Benoit Coulombe

Summary

Affiliation: Clinical Research Institute of Montreal
Country: Canada

Publications

  1. pmc Photo-cross-linking of a purified preinitiation complex reveals central roles for the RNA polymerase II mobile clamp and TFIIE in initiation mechanisms
    Diane Forget
    Laboratory of Gene Transcription, Institut de Recherches Cliniques de Montreal, Montreal, Quebec, Canada H2W 1R7
    Mol Cell Biol 24:1122-31. 2004
  2. pmc Steps towards a repertoire of comprehensive maps of human protein interaction networks: the Human Proteotheque Initiative (HuPI)
    Benoit Coulombe
    Gene Transcription and Proteomics Laboratory and Proteomics Discovery Platform, Institut de Recherches Cliniques de Montreal, Montreal, Quebec, Canada
    Biochem Cell Biol 86:149-56. 2008
  3. pmc Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase
    Maria L Kireeva
    Department of Biochemistry and Molecular Biology, Michigan State University, E, Lansing, MI, 48824 1319, USA
    BMC Biophys 5:11. 2012
  4. pmc Mapping the disease protein interactome: toward a molecular medicine GPS to accelerate drug and biomarker discovery
    Benoit Coulombe
    Institut de recherches cliniques de Montréal IRCM, Montréal, Québec, Canada
    J Proteome Res 10:120-5. 2011
  5. pmc Functional dissection of the catalytic mechanism of mammalian RNA polymerase II
    Benoit Coulombe
    Gene Transcription Laboratory, Institute de recherche cliniques de Montréal, QC, Canada
    Biochem Cell Biol 83:497-504. 2005
  6. pmc Genomic location of the human RNA polymerase II general machinery: evidence for a role of TFIIF and Rpb7 at both early and late stages of transcription
    Marilena Cojocaru
    Institut de Recherches Cliniques de Montreal, 110 avenue des Pins Ouest, Montreal, QC, Canada H2W 1R7
    Biochem J 409:139-47. 2008
  7. pmc Discovery of cell compartment specific protein-protein interactions using affinity purification combined with tandem mass spectrometry
    Mathieu Lavallée-Adam
    McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montreal, Quebec H3A 2B4, Canada
    J Proteome Res 12:272-81. 2013
  8. pmc Nuclear import of RNA polymerase II is coupled with nucleocytoplasmic shuttling of the RNA polymerase II-associated protein 2
    Diane Forget
    Institut de recherches cliniques de Montreal IRCM, Montreal, Quebec, Canada H2W 1R7, McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montreal, Quebec, Canada H3A 2B4
    Nucleic Acids Res 41:6881-91. 2013
  9. 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
  10. pmc Human papillomavirus E1 helicase interacts with the WD repeat protein p80 to promote maintenance of the viral genome in keratinocytes
    Alexandra Côté-Martin
    Laboratory of Molecular Virology, Institut de Recherches Cliniques de Montreal, 110 Pine Avenue West, Montreal, Quebec, Canada
    J Virol 82:1271-83. 2008

