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Benoit Coulombe
Laboratory of Gene Transcription and Proteomics, Clinical Research Institute of Montreal, Montreal, Canada

Faculty Member: CELL BIOLOGY > Control of gene expression [ since 11 February 2003 ]
[ Biography ] [ Homepage ] [ Evaluations ]
Biography

BENOIT COULOMBE
Clinical Research Institute of Montreal
Montreal, Quebec, Canada
Tel: (514) 987-5662 / Fax: (514) 987-5663
E-mail: benoit.coulombe@ircm.qc.ca
URL: http://www.ircm.qc.ca/en/recherche/statique/unite14.html

RESEARCH INTERESTS:
My objective is to develop a detailed understanding of the mechanisms by which the information contained into the human genome is decoded to produce the mRNA molecules used for protein synthesis. More specifically, I seek to understand how the activity of RNA polymerase II is regulated by the multiple interactions of the enzyme with the DNA template, the nascent RNA and the regulatory proteins; and how RNA polymerase II interacts with other molecular machines to orchestrate nuclear processes such as pre-mRNA maturation and transport as well as DNA replication and repair. My research is directed toward both transcription of individual genes, using biochemistry and molecular biology to unravel the molecular details of the transcription reaction, and the analysis of transcription at the genome wide level, using genomics and proteomics to decipher regulatory networks of gene expression. Because transcriptional deregulations lead to diseases such as cancer and genetic dysfunctions and because many microbes use the transcription machinery of their host to transcribe and replicate their own genome, my research helps identifying novel molecular targets for drug discovery.

Home page

http://www.ircm.qc.ca/en/recherche/statique/unite14.html

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Evaluations

Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches.
McClellan AJ, Xia Y, …, Gerstein M, Frydman J
Cell 2007 Oct 5 131(1):121-35 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Benoit Coulombe / Frederick Hughson
Evaluated 22 Oct 2007

The minimum information required for reporting a molecular interaction experiment (MIMIx).
Orchard S, Salwinski L, …, Cesareni G, Hermjakob H
Nat Biotechnol 2007 Aug 25(8):894-8 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Benoit Coulombe / Richard Willson
Evaluated 5 Sep 2007

The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics.
Yu H, Kim PM, …, Trifonov V, Gerstein M
PLoS Comput Biol 2007 Apr 20 3(4):e59 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Benoit Coulombe
Evaluated 8 May 2007

Proteome survey reveals modularity of the yeast cell machinery.
Gavin AC, Aloy P, …, Russell RB, Superti-Furga G
Nature 2006 Mar 30 440(7084):631-6 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fabio Piano / Benoit Coulombe
Evaluated 27 Jul 2006

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
Krogan NJ, Cagney G, …, Emili A, Greenblatt JF
Nature 2006 Mar 30 440(7084):637-43 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Daniel Chamovitz / Benoit Coulombe / Fabio Piano
Evaluated 16 May 2006

Exon tethering in transcription by RNA polymerase II.
Dye MJ, Gromak N, Proudfoot NJ
Mol Cell 2006 Mar 17 21(6):849-59 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Lawrence Chasin / Benoit Coulombe / Miles Wilkinson
Evaluated 29 Mar 2006

The mechanism of DNA replication primer synthesis by RNA polymerase.
Zenkin N, Naryshkina T, Kuznedelov K, Severinov K
Nature 2006 Feb 2 439(7076):617-20 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Benoit Coulombe
Evaluated 17 Mar 2006

A posttranscriptional role for the yeast Paf1-RNA polymerase II complex is revealed by identification of primary targets.
Penheiter KL, Washburn TM, …, Hoffman MG, Jaehning JA
Mol Cell 2005 Oct 28 20(2):213-23 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Daniel Reines / Benoit Coulombe
Evaluated 21 Nov 2005

The proteasome regulatory particle alters the SAGA coactivator to enhance its interactions with transcriptional activators.
Lee D, Ezhkova E, …, Tansey WP, Workman JL
Cell 2005 Nov 4 123(3):423-36 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Susan Forsburg / Benoit Coulombe / Rivka Dikstein / Cheng-Ming Chiang / Dinah Singer / Tony Weil / Michael Meisterernst
Evaluated 15 Nov 2005

A core promoter element downstream of the TATA box that is recognized by TFIIB.
Deng W, Roberts SG
Genes Dev 2005 Oct 15 19(20):2418-23 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Cheng-Ming Chiang / Benoit Coulombe
Evaluated 4 Nov 2005

Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II.
Baillat D, Hakimi MA, …, Cooch N, Shiekhattar R
Cell 2005 Oct 21 123(2):265-76 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Benoit Coulombe
Evaluated 31 Oct 2005

A ratchet mechanism of transcription elongation and its control.
Bar-Nahum G, Epshtein V, …, Mustaev A, Nudler E
Cell 2005 Jan 28 120(2):183-93 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Benoit Coulombe
Evaluated 18 Feb 2005

Interaction network containing conserved and essential protein complexes in Escherichia coli.
Butland G, Peregrín-Alvarez JM, …, Greenblatt J, Emili A
Nature 2005 Feb 3 433(7025):531-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Tracy Palmer / Benoit Coulombe
Evaluated 14 Feb 2005

