recruitment of NRDE factors that inhibit RNAP II during the elongation phase of transcription...
  80. ncbi Loss of human ribosomal gene CpG methylation enhances cryptic RNA polymerase II transcription and disrupts ribosomal RNA processing
    Thérèse Gagnon-Kugler
    Cancer Research Centre, CHUQ HDQ Research Centre, Pavillon St Patrick, 9 rue McMahon, Quebec, QC G1R 3S3, Canada
    Mol Cell 35:414-25. 2009
    ..Reactivation of the rRNA genes is associated with their cryptic transcription by RNA polymerase II. Ectopic expression of cryptic rRNA gene transcripts recapitulates the defects associated with loss of CpG ..
  81. pmc The Paf1 complex: platform or player in RNA polymerase II transcription?
    Judith A Jaehning
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
    Biochim Biophys Acta 1799:379-88. 2010
    The Paf1 complex (Paf1C), composed of the proteins Paf1, Ctr9, Cdc73, Rtf1, and Leo1, accompanies RNA polymerase II (pol II) from the promoter to the 3' end formation site of mRNA and snoRNA encoding genes; it is also found associated ..
  82. ncbi Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II
    David Baillat
    The Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsylvania 19104, USA
    Cell 123:265-76. 2005
    The C-terminal domain (CTD) of RNA polymerase II (RNAPII) is an essential component of transcriptional regulation and RNA processing of protein-coding genes...
  83. ncbi Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability
    Xialu Li
    Department of Biological Sciences, Columbia University, New York, New York 10027, USA
    Cell 122:365-78. 2005
    ..Our results support a model by which recruitment of ASF/SF2 to nascent transcripts by RNA polymerase II prevents formation of mutagenic R loop structures.
  84. ncbi Dynamic regulation of pol II transcription by the mammalian Mediator complex
    Sohail Malik
    Laboratory of Biochemistry and Molecular Biology, Rockefeller University, 1230 York Ave, New York, NY 10021, USA
    Trends Biochem Sci 30:256-63. 2005
    Mammalian Mediator is a key coactivator that enables transcriptional activators to regulate transcription by RNA polymerase II (pol II). Like the yeast complex to which it is phylogenetically related, it contains up to 30 subunits...
  85. ncbi RNA polymerase II subunits link transcription and mRNA decay to translation
    Liat Harel-Sharvit
    Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion Israel Institute of Technology, Haifa, 31096, Israel
    Cell 143:552-63. 2010
    ..Efficient translation in the cytoplasm depends on association of Rpb4/7 with RNA polymerase II (Pol II) in the nucleus, leading to a model in which Pol II remotely controls translation...
  86. ncbi HSP90 and its R2TP/Prefoldin-like cochaperone are involved in the cytoplasmic assembly of RNA polymerase II
    Séverine Boulon
    Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK
    Mol Cell 39:912-24. 2010
    ..However, the mechanism by which RNA polymerase II is assembled from its 12 subunits remains unclear...
  87. ncbi Crosstalk between mRNA 3' end processing and transcription initiation
    Christophe K Mapendano
    Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology, Aarhus University, C F Møllers Allé 3, Building 1130, DK 8000 Aarhus, Denmark
    Mol Cell 40:410-22. 2010
    ..Readthrough RNA polymerase II (RNAPII) engaged on polyadenylation site-mutated transcription units sequester the transcription initiation/..
  88. ncbi A slow RNA polymerase II affects alternative splicing in vivo
    Manuel De la Mata
    Laboratorio de Fisiologia y Biologia Molecular, Departamento de Fisiologia, Biologia Molecular y Celular, IFIBYNE CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellon 2, Buenos Aires, Argentina
    Mol Cell 12:525-32. 2003
    ..These results provide a direct proof for the elongation control of alternative splicing in vivo...
  89. ncbi In vivo dynamics of RNA polymerase II transcription
    Xavier Darzacq
    Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Nat Struct Mol Biol 14:796-806. 2007
    ..Photobleaching of fluorescent RNA polymerase II revealed several kinetically distinct populations of the enzyme interacting with a specific gene...