Collaborators

  • Mathieu Blanchette
  • Jacques Archambault
  • Guy G Poirier
  • Francois Robert
  • Vincent Ferretti
  • Vincent Giguere
  • Jerry L Workman
  • Benoit Chabot
  • Xiaoyu Chen
  • Gordon Chua
  • Mikhail Kashlev
  • D H Price
  • Marie Soleil Gauthier
  • Philippe Cloutier
  • Diane Forget
  • Mathieu Lavallée-Adam
  • Denis Faubert
  • Annie Bouchard
  • Céline Domecq
  • Célia Jeronimo
  • Marilena Cojocaru
  • Racha Al-Khoury
  • Marie France Langelier
  • Jack Greenblatt
  • Vincent Trinh
  • Dominique Bergeron
  • Thomas M Durcan
  • Maria L Kireeva
  • Andrée Anne Lacombe
  • Zachary F Burton
  • Christian Poitras
  • Alexandra Côté-Martin
  • Laimonis A Laimins
  • Hélène Sénéchal
  • Timothy R Hughes
  • Cynthia Therien
  • Dania Baali
  • Angels Tapias
  • Edward A Fon
  • Priti Gros
  • Gian Luca McLelland
  • Matthew Y Tang
  • Eman A Dashti
  • Miguel A Aguileta
  • Thomas A Shaler
  • Joëlle R Pérusse
  • Justine Rousseau
  • Kristopher Opron
  • Robert I Cukier
  • Steve A Seibold
  • Katayoun Varzavand
  • Jeff J Cooper
  • Maria Kireeva
  • Heng Jiang
  • Simon Joubert
  • Claudia M D'Abramo
  • Michaël Lehoux
  • Pierre Cote
  • Cary Moody
  • Amelie Fradet-Turcotte
  • Qintong Li
  • Sylvie Bourassa
  • Mahel Zeghouf
  • Frederic Coin
  • Armaity P Davierwala
  • Veronica Canadien
  • Jeff Pootoolal
  • Jean Marc Egly
  • Jacqueline H Enzlin
  • Dawn P Richards
  • ORLANDO D SCHARER
  • Mark Chandy
  • Jerome Auriol
  • Sanie Mnaimneh
  • Bryan K Beattie

