Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme.
We have performed a survey of soluble human protein complexes containing components of the transcription and RNA processing machineries using protein affinity purification coupled to mass spectrometry. Thirty-two tagged polypeptides yielded a network of 805 high-confidence interactions. Remarkably, the network is significantly enriched in proteins that regulate the formation of protein complexes, including a number of previously uncharacterized proteins for which we have inferred functions. The RNA polymerase II (RNAP II)-associated proteins (RPAPs) are physically and functionally associated with RNAP II, forming an interface between the enzyme and chaperone/scaffolding proteins. BCDIN3 is the 7SK snRNA methylphosphate capping enzyme (MePCE) present in an snRNP complex containing both RNA processing and transcription factors, including the elongation factor P-TEFb. Our results define a high-density protein interaction network for the mammalian transcription machinery and uncover multiple regulatory factors that target the transcription machinery.
Jeronimo
Célia
C
Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada.
Forget
Diane
D
Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada.
Bouchard
Annie
A
Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada.
Li
Qintong
Q
Biochemistry Department, University of Iowa, Iowa City, IA 52242-1109, USA.
Chua
Gordon
G
Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5G 1L6, Canada.
Poitras
Christian
C
Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada.
Thérien
Cynthia
C
Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada.
Bergeron
Dominique
D
Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada.
Bourassa
Sylvie
S
Centre hospitalier universitaire de Québec, Université Laval, Québec, QC G1V 4G2, Canada.
Greenblatt
Jack
J
Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5G 1L6, Canada.
Chabot
Benoit
B
Département de microbiologie et infectiologie, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada.
Poirier
Guy G
GG
Centre hospitalier universitaire de Québec, Université Laval, Québec, QC G1V 4G2, Canada.
Hughes
Timothy R
TR
Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5G 1L6, Canada.
Blanchette
Mathieu
M
McGill Centre for Bioinformatics, McGill University, Montréal, QC H3A 2B4, Canada.
Price
David H
DH
Biochemistry Department, University of Iowa, Iowa City, IA 52242-1109, USA.
Coulombe
Benoit
B
Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada. Electronic address: benoit.coulombe@ircm.qc.ca.
D000595:Amino Acid Sequence; D002352:Carrier Proteins / Q000737:chemistry / Q000378:metabolism; D002460:Cell Line; D006801:Humans; D066298:In Vitro Techniques; D046911:Macromolecular Substances; D008969:Molecular Sequence Data; D009713:Nucleotidyltransferases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D025941:Protein Interaction Mapping; D034622:RNA Interference; D012319:RNA Polymerase II / Q000737:chemistry / Q000378:metabolism; D012323:RNA Processing, Post-Transcriptional; D017411:Ribonucleoproteins, Small Nuclear / Q000737:chemistry / Q000378:metabolism; D014158:Transcription, Genetic; D000098556:mRNA Guanylyltransferases
D002352:Carrier Proteins; D046911:Macromolecular Substances; D017411:Ribonucleoproteins, Small Nuclear; D009713:Nucleotidyltransferases; D012319:RNA Polymerase II; D000098556:mRNA Guanylyltransferases