  90. ncbi Mediator and the mechanism of transcriptional activation
    Roger D Kornberg
    Department of Structural Biology, Stanford School of Medicine, Stanford, CA 94305, USA
    Trends Biochem Sci 30:235-9. 2005
    Mediator was discovered because of its activity in a yeast RNA polymerase II (pol II) transcription system - it is needed for the system to respond to a transcriptional activator...
  91. pmc Close association of RNA polymerase II and many transcription factors with Pol III genes
    Debasish Raha
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 107:3639-44. 2010
    ..These results indicate that, contrary to previous expectations, polymerases can often work with one another to globally coordinate gene expression...
  92. ncbi FACT facilitates transcription-dependent nucleosome alteration
    Rimma Belotserkovskaya
    Howard Hughes Medical Institute, Department of Biochemistry, Division of Nucleic Acids Enzymology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854, USA
    Science 301:1090-3. 2003
    ..facilitates chromatin transcription) complex is required for transcript elongation through nucleosomes by RNA polymerase II (Pol II) in vitro...
  93. pmc RNF20 inhibits TFIIS-facilitated transcriptional elongation to suppress pro-oncogenic gene expression
    Efrat Shema
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Mol Cell 42:477-88. 2011
    ..those genes by interfering with chromatin recruitment of TFIIS, a factor capable of relieving stalled RNA polymerase II. RNF20 inhibits the interaction between TFIIS and the PAF1 complex and hinders transcriptional elongation...
  94. ncbi Transcription by RNA polymerase III: more complex than we thought
    Robert J White
    Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
    Nat Rev Genet 12:459-63. 2011
    ..Here I describe these novel insights and consider their implications and the questions that remain...
  95. pmc RNA polymerase II kinetics in polo polyadenylation signal selection
    Pedro A B Pinto
    Cell Activation and Gene Expression Group, IBMC Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
    EMBO J 30:2431-44. 2011
    ..site selection functions to provide the correct levels of protein expression necessary for histoblast proliferation, and that the kinetics of RNA polymerase II have an important role in the mechanism of alternative polyadenylation.
  96. ncbi Active genes dynamically colocalize to shared sites of ongoing transcription
    Cameron S Osborne
    Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, CB2 4AT, UK
    Nat Genet 36:1065-71. 2004
    ..Indeed, nascent RNA production and RNA polymerase II seem to be localized into discrete foci or 'transcription factories'...
  97. pmc NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly
    Daniel A Gilchrist
    Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
    Genes Dev 22:1921-33. 2008
    The Negative Elongation Factor (NELF) is a transcription regulatory complex that induces stalling of RNA polymerase II (Pol II) during early transcription elongation and represses expression of several genes studied to date, including ..
  98. pmc Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs
    Emily Brookes
    Genome Function Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
    Cell Stem Cell 10:157-70. 2012
    ..Polycomb silencing in embryonic stem cells (ESCs) can be accompanied by active chromatin and primed RNA polymerase II (RNAPII), but the relationship between PRCs and RNAPII remains unclear genome-wide...
  99. pmc Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data
    David L Corcoran
    Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
    PLoS ONE 4:e5279. 2009
    ..coding genes) are co-transcribed with their host genes and most intergenic miRNAs transcribed from their own RNA polymerase II (Pol II) promoter...
  100. pmc Jarid2 is a PRC2 component in embryonic stem cells required for multi-lineage differentiation and recruitment of PRC1 and RNA Polymerase II to developmental regulators
    David Landeira
    Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN UK
    Nat Cell Biol 12:618-24. 2010
    ..subsequent stages in development are enriched at their promoters for PRC1, PRC2 and Ser 5-phosphorylated RNA Polymerase II (RNAP), and contain domains of 'bivalent' chromatin (enriched for H3K4me3; histone H3 di- or trimethylated ..
  101. pmc How eukaryotic genes are transcribed
    Bryan J Venters
    Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Crit Rev Biochem Mol Biol 44:117-41. 2009
    ..factors; (3) chromatin remodeling coupled to promoter assembly of the general transcription factors and RNA polymerase II; and (4) phosphorylation states of RNA polymerase II coupled to chromatin modification states during ..