Detail Information

Publications34

  1. pmc Photo-cross-linking of a purified preinitiation complex reveals central roles for the RNA polymerase II mobile clamp and TFIIE in initiation mechanisms
    Diane Forget
    Laboratory of Gene Transcription, Institut de Recherches Cliniques de Montreal, Montreal, Quebec, Canada H2W 1R7
    Mol Cell Biol 24:1122-31. 2004
    ..These results support the central roles of the mobile clamp of RNAP II and TFIIE in transcription initiation...
  2. pmc Steps towards a repertoire of comprehensive maps of human protein interaction networks: the Human Proteotheque Initiative (HuPI)
    Benoit Coulombe
    Gene Transcription and Proteomics Laboratory and Proteomics Discovery Platform, Institut de Recherches Cliniques de Montreal, Montreal, Quebec, Canada
    Biochem Cell Biol 86:149-56. 2008
    ..The process governing the evolution of HuPI towards becoming a repository of accurate and complete protein interaction maps is described...
  3. pmc Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase
    Maria L Kireeva
    Department of Biochemistry and Molecular Biology, Michigan State University, E, Lansing, MI, 48824 1319, USA
    BMC Biophys 5:11. 2012
    ..abstract:..
  4. pmc Mapping the disease protein interactome: toward a molecular medicine GPS to accelerate drug and biomarker discovery
    Benoit Coulombe
    Institut de recherches cliniques de Montréal IRCM, Montréal, Québec, Canada
    J Proteome Res 10:120-5. 2011
    ....
  5. pmc Functional dissection of the catalytic mechanism of mammalian RNA polymerase II
    Benoit Coulombe
    Gene Transcription Laboratory, Institute de recherche cliniques de Montréal, QC, Canada
    Biochem Cell Biol 83:497-504. 2005
    ..Both in vitro and in vivo analyses of these mutants revealed novel features of the catalytic mechanisms involving this enzyme...
  6. pmc Genomic location of the human RNA polymerase II general machinery: evidence for a role of TFIIF and Rpb7 at both early and late stages of transcription
    Marilena Cojocaru
    Institut de Recherches Cliniques de Montreal, 110 avenue des Pins Ouest, Montreal, QC, Canada H2W 1R7
    Biochem J 409:139-47. 2008
    ..Together, our results provide for the first time a general picture of GTF function during the RNAPII transcription reaction in live mammalian cells and show that TFIIF and Rpb7 are involved in both early and late transcriptional stages...
  7. pmc Discovery of cell compartment specific protein-protein interactions using affinity purification combined with tandem mass spectrometry
    Mathieu Lavallée-Adam
    McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montreal, Quebec H3A 2B4, Canada
    J Proteome Res 12:272-81. 2013
    ..Finally, we demonstrate that this improvement in sensitivity leads to the discovery of novel interactions of RNAP II carboxyl-terminal domain (CTD) interacting domain (CID) proteins with POLR2A...
  8. pmc Nuclear import of RNA polymerase II is coupled with nucleocytoplasmic shuttling of the RNA polymerase II-associated protein 2
    Diane Forget
    Institut de recherches cliniques de Montreal IRCM, Montreal, Quebec, Canada H2W 1R7, McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montreal, Quebec, Canada H3A 2B4
    Nucleic Acids Res 41:6881-91. 2013
    ....
  9. 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
    ..A model for RNAPII biogenesis is presented...
  10. pmc Human papillomavirus E1 helicase interacts with the WD repeat protein p80 to promote maintenance of the viral genome in keratinocytes
    Alexandra Côté-Martin
    Laboratory of Molecular Virology, Institut de Recherches Cliniques de Montreal, 110 Pine Avenue West, Montreal, Quebec, Canada
    J Virol 82:1271-83. 2008
    ..These findings suggest that the interaction of E1 with p80 is required for efficient maintenance of the viral episome in undifferentiated keratinocytes...
  11. pmc Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme
    Célia Jeronimo
    Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de Recherches Cliniques de Montreal, Montreal, QC, Canada
    Mol Cell 27:262-74. 2007
    ..Our results define a high-density protein interaction network for the mammalian transcription machinery and uncover multiple regulatory factors that target the transcription machinery...
  12. pmc The highly conserved glutamic acid 791 of Rpb2 is involved in the binding of NTP and Mg(B) in the active center of human RNA polymerase II
    Marie France Langelier
    Laboratory of Gene Transcription, Institut de Recherches Cliniques de Montreal, 110 avenue des Pins Ouest, Montreal, Quebec, Canada H2W 1R7
    Nucleic Acids Res 33:2629-39. 2005
    ....
