Interaction Networks of the Molecular Machines That Decode, Replicate, and Maintain the Integrity of the Human Genome *

The interaction of many proteins with genomic DNA is required for the expression, replication, and maintenance of the integrity of mammalian genomes. These proteins participate in processes as diverse as gene transcription and mRNA processing, as well as in DNA replication, recombination, and repair. This intricate system, where the various nuclear machineries interact with one another and bind to either common or distinct DNA regions to create an impressive network of protein-protein and protein-DNA interactions, is made even more complex by the need for a very stringent control in order to ensure normal cell growth and differentiation. A general methodology based on the in vivo pull-down of tagged components of nuclear machines and regulatory proteins was used to study genome-wide protein-protein and protein-DNA interactions in mammalian cells. In particular, this approach has been used in defining the interaction networks (or “interactome”) formed by RNA polymerase II, a molecular machine that decodes the human genome. In addition, because this methodology allows for the purification of variant forms of tagged complexes having site-directed mutations in key elements, it can also be used for deciphering the relationship between the structure and the function of the molecular machines, such as RNA polymerase II, that by binding DNA play a central role in the pathway from the genome to the organism.

[1]  T. Hughes,et al.  RPAP1, a Novel Human RNA Polymerase II-Associated Protein Affinity Purified with Recombinant Wild-Type and Mutated Polymerase Subunits , 2004, Molecular and Cellular Biology.

[2]  B. Coulombe,et al.  Photo-Cross-Linking of a Purified Preinitiation Complex Reveals Central Roles for the RNA Polymerase II Mobile Clamp and TFIIE in Initiation Mechanisms , 2004, Molecular and Cellular Biology.

[3]  N. Krogan,et al.  Transitions in RNA polymerase II elongation complexes at the 3′ ends of genes , 2004, The EMBO journal.

[4]  M. Gerstein,et al.  A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data , 2003, Science.

[5]  P. Cramer,et al.  Architecture of the RNA Polymerase II-TFIIS Complex and Implications for mRNA Cleavage , 2003, Cell.

[6]  I. Simon,et al.  Systematic analysis of essential yeast TAFs in genome‐wide transcription and preinitiation complex assembly , 2003, The EMBO journal.

[7]  Roger D Kornberg,et al.  Complete, 12-subunit RNA polymerase II at 4.1-Å resolution: Implications for the initiation of transcription , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[8]  D. Reinberg,et al.  FCP 1 , a Phosphatase Specific for the Heptapeptide Repeat of the Largest Subunit of RNA Polymerase II , Stimulates Transcription Elongation , 2002 .

[9]  Nicola J. Rinaldi,et al.  Supporting online material for : Transcriptional Regulatory Networks in Saccharomyces cerevisiae , 2002 .

[10]  Mark Gerstein,et al.  Bridging structural biology and genomics: assessing protein interaction data with known complexes. , 2002, Drug discovery today.

[11]  G. Cagney,et al.  RNA Polymerase II Elongation Factors of Saccharomyces cerevisiae: a Targeted Proteomics Approach , 2002, Molecular and Cellular Biology.

[12]  B. Snel,et al.  Comparative assessment of large-scale data sets of protein–protein interactions , 2002, Nature.

[13]  Gary D Bader,et al.  Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.

[14]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[15]  B. Séraphin,et al.  The tandem affinity purification (TAP) method: a general procedure of protein complex purification. , 2001, Methods.

[16]  P. Cramer,et al.  Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution , 2001, Science.

[17]  R. Ozawa,et al.  A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[18]  V. Orlando,et al.  Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation. , 2000, Trends in biochemical sciences.

[19]  James R. Knight,et al.  A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.

[20]  C. Peterson,et al.  Transcriptional Regulation in Eukaryotes: Concepts, Strategies and Techniques , 2000 .

[21]  B. Séraphin,et al.  A generic protein purification method for protein complex characterization and proteome exploration , 1999, Nature Biotechnology.

[22]  B. Coulombe,et al.  DNA Bending and Wrapping around RNA Polymerase: a “Revolutionary” Model Describing Transcriptional Mechanisms , 1999, Microbiology and Molecular Biology Reviews.

[23]  Michael R. Green,et al.  Dissecting the Regulatory Circuitry of a Eukaryotic Genome , 1998, Cell.

[24]  J. Greenblatt,et al.  FCP1, the RAP74-Interacting Subunit of a Human Protein Phosphatase That Dephosphorylates the Carboxyl-terminal Domain of RNA Polymerase IIO* , 1998, The Journal of Biological Chemistry.

[25]  F. Robert,et al.  Wrapping of promoter DNA around the RNA polymerase II initiation complex induced by TFIIF. , 1998, Molecular cell.

[26]  Michael Hampsey,et al.  Molecular Genetics of the RNA Polymerase II General Transcriptional Machinery , 1998, Microbiology and Molecular Biology Reviews.

[27]  F. Robert,et al.  RAP74 induces promoter contacts by RNA polymerase II upstream and downstream of a DNA bend centered on the TATA box. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[28]  T Lagrange,et al.  The general transcription factors of RNA polymerase II. , 1996, Genes & development.

[29]  K. Struhl,et al.  TBP-associated factors are not generally required for transcriptional activation in yeast , 1996, Nature.

[30]  S. Fields,et al.  Protein-protein interactions: methods for detection and analysis , 1995, Microbiological reviews.

[31]  S. Fields,et al.  A novel genetic system to detect protein–protein interactions , 1989, Nature.

[32]  John J. Wyrick,et al.  Genome-wide location and function of DNA binding proteins. , 2000, Science.

[33]  R. Young,et al.  RNA polymerase II. , 1991, Annual review of biochemistry.