Research Grants70

  1. Lung Lysyl Oxidase Regulation by Metal Ion Homeostasis
    Wande Li; Fiscal Year: 2013
    ..mechanisms for Cd silencing of the LO gene at the transcriptional level by examining Cd modulation of RNA polymerase II- directed LO pre-mRNA synthesis and processing, and of the LO promoter activation regulated by the core ..
  2. Med1 in Liver Metabolism, Regeneration and Cancer
    Janardan K Reddy; Fiscal Year: 2013
    ..The Mediator complex is necessary for the expression of RNA polymerase II (PoI II)-transcribed genes...
  3. Vitamin D Hormone Signaling in Bone Mineral Homeostasis
    Mark R Haussler; Fiscal Year: 2010
    ..complexes that either repress or induce DNA transcription by chromatin remodeling and linkage to RNA polymerase II. Cultured 1,25(OH)2D3target cells will be used as model systems for Specific Aims designed to elucidate the ..
  4. Tat and CDK9 on gene expression alterations coupled to HIV-1 Associated Dementia
    Xavier Grana; Fiscal Year: 2010
    ..by Tat to TAR, an RNA element in the nascent HIV-1 transcript, where CDK9 is positioned to phosphorylate RNA polymerase II (RNAPII) and negative elongation factors, strongly activating HIV-1 transcription...
  5. MOLECULAR MECHANISMS OF COMPLEX MIXTURE TOXICITY
    Alvaro Puga; Fiscal Year: 2013
    ..These changes inhibit recruitment of RNA polymerase II to the Cyp1a1 promoter, block BaP-inducible gene expression and stimulate the formation of BPDE-DNA adducts...
  6. Role of Retroelements in Environmental Atherogenesis
    Kenneth S Ramos; Fiscal Year: 2010
    ..is hypothesized that L1 activation is mediated via epigenetic mechanisms that increase promoter activity and RNA polymerase II efficiency...
  7. MECHANISMS OF EUKARYOTIC TRANSCRIPTIONAL REGULATION
    Michael R Green; Fiscal Year: 2013
    ..Transcription initiation by RNA polymerase II involves the assembly of general transcription factors on the core promoter to form a preinitiation complex (..
  8. CHEMISTRY AND BIOLOGY OF PLATINUM ANTICANCER DRUGS
    Stephen J Lippard; Fiscal Year: 2013
    ..Because cisplatin blocks RNA polymerase II, which triggers apoptosis and initiates nucleotide excision repair, transcription inhibition by Pt-DNA ..
  9. Molecular Biology of Human Erythrocyte Alpha Spectrin
    Patrick G Gallagher; Fiscal Year: 2013
    ..Integration of mRNA transcript composition, genomic organization, RNA polymerase II binding, transcription factor and regulatory protein binding, and histone architecture will provide detailed ..
  10. ANALYSIS OF TRYPANOSOME MRNA SYNTHESIS BY GENE TRANSFER
    Vivian Bellofatto; Fiscal Year: 2010
    ..For example, Trypanosoma brucei and other members of the trypanosomatid family contain an unusual RNA polymerase II enzyme and what appears to be an abridged set of transcription factors...
  11. Roles of RNA Polymerases IV and V in siRNA-mediated gene silencing
    CRAIG STUART PIKAARD; Fiscal Year: 2013
    ..Affinity purification and mass spec analyses revealed that Pol IV and Pol V are specialized forms of RNA Polymerase II, with half of their twelve subunits encoded by the same genes...
  12. Novel CTD inhibitors with synthetic lethality to oncogenic Ras for cancer therapy
    Bingliang Fang; Fiscal Year: 2013
    ..or -231 led to suppression of the phosphorylation of the C-terminal domain (CTD) of the largest subunit of RNA polymerase II, whish is consistent with previous reports that the continuous activity of RNA polymerase II is required to ..
  13. Mechanisms of TGFB Signal Transduction
    Akiko Hata; Fiscal Year: 2013
    ..recruitment of Brg1 to VSMC-specific gene promoters, thereby resulting in inhibition of recruitment of RNA polymerase II (Pol II) and transcription...
  14. Genomic Enhancers at 8q24 and Prostate Cancer
    Gerhard A Coetzee; Fiscal Year: 2013
    ..all the risk regions was profiled for RNA expression, histone modifications and locations occupied by RNA polymerase II and the androgen receptor...