Histone demethylation mediated by the nuclear amine oxidase homolog LSD1.
Shi Y, Lan F, …, Casero RA, Shi Y
Cell 2004 Dec 29 119(7):941-53 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Steven Henikoff / Thomas Jenuwein / Chris Sander / Winship Herr / Dinah Singer / Robert Dutnall / Eric Selker / Frank Lyko / Daniel Reines / Benoit Coulombe / Robin Allshire
Evaluated 20 Jan 2005

Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center.
Westover KD, Bushnell DA, Kornberg RD
Cell 2004 Nov 12 119(4):481-9 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Robert Dutnall / Daniel Reines / Ronald Conaway / Benoit Coulombe
Evaluated 12 Jan 2005

MicroRNA genes are transcribed by RNA polymerase II.
Lee Y, Kim M, …, Baek SH, Kim VN
EMBO J 2004 Oct 13 23(20):4051-60 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Marjori Matzke / Benoit Coulombe / Elsebet Lund
Evaluated 1 Oct 2004

Gene loops juxtapose promoters and terminators in yeast.
O'Sullivan JM, Tan-Wong SM, …, Mellor J, Proudfoot NJ
Nat Genet 2004 Sep 36(9):1014-8 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Benoit Coulombe / Robert Fisher
Evaluated 31 Aug 2004

Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription.
Perederina A, Svetlov V, …, Artsimovitch I, Vassylyev DG
Cell 2004 Aug 6 118(3):297-309 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Benoit Coulombe
Evaluated 19 Aug 2004

Cleavage and proteasome-mediated degradation of the basal transcription factor TFIIA.
Høiby T, Mitsiou DJ, …, Tempst P, Stunnenberg HG
EMBO J 2004 Aug 4 23(15):3083-91 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Benoit Coulombe
Evaluated 23 Jul 2004

A tethered catalysis, two-hybrid system to identify protein-protein interactions requiring post-translational modifications.
Guo D, Hazbun TR, …, Fields S, Kuo MH
Nat Biotechnol 2004 Jul 22(7):888-92 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Benoit Coulombe / Thomas Kodadek / Igor Stagljar
Evaluated 21 Jul 2004

Evidence for dynamically organized modularity in the yeast protein-protein interaction network.
Han JD, Bertin N, …, Roth FP, Vidal M
Nature 2004 Jul 1 430(6995):88-93 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Benoit Coulombe
Evaluated 21 Jul 2004

A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A.
Giglia-Mari G, Coin F, …, Hoeijmakers JH, Vermeulen W
Nat Genet 2004 Jul 36(7):714-9 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Benoit Coulombe / Errol C. Friedberg
Evaluated 20 Jul 2004

Recognition of RNA polymerase II carboxy-terminal domain by 3'-RNA-processing factors.
Meinhart A, Cramer P
Nature 2004 Jul 8 430(6996):223-6 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Benoit Coulombe / Gabriele Varani / Elena Conti
Evaluated 20 Jul 2004

Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways.
Parsons AB, Brost RL, …, Hughes TR, Boone C
Nat Biotechnol 2004 Jan 22(1):62-9 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Andrew Emili / Benoit Coulombe
Evaluated 28 Jan 2004

Donation of catalytic residues to RNA polymerase active center by transcription factor Gre.
Sosunova E, Sosunov V, …, Goldfarb A, Mustaev A
Proc Natl Acad Sci U S A 2003 Dec 23 100(26):15469-74 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Benoit Coulombe
Evaluated 9 Jan 2004

Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage.
Kettenberger H, Armache KJ, Cramer P
Cell 2003 Aug 8 114(3):347-57 [abstract on PubMed] [related articles] [order article]
Selected by | Ronald Conaway / Benoit Coulombe / Richard Maraia / Michael Meisterernst
Evaluated 29 Aug 2003

Crystal structure of a transcription factor IIIB core interface ternary complex.
Juo ZS, Kassavetis GA, …, Geiduschek EP, Sigler PB
Nature 2003 Apr 3 422(6931):534-9 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Benoit Coulombe / Gourisankar Ghosh
Evaluated 4 Apr 2003

NTP-driven translocation by human RNA polymerase II.
Nedialkov YA, Gong XQ, …, Yan H, Burton ZF
J Biol Chem 2003 May 16 278(20):18303-12 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Benoit Coulombe
Evaluated 31 Mar 2003

In vivo characterization of regulatory polymorphisms by allele-specific quantification of RNA polymerase loading.
Knight JC, Keating BJ, Rockett KA, Kwiatkowski DP
Nat Genet 2003 Apr 33(4):469-75 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Benoit Coulombe
Evaluated 20 Mar 2003

Visualizing RNA extrusion and DNA wrapping in transcription elongation complexes of bacterial and eukaryotic RNA polymerases.
Rivetti C, Codeluppi S, Dieci G, Bustamante C
J Mol Biol 2003 Mar 7 326(5):1413-26 [abstract on PubMed] [related articles] [order article]
Selected by | Benoit Coulombe / Daniel Reines
Evaluated 10 Mar 2003

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