  13. pmc PReMod: a database of genome-wide mammalian cis-regulatory module predictions
    Vincent Ferretti
    McGill University and Genome Quebec Innovation Center, 740 Dr Penfield, Montreal, QC, Canada H3A 1A4
    Nucleic Acids Res 35:D122-6. 2007
    ..It also provides a visual depiction of the chromosomal context of the selected pCRMs in terms of neighboring pCRMs and genes, all of which are linked to the UCSC Genome Browser and the NCBI. PReMod: http://genomequebec.mcgill.ca/PReMod...
  14. pmc High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNA polymerase II-associated complexes
    Philippe Cloutier
    Institut de Recherches Cliniques de Montreal, Montreal Quebec, Canada
    Methods 48:381-6. 2009
    ....
  15. pmc RPAP1, a novel human RNA polymerase II-associated protein affinity purified with recombinant wild-type and mutated polymerase subunits
    Célia Jeronimo
    Laboratory of Gene Transcription, Institut de Recherches Cliniques de Montreal, Montreal, Quebec, Canada H2W 1R7
    Mol Cell Biol 24:7043-58. 2004
    ....
  16. pmc Transcription factor IIS cooperates with the E3 ligase UBR5 to ubiquitinate the CDK9 subunit of the positive transcription elongation factor B
    Marilena Cojocaru
    Institut de Recherches Cliniques de Montreal, Montreal, Quebec H2W 1R7, Canada
    J Biol Chem 286:5012-22. 2011
    ..Together, these results identify UBR5 as a novel E3 ligase that regulates transcription and define an additional function of TFIIS in the regulation of CDK9...
  17. pmc Use of site-specific protein-DNA photocrosslinking of purified complexes to analyze the topology of the RNA polymerase II transcription initiation complex
    Diane Forget
    Gene Transcription and Proteomics Laboratory, Institut de Recherches Cliniques de Montreal, 110, avenue des Pins Ouest, Montreal, QC, Canada, H2W 1R7
    Methods Mol Biol 543:439-51. 2009
    ..The specific complexes are localized on the gel, purified, and processed for the identification of the crosslinked polypeptides...
  18. pmc Modeling contaminants in AP-MS/MS experiments
    Mathieu Lavallée-Adam
    McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montréal, Canada
    J Proteome Res 10:886-95. 2011
    ..Our approach will thus allow improved accuracy in PPI identification while reducing the number of control experiments required...
  19. pmc Structural perspective on mutations affecting the function of multisubunit RNA polymerases
    Vincent Trinh
    Gene Transcription Laboratory, Institut de Recherches Cliniques de Montreal, 110 ave des Pins ouest, Montreal, Quebec, Canada
    Microbiol Mol Biol Rev 70:12-36. 2006
    ....
  20. pmc Detection of locally over-represented GO terms in protein-protein interaction networks
    Mathieu Lavallée-Adam
    McGill Centre for Bioinformatics and School of Computer Science, Montreal, Quebec, Canada
    J Comput Biol 17:443-57. 2010
    ..When applied to these two biological networks, our approach recovers many known complexes and pathways, but also suggests potential functions for many subnetworks. Online Supplementary Material is available at www.liebertonline.com...
  21. pmc Interaction networks of the molecular machines that decode, replicate, and maintain the integrity of the human genome
    Benoit Coulombe
    Laboratory of Gene Transcription, Institut de Recherches Cliniques de Montreal, 110 avenue des Pins Ouest, Montreal, Quebec, Canada H2W 1R7
    Mol Cell Proteomics 3:851-6. 2004
    ....
  22. ncbi request reprint Amino acid substitutions that specifically impair the transcriptional activity of papillomavirus E2 affect binding to the long isoform of Brd4
    Hélène Sénéchal
    Laboratory of Molecular Virology, Institut de Recherches Cliniques de Montreal, 110 Pine Avenue West, Montreal, Quebec, Canada H2W 1R7
    Virology 358:10-7. 2007
    ..Since these amino acids are located near each other in the 3-dimensional structure of the TAD, we suggest that they define a conserved surface involved in binding Brd4 to regulate viral gene transcription...
  23. pmc Site-directed mutagenesis, purification and assay of Saccharomyces cerevisiae RNA polymerase II
    Céline Domecq
    Institut de Recherches Cliniques de Montreal, 110, Montreal, Que, Canada H2W 1R7
    Protein Expr Purif 69:83-90. 2010
    ..Mutations are also analyzed within the active site region indicating key residues for catalysis and the importance of a Rpb2 R983-E1028 ion pair. Rpb2 R983Q and E1028Q are defective in escape from a transcriptional stall...
  24. pmc A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity
    Philippe Cloutier
    Institut de recherches cliniques de Montreal IRCM, Montreal, Quebec, Canada
    PLoS Genet 9:e1003210. 2013