  15. Regulation of insulator function and globin gene expression by USF and associated
    Suming Huang; Fiscal Year: 2013
    ..in the -globin gene promoter and previous work has shown that USF is required for efficient recruitment of RNA polymerase II (Pol II) to LCR element HS2 and to the -globin gene promoter...
  16. Mechanisms in transcriptional regulation during cardiac hypertrophy
    Maha Abdellatif; Fiscal Year: 2013
    ..Additionally, we do not know the mode of transcriptional regulation - de novo RNA polymerase II (pol II) recruitment vs. the release of paused pol II - or the regulators involved...
  17. Regulation of KSHV Latency
    Paul M Lieberman; Fiscal Year: 2013
    ..We have also found that these CTCF sites in the latency control region are important for the programming of RNA polymerase II elongation and mRNA processing...
  18. ROLE OF COREGULATORS IN STEROID HORMONE-REGULATED TRANSCRIPTION
    Michael R Stallcup; Fiscal Year: 2013
    ..promoter;the SWI/SNF complex remodels chromatin in an ATP-dependent manner;and the Mediator complex recruits RNA polymerase II. We have recently discovered two SRC-associated coregulators which are required for recruitment of the SWI/..
  19. RNA polymerase II Elongation Complex: Structure and Function
    Daniel Reines; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Transcription elongation and termination by RNA polymerase II are complex processes that determine the fate of the primary transcript thereby regulate gene expression...
  20. Post-translational regulation of MLL in leukemogenesis
    ANDREW GEORGE MUNTEAN; Fiscal Year: 2013
    ..PAFc is a transcription activation complex that associates with RNA polymerase II and promotes histone H2B ubiquitination (a prerequisite for H3 lysine 4 and 79 methylation)...
  21. Post-translational regulation of MLL in leukemogenesis
    ANDREW GEORGE MUNTEAN; Fiscal Year: 2012
    ..PAFc is a transcription activation complex that associates with RNA polymerase II and promotes histone H2B ubiquitination (a prerequisite for H3 lysine 4 and 79 methylation)...
  22. Molecular Analysis of Pericentric Sister Chromatid Cohesion
    PAUL CONNOR MEGEE; Fiscal Year: 2013
    ..The contribution of RNA polymerase II-dependent transcription in the establishment of cohesin loader distributions will be examined following ..
  23. ANALYSIS OF CHROMATIN REMODELING IN MAMMARY GLAND DEVELOPMENT USING TILING ARRAYS
    Monique Rijnkels; Fiscal Year: 2009
    ..These studies will provide a foundation for understanding the mechanisms that determine differentiation and organogenesis of specific tissues. ..
  24. Live cell imaging of IgH and c-Myc gene loci and the role of nuclear organization
    Mark T Groudine; Fiscal Year: 2010
    ..the IgH and c-Myc loci often colocalize in shared transcription factories (sites of concentrated active RNA polymerase II), and IgH and c-Myc are frequent translocation partners in plasmacytomas and Burkitt lymphoma...
  25. Structural Studies of RNA Maturation and Processing
    Christopher D Lima; Fiscal Year: 2013
    ..Capping activities are recruited to the transcription apparatus through interactions with RNA polymerase II (RNAP II) after it is phosphorylated on serine residues within its C-terminal tandem heptapeptide repeats ..
  26. RNA polymerase II transcription in trypanosomes
    ARTHUR GUNZL; Fiscal Year: 2013
    ..data show that these proteins form a transcription pre-initiation complex at the SLRNA promoter and recruit RNA polymerase II for accurate transcription initiation...
  27. The role of the nucleoporin Nup98 in gene regulation
    Martin W Hetzer; Fiscal Year: 2013
    ..analyzed by chromatin immune- precipitation to investigate which binding partners, histone modifications and RNA polymerase II phosphorylation events depend on Nup98...
  28. RNA CONFORMATION AND CATALYSIS
    David P Bartel; Fiscal Year: 2013
    ..the hypothesis that silencing is post- transcriptional, RNAi-mutant strains will be monitored for changes in RNA Polymerase II binding, mRNA turnover, and the correspondence between sequenced siRNAs and mRNA degradation fragments...
