Katsuhiko Murakami

Katsuhiko Murakami

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Katsuhiko Murakami

Publications by authors named "Katsuhiko Murakami"

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Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase.

Nucleic Acids Res 2020 Jan 22. Epub 2020 Jan 22.

Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1093/nar/gkz1221DOI Listing
January 2020

Structure and function of an unusual flavodoxin from the domain .

Proc Natl Acad Sci U S A 2019 Dec 4;116(51):25917-25922. Epub 2019 Dec 4.

Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802;

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http://dx.doi.org/10.1073/pnas.1908578116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6926009PMC
December 2019

Region 3.2 of the σ factor controls the stability of rRNA promoter complexes and potentiates their repression by DksA.

Nucleic Acids Res 2018 11;46(21):11477-11487

Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.

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http://dx.doi.org/10.1093/nar/gky919DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265461PMC
November 2018

Minimalism and functionality: Structural lessons from the heterodimeric N4 bacteriophage RNA polymerase II.

J Biol Chem 2018 08 10;293(35):13616-13625. Epub 2018 Jul 10.

From the Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802

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http://dx.doi.org/10.1074/jbc.RA118.003447DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6120196PMC
August 2018

Structure-function comparisons of (p)ppApp vs (p)ppGpp for Escherichia coli RNA polymerase binding sites and for rrnB P1 promoter regulatory responses in vitro.

Biochim Biophys Acta Gene Regul Mech 2018 08 18;1861(8):731-742. Epub 2018 Jul 18.

Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland. Electronic address:

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http://dx.doi.org/10.1016/j.bbagrm.2018.07.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6114088PMC
August 2018

An Introduction to the Structure and Function of the Catalytic Core Enzyme of RNA Polymerase.

EcoSal Plus 2018 08;8(1)

Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802.

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http://dx.doi.org/10.1128/ecosalplus.ESP-0004-2018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6095464PMC
August 2018

Biomarker discovery by integrated joint non-negative matrix factorization and pathway signature analyses.

Sci Rep 2018 06 27;8(1):9743. Epub 2018 Jun 27.

Human Genome Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan.

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http://dx.doi.org/10.1038/s41598-018-28066-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6021419PMC
June 2018

Cryo-EM structure of σ RNA polymerase and promoter DNA complex revealed a role of σ non-conserved region during the open complex formation.

J Biol Chem 2018 05 26;293(19):7367-7375. Epub 2018 Mar 26.

From the Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802 and

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http://dx.doi.org/10.1074/jbc.RA118.002161DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5949986PMC
May 2018

Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA.

Mol Cell 2018 03 22;69(5):828-839.e5. Epub 2018 Feb 22.

Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2018.01.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5837818PMC
March 2018

X-ray crystal structure of a reiterative transcription complex reveals an atypical RNA extension pathway.

Proc Natl Acad Sci U S A 2017 08 26;114(31):8211-8216. Epub 2017 Jun 26.

Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802;

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http://dx.doi.org/10.1073/pnas.1702741114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5547606PMC
August 2017

Structural basis for rifamycin resistance of bacterial RNA polymerase by the three most clinically important RpoB mutations found in Mycobacterium tuberculosis.

Mol Microbiol 2017 03 10;103(6):1034-1045. Epub 2017 Jan 10.

Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.

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http://dx.doi.org/10.1111/mmi.13606DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5344776PMC
March 2017

Novel Chemical Scaffolds for Inhibition of Rifamycin-Resistant RNA Polymerase Discovered from High-Throughput Screening.

SLAS Discov 2017 03 27;22(3):287-297. Epub 2016 Dec 27.

1 Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1177/2472555216679994DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5323270PMC
March 2017

NusG Is a Sequence-specific RNA Polymerase Pause Factor That Binds to the Non-template DNA within the Paused Transcription Bubble.

J Biol Chem 2016 Mar 7;291(10):5299-308. Epub 2016 Jan 7.

