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  • 1
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    Translocation dynamics of RNA polymerase [Biophysics and Computational Biology] (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-05-28
    Description: Translocation of RNA polymerase (RNAP) is a robust target for regulation of gene expression in prokaryotes and eukaryotes (1–3). During elongation, RNAP frequently encounters a broad range of DNA/RNA conformations (RNA hairpins, curved and cruciform DNA), DNA-binding proteins, DNA lesions, and misincorporation events at the 3′ ends of the RNA....
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    Blocking of the initiation-to-elongation transition by a transdominant RNA polymerase mutation (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-05-25
    Description: RNA polymerase, the principal enzyme of gene expression, possesses structural features conserved in evolution. A substitution of an evolutionarily invariant amino acid (Lys1065----Arg) in the beta subunit of Escherichia coli RNA polymerase apparently disrupts its catalytic center. The mutant protein inhibited cell growth when expressed from an inducible promoter. The assembled holoenzyme carrying the mutant subunit formed stable promoter complexes that continuously synthesized promoter-specific dinucleotides but that did not enter the elongation step. The mutant polymerase inhibited transcription by blocking the access of the wild-type enzyme to promoters.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kashlev, M -- Lee, J -- Zalenskaya, K -- Nikiforov, V -- Goldfarb, A -- GM30717/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 May 25;248(4958):1006-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Genetics, U.S.S.R. Academy of Sciences, Moscow.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1693014" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; DNA Mutational Analysis ; DNA-Directed RNA Polymerases/*genetics/metabolism ; Escherichia coli/enzymology/genetics ; Genes, Dominant ; Molecular Sequence Data ; Promoter Regions, Genetic ; RNA/biosynthesis ; Structure-Activity Relationship
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-10-04
    Description: Alternative splicing of pre-messenger RNA is a key feature of transcriptome expansion in eukaryotic cells, yet its regulation is poorly understood. Spliceosome assembly occurs co-transcriptionally, raising the possibility that DNA structure may directly influence alternative splicing. Supporting such an association, recent reports have identified distinct histone methylation patterns, elevated nucleosome occupancy and enriched DNA methylation at exons relative to introns. Moreover, the rate of transcription elongation has been linked to alternative splicing. Here we provide the first evidence that a DNA-binding 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. We further show that CTCF binding to CD45 exon 5 is inhibited by DNA methylation, leading to reciprocal effects on exon 5 inclusion. These findings provide a mechanistic basis for developmental regulation of splicing outcome through heritable epigenetic marks.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shukla, Sanjeev -- Kavak, Ersen -- Gregory, Melissa -- Imashimizu, Masahiko -- Shutinoski, Bojan -- Kashlev, Mikhail -- Oberdoerffer, Philipp -- Sandberg, Rickard -- Oberdoerffer, Shalini -- Intramural NIH HHS/ -- England -- Nature. 2011 Nov 3;479(7371):74-9. doi: 10.1038/nature10442.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Cancer Research, Mouse Cancer Genetics Program, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21964334" target="_blank"〉PubMed〈/a〉
    Keywords: *Alternative Splicing ; Animals ; Antigens, CD45/genetics ; Cell Line ; Cells, Cultured ; *DNA Methylation ; Epigenesis, Genetic ; Exons/genetics ; Genome, Human/genetics ; Humans ; Mice ; Protein Binding ; RNA Polymerase II/*metabolism ; RNA Splice Sites/genetics ; RNA, Messenger/genetics/metabolism ; Repressor Proteins/*metabolism ; Saccharomyces cerevisiae/enzymology ; *Transcription, Genetic/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Mapping of catalytic residues in the RNA polymerase active center (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-07-05
    Description: When the Mg2+ ion in the catalytic center of Escherichia coli RNA polymerase (RNAP) is replaced with Fe2+, hydroxyl radicals are generated. In the promoter complex, such radicals cleave template DNA near the transcription start site, whereas the beta' subunit is cleaved at a conserved motif NADFDGD (Asn-Ala-Asp-Phe-Asp-Gly-Asp). Substitution of the three aspartate residues with alanine creates a dominant lethal mutation. The mutant RNAP is catalytically inactive but can bind promoters and form an open complex. The mutant fails to support Fe2+-induced cleavage of DNA or protein. Thus, the NAD-FDGD motif is involved in chelation of the active center Mg2+.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zaychikov, E -- Martin, E -- Denissova, L -- Kozlov, M -- Markovtsov, V -- Kashlev, M -- Heumann, H -- Nikiforov, V -- Goldfarb, A -- Mustaev, A -- New York, N.Y. -- Science. 1996 Jul 5;273(5271):107-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Limnological Institute, Russian Academy of Sciences, Irkutsk, Russia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8658176" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Aspartic Acid/metabolism ; Binding Sites ; DNA/metabolism ; DNA-Directed RNA Polymerases/*chemistry/genetics/*metabolism ; Dithiothreitol/pharmacology ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/*enzymology ; Ferrous Compounds/metabolism ; Hydroxyl Radical ; Magnesium/metabolism ; Molecular Sequence Data ; Mutagenesis ; Promoter Regions, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Discontinuous mechanism of transcription elongation (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-08-05