  29. Epigenome Mapping in Cortical Interneurons
    Schahram Akbarian; Fiscal Year: 2013
    ..sequences including those further removed from proximal promoters (H3K4me1), and a mark associated with RNA polymerase II activity and transcriptional elongation across coding and non-coding regions (H3K36me3)...
  30. Dynamic Mechanisms of Vitamin D-Induced Gene Expression
    J Wesley Pike; Fiscal Year: 2012
    ..role of 1,25(OH)2D3 in the regulation of transcription factor co-recruitment, epigenetic modification and RNA polymerase II modulation will be assessed...
  31. Nuclear Function of Abl in DNA Damage Response
    Jean Y J Wang; Fiscal Year: 2012
    ..Through tyrosine phosphorylation of the C-terminal repeated domain (CTD) of RNA polymerase II, we have found that Abl regulates RNA splicing in genotoxin-treated cells...
  32. Persistent microRNA changes in serum of cancer-free breast cancer patients
    Harikrishna Nakshatri; Fiscal Year: 2012
    ..Recruitment of modified histones and RNA polymerase II/III to regulatory regions of U6, 5S, and select microRNA genes in liver and lungs will be measured in ..
  33. RNA Polymerase Transcription Past DNA Adducts
    David A Scicchitano; Fiscal Year: 2013
    ..There are three specific aims to address these goals. We will: (1) investigate RNA polymerase II transcription past select DNA adducts;(2) determine the base sequence of the mRNA produced via bypass of ..
  34. Functions of nuclear non-canonical poly(A) polymerases in Trypanosomes
    Ruslan Aphasizhev; Fiscal Year: 2010
    ..to environmental conditions in mammalian and insect hosts do not include transcription initiation control of RNA polymerase II (Pol II) activity on protein-encoding genes...
  35. Mediator and epigenetic control of neuronal gene expression and differentiation
    Thomas G Boyer; Fiscal Year: 2013
    ..Mediator is a multiprotein interface between gene-specific transcription factors and the eukaryotic RNA polymerase II general transcription machinery...
  36. The Role of a New Cleavage and Polyadenylation Specificity Factor (CPSF73-II)
    Qingshun Q Li; Fiscal Year: 2010
    ..Polyadenylation Specificity Factor (CPSF) complex is required for the cleavage and polyadenylation of most RNA polymerase II-synthesized pre-mRNA transcripts...
  37. The CAK Network in Metazoan Cell Cycle Regulation
    Robert P Fisher; Fiscal Year: 2010
    ..provided by applicant): Cyclin-dependent kinases (CDKs) control cell division and transcription by RNA polymerase II (Pol II), and are themselves stringently regulated...
  38. The Pox Virion Molecular Interactome
    Paul D Gershon; Fiscal Year: 2013
    ..architectures of elaborate cellular assemblies such as the nuclear pore complex, 20S proteasome and RNA polymerase II. Aim 1 of this proposal seeks to identify directly juxtaposed proteins within the virion core via covalent ..
  39. Acute Renal Failure: Mechanisms and Adaptive Responses
    Richard A Zager; Fiscal Year: 2013
    ..occur at test gene promoter regions, and whether hyper-recruitment of relevant transcription factors and of RNA polymerase II (Pol II) to them result;3...
  40. Genetic Regulation of Metabolic and Fibrotic Programs in Hypertrophic Heart
    M A Q Siddiqui; Fiscal Year: 2013
    ..the activity of P-TEFb (P-Transcriptional Elongation Factor b), a transcriptional regulator that activates RNA polymerase II to transcribe genes...
  41. Facilitating large scale biomass generation: acquisition of an automated 100 L fe
    Roger D Kornberg; Fiscal Year: 2010
    ..Kornberg and colleagues investigate the structure and regulation of the RNA polymerase II transcription machinery from the yeast Saccharomyces cerevisiae...
  42. Repair of oxidative damage in mammalian genomes
    Tapas K Hazra; Fiscal Year: 2010
    ..The stable interaction of NEIL2 with RNA Polymerase II (Pol II) and heterogeneous nuclear ribonucleo protein (hnRNP-U), and the significant increase in endogenous ..