From the Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802

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http://dx.doi.org/10.1074/jbc.M115.704189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4777861PMC
March 2016

Structural and mutational analysis of archaeal ATP-dependent RNA ligase identifies amino acids required for RNA binding and catalysis.

Nucleic Acids Res 2016 Mar 20;44(5):2337-47. Epub 2016 Feb 20.

Department of Biological Sciences, State University of New York, Buffalo, NY 14260, USA Department of Infection Biology, Graduate School of Comprehensive Human Sciences, Faculty of Medicine, University of Tsukuba, Ibaraki 305-8575, Japan

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http://dx.doi.org/10.1093/nar/gkw094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4797309PMC
March 2016

TRANSCRIPTION. Structures of the RNA polymerase-σ54 reveal new and conserved regulatory strategies.

Science 2015 Aug;349(6250):882-5

Centre for Structural Biology, Imperial College London, South Kensington SW7 2AZ, UK. Department of Medicine, Imperial College London, South Kensington SW7 2AZ, UK.

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http://dx.doi.org/10.1126/science.aab1478DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681505PMC
August 2015

Recent functional insights into the role of (p)ppGpp in bacterial physiology.

Nat Rev Microbiol 2015 May 8;13(5):298-309. Epub 2015 Apr 8.

Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.

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http://dx.doi.org/10.1038/nrmicro3448DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4659695PMC
May 2015

Structural biology of bacterial RNA polymerase.

Biomolecules 2015 May 11;5(2):848-64. Epub 2015 May 11.

Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.3390/biom5020848DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4496699PMC
May 2015

X-ray crystal structures of Escherichia coli RNA polymerase with switch region binding inhibitors enable rational design of squaramides with an improved fraction unbound to human plasma protein.

J Med Chem 2015 Apr 23;58(7):3156-71. Epub 2015 Mar 23.

†Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.

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http://dx.doi.org/10.1021/acs.jmedchem.5b00050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4658208PMC
April 2015

The X-ray crystal structure of the euryarchaeal RNA polymerase in an open-clamp configuration.

Nat Commun 2014 Oct 14;5:5132. Epub 2014 Oct 14.

Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1038/ncomms6132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4657547PMC
October 2014

Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme.

J Biol Chem 2014 Aug 27;289(35):24549-59. Epub 2014 Jun 27.

From the Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802,

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http://dx.doi.org/10.1074/jbc.M114.584037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4148879PMC
August 2014

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

J Biomed Semantics 2014 Feb 5;5(1). Epub 2014 Feb 5.

Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1186/2041-1480-5-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978116PMC
February 2014

Inactivation of the bacterial RNA polymerase due to acquisition of secondary structure by the ω subunit.

J Biol Chem 2013 Aug 10;288(35):25076-87. Epub 2013 Jul 10.

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.

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http://dx.doi.org/10.1074/jbc.M113.468520DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3757172PMC
August 2013

Differential regulation by ppGpp versus pppGpp in Escherichia coli.

Nucleic Acids Res 2013 Jul 25;41(12):6175-89. Epub 2013 Apr 25.

Laboratory of Molecular Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1093/nar/gkt302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3695517PMC
July 2013

PCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from h-invitational protein-protein interactions integrative dataset.

BMC Syst Biol 2012 12;6 Suppl 2:S7. Epub 2012 Dec 12.

Integrated Databases and Systems Biology Team, Biological Information Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.

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http://dx.doi.org/10.1186/1752-0509-6-S2-S7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3521179PMC
June 2013

X-ray crystal structures of the Escherichia coli RNA polymerase in complex with benzoxazinorifamycins.

J Med Chem 2013 Jun 31;56(11):4758-63. Epub 2013 May 31.

Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1021/jm4004889DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3745299PMC
June 2013

X-ray crystal structure of Escherichia coli RNA polymerase σ70 holoenzyme.

J Biol Chem 2013 Mar 6;288(13):9126-34. Epub 2013 Feb 6.

Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1074/jbc.M112.430900DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3610985PMC
March 2013

Watching the bacteriophage N4 RNA polymerase transcription by time-dependent soak-trigger-freeze X-ray crystallography.

J Biol Chem 2013 Feb 12;288(5):3305-11. Epub 2012 Dec 12.

Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1074/jbc.M112.387712DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561550PMC
February 2013

H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery.

Nucleic Acids Res 2013 Jan 28;41(Database issue):D915-9. Epub 2012 Nov 28.

Integrated Database and Systems Biology Team, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Aomi 2-4-7, Koto-ku, Tokyo 135-0064, Japan.

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http://dx.doi.org/10.1093/nar/gks1245DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531145PMC
January 2013

MreA functions in the global regulation of methanogenic pathways in Methanosarcina acetivorans.

mBio 2012 31;3(4):e00189-12. Epub 2012 Jul 31.

Department of Biochemistry and Molecular Biology, the Pennsylvania State University, University Park, PA, USA.

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http://mbio.asm.org/content/3/4/e00189-12.full.pdf
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http://mbio.asm.org/cgi/doi/10.1128/mBio.00189-12
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http://dx.doi.org/10.1128/mBio.00189-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3419521PMC
October 2012

Time-resolved events on the reaction pathway of transcript initiation by a single-subunit RNA polymerase: Raman crystallographic evidence.

J Am Chem Soc 2011 Aug 27;133(32):12544-55. Epub 2011 Jul 27.

Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States.

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http://pubs.acs.org/doi/abs/10.1021/ja201557w
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http://dx.doi.org/10.1021/ja201557wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154994PMC
August 2011

X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides.

Proc Natl Acad Sci U S A 2011 Mar 14;108(9):3566-71. Epub 2011 Feb 14.

Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1073/pnas.1016691108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048110PMC
March 2011

Archaeal RNA polymerase and transcription regulation.

Crit Rev Biochem Mol Biol 2011 Feb;46(1):27-40

Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.3109/10409238.2010.538662DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3076279PMC
February 2011

RNA polymerase and transcription elongation factor Spt4/5 complex structure.

Proc Natl Acad Sci U S A 2011 Jan 27;108(2):546-50. Epub 2010 Dec 27.

Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1073/pnas.1013828108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3021056PMC
January 2011

Functional analysis of the three TATA binding protein homologs in Methanosarcina acetivorans.

J Bacteriol 2010 Mar 15;192(6):1511-7. Epub 2010 Jan 15.

Department of Biochemistry and Molecular Biology and Center for Microbial Structural Biology, 205 South Frear Laboratory, The Pennsylvania State University, University Park, PA 16802, USA.

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http://jb.asm.org/cgi/doi/10.1128/JB.01165-09
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http://dx.doi.org/10.1128/JB.01165-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832540PMC
March 2010

G-compass: a web-based comparative genome browser between human and other vertebrate genomes.

Bioinformatics 2009 Dec 21;25(24):3321-2. Epub 2009 Oct 21.

Japan Biological Information Research Center, Japan Biological Informatics Consortium, Aomi 2-42, Koto-ku, Tokyo 135-0064, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btp594DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788932PMC
December 2009

Archaeal RNA polymerase.

Curr Opin Struct Biol 2009 Dec 31;19(6):724-31. Epub 2009 Oct 31.

Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1016/j.sbi.2009.10.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806685PMC
December 2009

Structural basis for DNA-hairpin promoter recognition by the bacteriophage N4 virion RNA polymerase.

Mol Cell 2008 Dec;32(5):707-17

Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1016/j.molcel.2008.11.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639713PMC
December 2008

Structural and biochemical characterization of flavoredoxin from the archaeon Methanosarcina acetivorans.

Biochemistry 2008 Nov 9;47(44):11528-35. Epub 2008 Oct 9.

Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1021/bi801012pDOI Listing
November 2008

X-ray crystal structure of the polymerase domain of the bacteriophage N4 virion RNA polymerase.

Proc Natl Acad Sci U S A 2008 Apr 24;105(13):5046-51. Epub 2008 Mar 24.

Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1073/pnas.0712325105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2278199PMC
April 2008

Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions.

BMC Genomics 2008 Mar 1;9:112. Epub 2008 Mar 1.

Integrated Database Group, Japan Biological Information Research Center (JBIRC), Japan Biological Informatics Consortium, Aomi 2-41, Koto-ku, Tokyo, 135-0064, Japan.

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http://dx.doi.org/10.1186/1471-2164-9-112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2292176PMC
March 2008

The X-ray crystal structure of RNA polymerase from Archaea.

Nature 2008 Feb 30;451(7180):851-4. Epub 2008 Jan 30.

Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://www.nature.com/articles/nature06530
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http://dx.doi.org/10.1038/nature06530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805805PMC
February 2008

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.

Authors:
Chisato Yamasaki Katsuhiko Murakami Yasuyuki Fujii Yoshiharu Sato Erimi Harada Jun-ichi Takeda Takayuki Taniya Ryuichi Sakate Shingo Kikugawa Makoto Shimada Motohiko Tanino Kanako O Koyanagi Roberto A Barrero Craig Gough Hong-Woo Chun Takuya Habara Hideki Hanaoka Yosuke Hayakawa Phillip B Hilton Yayoi Kaneko Masako Kanno Yoshihiro Kawahara Toshiyuki Kawamura Akihiro Matsuya Naoki Nagata Kensaku Nishikata Akiko Ogura Noda Shin Nurimoto Naomi Saichi Hiroaki Sakai Ryoko Sanbonmatsu Rie Shiba Mami Suzuki Kazuhiko Takabayashi Aiko Takahashi Takuro Tamura Masayuki Tanaka Susumu Tanaka Fusano Todokoro Kaori Yamaguchi Naoyuki Yamamoto Toshihisa Okido Jun Mashima Aki Hashizume Lihua Jin Kyung-Bum Lee Yi-Chueh Lin Asami Nozaki Katsunaga Sakai Masahito Tada Satoru Miyazaki Takashi Makino Hajime Ohyanagi Naoki Osato Nobuhiko Tanaka Yoshiyuki Suzuki Kazuho Ikeo Naruya Saitou Hideaki Sugawara Claire O'Donovan Tamara Kulikova Eleanor Whitfield Brian Halligan Mary Shimoyama Simon Twigger Kei Yura Kouichi Kimura Tomohiro Yasuda Tetsuo Nishikawa Yutaka Akiyama Chie Motono Yuri Mukai Hideki Nagasaki Makiko Suwa Paul Horton Reiko Kikuno Osamu Ohara Doron Lancet Eric Eveno Esther Graudens Sandrine Imbeaud Marie Anne Debily Yoshihide Hayashizaki Clara Amid Michael Han Andreas Osanger Toshinori Endo Michael A Thomas Mika Hirakawa Wojciech Makalowski Mitsuteru Nakao Nam-Soon Kim Hyang-Sook Yoo Sandro J De Souza Maria de Fatima Bonaldo Yoshihito Niimura Vladimir Kuryshev Ingo Schupp Stefan Wiemann Matthew Bellgard Masafumi Shionyu Libin Jia Danielle Thierry-Mieg Jean Thierry-Mieg Lukas Wagner Qinghua Zhang Mitiko Go Shinsei Minoshima Masafumi Ohtsubo Kousuke Hanada Peter Tonellato Takao Isogai Ji Zhang Boris Lenhard Sangsoo Kim Zhu Chen Ursula Hinz Anne Estreicher Kenta Nakai Izabela Makalowska Winston Hide Nicola Tiffin Laurens Wilming Ranajit Chakraborty Marcelo Bento Soares Maria Luisa Chiusano Yutaka Suzuki Charles Auffray Yumi Yamaguchi-Kabata Takeshi Itoh Teruyoshi Hishiki Satoshi Fukuchi Ken Nishikawa Sumio Sugano Nobuo Nomura Yoshio Tateno Tadashi Imanishi Takashi Gojobori

Nucleic Acids Res 2008 Jan 18;36(Database issue):D793-9. Epub 2007 Dec 18.