    ....
  25. doi request reprint Methylation of the DNA/RNA-binding protein Kin17 by METTL22 affects its association with chromatin
    Philippe Cloutier
    Institut de recherches cliniques de Montreal IRCM, Montreal, Quebec H2W 1R7, Canada
    J Proteomics 100:115-24. 2014
    ..These results are discussed in view of the putative cellular function of Kin17...
  26. pmc Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression
    Mathieu Blanchette
    McGill Centre for Bioinformatics, Montreal, Quebec, Canada, H3A 2B4
    Genome Res 16:656-68. 2006
    ..The set of predicted CRMs, which is made available as a public database called PReMod (http://genomequebec.mcgill.ca/PReMod), will help analyze regulatory mechanisms in specific biological systems...
  27. pmc New insights into the biogenesis of nuclear RNA polymerases?
    Philippe Cloutier
    Laboratory of Gene Transcription and Proteomics, Institut de Recherches Cliniques de Montreal, 110 avenue des Pins Ouest, Montreal, QC H2W 1R7, Canada
    Biochem Cell Biol 88:211-21. 2010
    ..One of the RPAPs, RPAP3, is part of an 11-subunit complex we termed the RPAP3/R2TP/prefoldin-like complex. Here, we review the literature on the subunits of this complex, which points to a role in nuclear RNAP biogenesis...
  28. ncbi request reprint Defining protein interactions that regulate disease progression
    Racha Al-Khoury
    Institut de Recherches Cliniques de Montreal, Montreal Quebec, Canada
    Expert Opin Ther Targets 13:13-7. 2009
    ..We also discuss some success stories in the modulation of disease-related protein-protein interactions using small molecules...
  29. pmc Site-specific protein-DNA photocross-linking of purified complexes: topology of the RNA polymerase II transcription initiation complex
    Diane Forget
    Laboratory of Gene Transcription, Clinical Research Institute of Montreal, 110 Pine Avenue West, Montreal, Quebec H2W 1R7, Canada
    Methods Enzymol 370:701-12. 2003
  30. doi request reprint Increased subcutaneous adipose tissue expression of genes involved in glycerolipid-fatty acid cycling in obese insulin-resistant versus -sensitive individuals
    Marie Soleil Gauthier
    Institut de Recherches Cliniques de Montréal M S G, J R P, M E L, B C, R R L, Montreal, QC H2W 1R7, Canada Montreal Diabetes Research Center at the Centre de Recherche du Centre Hospitalier de l Université de Montréal CRCHUM M S G, M E L, R S, S R M M, M P, R R L, Montreal, QC H2X 0A9, Canada McGill University and Centre d Innovation Génome Québec R S, Montreal, QC H3A 0G1, Canada Molecular Nutrition Unit at the CRCHUM S R M M, M P, Montreal, QC H2X 0A9, Canada Diabetes and Metabolism Research Unit N B R, and Department of Medicine and Section of Endocrinology N B R, Boston University School of Medicine, Boston, Massachusetts 02118 Departments of Biochemistry B C, M P and Nutrition M E L, M P, R R L, Faculty of Medicine, Universite de Montreal, Montreal, QC H3C 3J7, Canada
    J Clin Endocrinol Metab 99:E2518-28. 2014
    ..Altered fatty-acid (FA) metabolism in sc adipose tissue (SAT) contributes to obesity-associated IR...
  31. pmc A human RNA polymerase II-containing complex associated with factors necessary for spliceosome assembly
    Francois Robert
    Laboratory of Gene Transcription, Institut de Recherches Cliniques de Montreal, 110 avenue des Pins Ouest, Montreal, Quebec H2W 1R7, Canada
    J Biol Chem 277:9302-6. 2002
    ....
  32. pmc USP8 regulates mitophagy by removing K6-linked ubiquitin conjugates from parkin
    Thomas M Durcan
    McGill Parkinson Program, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
    EMBO J 33:2473-91. 2014
    ..This work uncovers a novel role for USP8-mediated deubiquitination of K6-linked ubiquitin conjugates from parkin in mitochondrial quality control. ..
  33. pmc Regulation of molecular chaperones through post-translational modifications: decrypting the chaperone code
    Philippe Cloutier
    Institut de Recherches Cliniques de Montreal, Quebec, Canada
    Biochim Biophys Acta 1829:443-54. 2013
    ..This review surveys the core information currently available as a starting point toward the more ambitious endeavor of deciphering the "chaperone code"...
  34. pmc Ordered conformational changes in damaged DNA induced by nucleotide excision repair factors
    Angels Tapias
    Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS INSERM ULP, BP 10142, 67404 Illkirch Cedex, Communaute Urbaine de Strasbourg, France
    J Biol Chem 279:19074-83. 2004
    ..XPG and XPF/ERCC1 endonucleases then cut the damaged DNA at the limit of the opened structure that was previously "labeled" by the positioning of XPC/HR23B and TFIIH...