  43. Characterization of CHD family chromodomains Implicated in Epigenetic Signaling
    Kimberly R Wiggins; Fiscal Year: 2010
    ..Recent studies have implicated CHD proteins in diverse roles such as facilitating transcription by RNA Polymerase II, assisting transcription co-repressor complexes, and regulating differentiation...
  44. Regulation of a Novel Trypanosome RNA Binding Protein by Arginine Methylation
    Kaylen Lott; Fiscal Year: 2013
    ..One unique aspect of kinetoplastid biology is the apparent absence of transcriptional control of RNA polymerase II. In the absence of transcriptional control, gene regulation relies largely on posttranscriptional processes ..
  45. The role of the interaction between the C-terminal domain of RNA pol II and a his
    Uchechi E Ukaegbu; Fiscal Year: 2012
    ..Studies have also shown that active transcription by RNA polymerase II is required for the maintenance of epigenetic memory of P...
  46. Role of chromatin structure in regulating gene silencing
    Mary Bryk; Fiscal Year: 2009
    ..factors, such as histones, histone-modifying enzymes, and silencing proteins, in regulating the silencing of RNA polymerase II-transcribed genes located in the ribosomal DNA locus (rDNA) of the budding yeast Saccharomyces cerevisiae...
  47. Specification of alternate siRNA biogenesis pathways in Arabidopsis
    TODD LUCAS BLEVINS; Fiscal Year: 2011
    ..e., precursor RNA synthesis. In fact, known RDR6 substrates derive from RNA polymerase II (Pol II) transcription, whereas repeat- associated siRNA biogenesis requires a plant-specific RNA polymerase ..
  48. Coupling of Transcription with Pre-mRNA Metabolism
    DAVID LEONARD BENTLEY; Fiscal Year: 2013
    ..mRNA synthesis requires transcription by RNA polymerase II (pol II) to produce a precursor that is matured by capping, splicing and cleavage/polyadenylation and ..
  49. GENESIS AND CONSEQUENCES OF ABERRANT DNA METHYLATION
    Paula M Vertino; Fiscal Year: 2013
    ..histone H4 modifications (H4K16 Ac;H4K20me3) and the complexes that catalyze these marks, in regulation of RNA polymerase II pausing dynamics at CpG island promoters...
  50. AIDS Opportunistic Infections: Virulence of C. glabrata
    Brendan Cormack; Fiscal Year: 2013
    ..hypothesize that they affect infection-specific transcription by altering the phosphorylation status of the RNA polymerase II C-terminal domain (CTD)...
  51. Transcriptional Architecture and Chromatin Landscape of Circadian Clocks in Aging
    Joseph S Takahashi; Fiscal Year: 2013
    ..wide-ranging and complex effects on genome-wide circadian transcriptional architecture, gene expression and RNA polymerase II recruitment and initiation as well as chromatin modifications involving histone methylation and acetylation...
  52. REGULATION OF DNA DAMAGE INDUCED GENES BY YEAST TAFIIS
    Joseph C Reese; Fiscal Year: 2013
    ..the last funding period we established it as a bona-fide elongation factor that directly activates arrested RNA polymerase II (RNAPII)...
  53. Mechanisms for Transcription-Coupled Repair in Human Cells
    Priscilla K Cooper; Fiscal Year: 2010
    ..and the CS phenotype;and (4) to define early steps in TCR and investigate a proposed remodeling of stalled RNA polymerase II by TCR proteins to enable repair...
  54. Genetic Analysis of the Nucleosome and RNA Polymerase II: A Systems Approach
    Nevan J Krogan; Fiscal Year: 2012
    ..essential, multisubunit, multifunctional complexes at the heart of gene expression and chromatin structure: RNA polymerase II (RNAPII) and the nucleosome...
  55. Identification of DNA Elements Governing Chromatin Function in C elegans
    Jason D Lieb; Fiscal Year: 2011
    ..126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination ..
  56. Role of Set2 and H3 methylation in chromatin function
    Brian D Strahl; Fiscal Year: 2013
    ..We, and others, have shown that Set2 associates with RNA polymerase II during transcription elongation, and that its methylation at H3K36 directs the recruitment of a histone ..