Japan Biological Information Research Center, Japan Biological Informatics Consortium, Japan.

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http://dx.doi.org/10.1093/nar/gkm999DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238988PMC
January 2008

The cyanobacterial principal sigma factor region 1.1 is involved in DNA-binding in the free form and in transcription activity as holoenzyme.

FEBS Lett 2006 Jun 12;580(14):3439-44. Epub 2006 May 12.

Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Japan.

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http://dx.doi.org/10.1016/j.febslet.2006.05.017DOI Listing
June 2006

Structure and function of lineage-specific sequence insertions in the bacterial RNA polymerase beta' subunit.

J Mol Biol 2005 Oct;353(1):138-54

The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.

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http://dx.doi.org/10.1016/j.jmb.2005.07.073DOI Listing
October 2005

Crystallographic analysis of Thermus aquaticus RNA polymerase holoenzyme and a holoenzyme/promoter DNA complex.

Methods Enzymol 2003 ;370:42-53

Rockefeller University, 1230 York Avenue, Box 224, New York, New York 10021, USA.

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http://dx.doi.org/10.1016/S0076-6879(03)70004-4DOI Listing
February 2004

Assessment of clusters of transcription factor binding sites in relationship to human promoter, CpG islands and gene expression.

BMC Genomics 2004 Feb 23;5(1):16. Epub 2004 Feb 23.

RIKEN Genomic Sciences Center, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, Kanagawa, JAPAN.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-5-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC375527PMC
February 2004

Catabolite activator protein: DNA binding and transcription activation.

Curr Opin Struct Biol 2004 Feb;14(1):10-20

Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854, USA.

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http://dx.doi.org/10.1016/j.sbi.2004.01.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2765107PMC
February 2004

Complete sequencing and characterization of 21,243 full-length human cDNAs.