    Description: During transcription elongation, three flexibly connected parts of RNA polymerase of Escherichia coli advance along the template so that the front-end domain is followed by the catalytic site which in turn is followed by the RNA product binding site. The advancing enzyme was found to maintain the same conformation throughout extended segments of the transcribed region. However, when the polymerase traveled across certain DNA sites that seemed to briefly anchor the front-end domain, cyclic shifting of the three parts, accompanied by buildup and relief of internal strain, was observed. Thus, elongation proceeded in alternating laps of monotonous and inchworm-like movement with the flexible RNA polymerase configuration being subject to direct sequence control.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nudler, E -- Goldfarb, A -- Kashlev, M -- GM49242/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Aug 5;265(5173):793-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Public Health Research Institute, New York, NY 10016.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8047884" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; DNA-Directed RNA Polymerases/*metabolism ; *Escherichia coli Proteins ; *Models, Genetic ; Molecular Sequence Data ; Movement ; Peptide Elongation Factors/metabolism ; Protein Conformation ; RNA, Messenger/metabolism ; RNA-Binding Proteins/metabolism ; Templates, Genetic ; Transcription Factors/metabolism ; Transcription, Genetic/*physiology ; Transcriptional Elongation Factors
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-08-01
    Description: 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. Our results indicate that the nucleosome behaves as a fluctuating barrier that locally increases pause density, slows pause recovery, and reduces the apparent pause-free velocity of Pol II. The polymerase, rather than actively separating DNA from histones, functions instead as a ratchet that rectifies nucleosomal fluctuations. We also obtained direct evidence that transcription through a nucleosome involves transfer of the core histones behind the transcribing polymerase via a transient DNA loop. The interplay between polymerase dynamics and nucleosome fluctuations provides a physical basis for the regulation of eukaryotic transcription.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2775800/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2775800/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hodges, Courtney -- Bintu, Lacramioara -- Lubkowska, Lucyna -- Kashlev, Mikhail -- Bustamante, Carlos -- GM32543/GM/NIGMS NIH HHS/ -- R37 GM032543/GM/NIGMS NIH HHS/ -- R37 GM032543-27/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 Jul 31;325(5940):626-8. doi: 10.1126/science.1172926.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Jason L. Choy Laboratory of Single-Molecule Biophysics and Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19644123" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Catalytic Domain ; DNA/genetics/*metabolism ; Diffusion ; Histones/metabolism ; Models, Genetic ; Nucleosomes/*metabolism ; Optical Tweezers ; RNA Polymerase II/chemistry/*metabolism ; RNA, Messenger/genetics/metabolism ; Saccharomyces cerevisiae/metabolism ; Templates, Genetic ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
    Electronic Resource
    Electronic Resource
    Histidine-tagged RNA polymerase: dissection of the transcription cycle using immobilized enzyme
    Amsterdam : Elsevier
    Gene 130 (1993), S. 9-14 
    Details
    ISSN: 0378-1119
    Keywords: RNA polymerase isolation ; Recombinant DNA ; elongation ; ternary complexes ; transcription initiation ; β' subunit
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0378-1119(93)90340-9
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    Paper (German National Licenses)
    Fulltext
  • 8
    Electronic Resource
    Electronic Resource
    Heat shock response in Escherichia coli promotes assembly of plasmid encoded RNA polymerase β-subunit into RNA polymerase (1989)
    Springer
    Molecular genetics and genomics 216 (1989), S. 469-474 
    Details
    ISSN: 1617-4623
    Keywords: Heat shock proteins ; Subunit assembly ; Aggregation ; RNA polymerase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Escherichia coli cells, carrying a rifampicin sensitive RNA polymerase β-subunit gene in the chromosome and a rifampicin resistant β-subunit gene placed under the control of a strong promoter in a multicopy plasmid, are unable to grow in the presence of rifampicin, despite the accumulation of large quantities of the resistant subunit. A major portion of the overproduced subunit is found in an insoluble form. Conditions known to induce the heat shock proteins (hsps), e.g. elevated temperature or the presence of ethanol in the growth medium, increase the amount of the plasmid-borne β-subunit which apparently assembles into active RNA polymerase and makes the plasmid bearing cells rifampicin resistant. Alternatively, plasmid-borne subunits assemble into RNA polymerase with low efficiency in rpoH mutant cells known to have reduced level of hsps. We suggest that the plasmid-borne subunit is poorly assembled into RNA polymerase and that hsps promote the assembly by interfering with β-subunit aggregation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00334392
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  • 9
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    Mechanism of sequence-specific pausing of bacterial RNA polymerase (2009)
    National Academy of Sciences
    Details
    Publication Date: 2009-04-24
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 10
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    Assembly of functional Escherichia coli RNA polymerase containing beta subunit fragments. (1995)
    National Academy of Sciences
    Details
    Publication Date: 1995-05-09
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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