  57. DEVELOPMENTAL BIOLOGY OF HUMAN ERYTHROPOIESIS
    Stuart H Orkin; Fiscal Year: 2013
    ..In Project 1 (H. Lodish, Project Leader) new transcription factors, RNA polymerase II elongation factors, and chromatin-modifying enzymes important for terminal red cell development will be ..
  58. mRNA Capping Enzymes
    STEWART H SHUMAN; Fiscal Year: 2013
    ..to nascent mRNAs by binding to the phosphorylated carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II), which is composed of a tandem array of heptapeptide repeats (consensus: Y1S2P3T4S5P6S7)...
  59. Functional Coupling of Steps in Genes Expression
    ROBIN E REED; Fiscal Year: 2013
    ..The protein FUS, which associates with U1 snRNP, SR proteins, and RNA polymerase II, was identified as a strong candidate for coupling transcription to splicing...
  60. Mechanisms of RSC recruitment and its role in transcription
    CHHABI KUMAR GOVIND; Fiscal Year: 2013
    ..Interestingly, RSC also interacts with RNA Polymerase II (Pol II), which suggests that the polymerase may target RSC to transcribed genes...
  61. Molecular Basis of mu-Opioid Receptor Gene Regulation
    Jane Ko; Fiscal Year: 2009
    ..Aim 4, we will examine whether PCBP directly interacts with the transcriptional machinery (including RNA polymerase II and auxiliary transcription factors, such as TFIID) in regulating MOR gene expression...
  62. Mechanism and targets of Sen1-dependent RNA polymerase II termination
    David A Brow; Fiscal Year: 2013
    ..Yet little is known about how non- coding RNAs are made and function. We discovered an RNA polymerase II (Pol II) termination pathway that influences the synthesis and function many non-coding RNAs...
  63. MECHANISMS OF YEAST TRANSCRIPTIONAL INITIATION
    Kevin Struhl; Fiscal Year: 2002
    ..but fail to respond to acidic activator proteins; are specifically defective either for transcription by RNA polymerase II or RNA polymerase III; show differential effects at TATA-containing vs TATA-less promoters; fail to support ..
  64. ROLE OF CELLULAR PROTEINS IN HPV TRANSCRIPTION
    Cheng Ming Chiang; Fiscal Year: 2004
    ..either with individually purified general transcription factors and cofactors or with a preassembled RNA polymerase II holoenzyme and TFIID (or TBP)...
  65. MOLECULAR GENETICS OF C. ELEGANS RNA POLYMERASE II
    DONALD RIDDLE; Fiscal Year: 1990
    ..The enzyme RNA polymerase II, which is responsible for the synthesis of messenger RNA, plays such a central role in cellular activity ..
  66. Cholinergic and cognitive decline in response to TrkA knockdown using RNAi
    Vinay Parikh; Fiscal Year: 2009
    ..will involve the construction of plasmids designed to express TrkA microRNA (miRNA) under the control of a RNA polymerase II promoter, and screening of TrkA miRNA sequences for suppression of TrkA receptor expression in rat ..
  67. Modification of RNA polymerase II by HSV-1 proteins
    Stephen Rice; Fiscal Year: 2006
    Infection of cells by herpes simplex virus type 1 (HSV-1) results in dramatic changes in RNA polymerase II (RNAP II) function, such that viral genes are highly transcribed in a regulated cascade, while host genes are transcriptionally ..
  68. MOLECULAR ANALYSIS OF TRANSCRIPTION IN NEUROSPORA
    Brett Tyler; Fiscal Year: 1990
    ..Recently I developed an RNA polymerase II in vitro transcription system for N...
  69. Functional Characterization of Nuclear Myosin I in Transcription
    Primal de Lanerolle; Fiscal Year: 2010
    ..Specifically, actin is necessary for pre-initiation complex formation by RNA polymerase II and actin binds to RNA polymerases I, II and III...
  70. Biochemical Analysis of RNA Polymerase II Transcription
    JESSICA DERMODY; Fiscal Year: 2007
    ..our understanding of the molecular interactions of the complexes involved in transcription initiation by RNA polymerase II. The transcription of DMA into RNA is a universal mechanism that is required of all cells for proper gene ..