Authors:
Toshio Ota Yutaka Suzuki Tetsuo Nishikawa Tetsuji Otsuki Tomoyasu Sugiyama Ryotaro Irie Ai Wakamatsu Koji Hayashi Hiroyuki Sato Keiichi Nagai Kouichi Kimura Hiroshi Makita Mitsuo Sekine Masaya Obayashi Tatsunari Nishi Toshikazu Shibahara Toshihiro Tanaka Shizuko Ishii Jun-ichi Yamamoto Kaoru Saito Yuri Kawai Yuko Isono Yoshitaka Nakamura Kenji Nagahari Katsuhiko Murakami Tomohiro Yasuda Takao Iwayanagi Masako Wagatsuma Akiko Shiratori Hiroaki Sudo Takehiko Hosoiri Yoshiko Kaku Hiroyo Kodaira Hiroshi Kondo Masanori Sugawara Makiko Takahashi Katsuhiro Kanda Takahide Yokoi Takako Furuya Emiko Kikkawa Yuhi Omura Kumi Abe Kumiko Kamihara Naoko Katsuta Kazuomi Sato Machiko Tanikawa Makoto Yamazaki Ken Ninomiya Tadashi Ishibashi Hiromichi Yamashita Katsuji Murakawa Kiyoshi Fujimori Hiroyuki Tanai Manabu Kimata Motoji Watanabe Susumu Hiraoka Yoshiyuki Chiba Shinichi Ishida Yukio Ono Sumiyo Takiguchi Susumu Watanabe Makoto Yosida Tomoko Hotuta Junko Kusano Keiichi Kanehori Asako Takahashi-Fujii Hiroto Hara Tomo-o Tanase Yoshiko Nomura Sakae Togiya Fukuyo Komai Reiko Hara Kazuha Takeuchi Miho Arita Nobuyuki Imose Kaoru Musashino Hisatsugu Yuuki Atsushi Oshima Naokazu Sasaki Satoshi Aotsuka Yoko Yoshikawa Hiroshi Matsunawa Tatsuo Ichihara Namiko Shiohata Sanae Sano Shogo Moriya Hiroko Momiyama Noriko Satoh Sachiko Takami Yuko Terashima Osamu Suzuki Satoshi Nakagawa Akihiro Senoh Hiroshi Mizoguchi Yoshihiro Goto Fumio Shimizu Hirokazu Wakebe Haretsugu Hishigaki Takeshi Watanabe Akio Sugiyama Makoto Takemoto Bunsei Kawakami Masaaki Yamazaki Koji Watanabe Ayako Kumagai Shoko Itakura Yasuhito Fukuzumi Yoshifumi Fujimori Megumi Komiyama Hiroyuki Tashiro Akira Tanigami Tsutomu Fujiwara Toshihide Ono Katsue Yamada Yuka Fujii Kouichi Ozaki Maasa Hirao Yoshihiro Ohmori Ayako Kawabata Takeshi Hikiji Naoko Kobatake Hiromi Inagaki Yasuko Ikema Sachiko Okamoto Rie Okitani Takuma Kawakami Saori Noguchi Tomoko Itoh Keiko Shigeta Tadashi Senba Kyoka Matsumura Yoshie Nakajima Takae Mizuno Misato Morinaga Masahide Sasaki Takushi Togashi Masaaki Oyama Hiroko Hata Manabu Watanabe Takami Komatsu Junko Mizushima-Sugano Tadashi Satoh Yuko Shirai Yukiko Takahashi Kiyomi Nakagawa Koji Okumura Takahiro Nagase Nobuo Nomura Hisashi Kikuchi Yasuhiko Masuho Riu Yamashita Kenta Nakai Tetsushi Yada Yusuke Nakamura Osamu Ohara Takao Isogai Sumio Sugano

Nat Genet 2004 Jan 21;36(1):40-5. Epub 2003 Dec 21.

Helix Research Institute, 1532-3 Yana, Kisarazu, Chiba 292-0812, Japan.

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Recruitment of sigma54-RNA polymerase to the Pu promoter of Pseudomonas putida through integration host factor-mediated positioning switch of alpha subunit carboxyl-terminal domain on an UP-like element.

J Biol Chem 2003 Jul 16;278(30):27695-702. Epub 2003 May 16.

Dipartimento di Genetica e Biologia dei Microrganismi, Università degli Studi di Milano, via Celoria 26, 20133 Milan, Italy.

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Oxidative damage to cellular and isolated DNA by homocysteine: implications for carcinogenesis.

Oncogene 2003 Jun;22(23):3530-8

Department of Environmental and Molecular Medicine, Mie University School of Medicine, Mie 514-8507, Japan.

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Bacterial RNA polymerases: the wholo story.

Curr Opin Struct Biol 2003 Feb;13(1):31-9

The Rockefeller University, Box 224, 1230 York Avenue, New York, NY 10021, USA.

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February 2003

Protein-protein and protein-DNA interactions of sigma70 region 4 involved in transcription activation by lambdacI.

J Mol Biol 2002 Nov;324(1):17-34

Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.

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http://dx.doi.org/10.1016/s0022-2836(02)01043-4DOI Listing
November 2002

Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution.

Science 2002 May;296(5571):1280-4

The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.

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http://dx.doi.org/10.1126/science.1069594DOI Listing
May 2002

Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex.

Science 2002 May;296(5571):1285-90

The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.

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http://dx.doi.org/10.1126/science.1069595DOI Listing
May 2002