title: Mapping of protein-protein interactions of E. coli RNA polymerase with microfluidic mechanical trapping.
abstract: The biophysical details of how transcription factors and other proteins interact with RNA polymerase are of great interest as they represent the nexus of how structure and function interact to regulate gene expression in the cell. We used an in vitro microfluidic approach to map interactions between a set of ninety proteins, over a third of which are transcription factors, and each of the four subunits of E. coli RNA polymerase, and we compared our results to those of previous large-scale studies. We detected interactions between RNA polymerase and transcription factors that earlier high-throughput screens missed; our results suggest that such interactions can occur without DNA mediation more commonly than previously appreciated.
authors.affiliation: Department of Applied Physics, Stanford University, Stanford, California, United States of America.
authors.forename: Steven R
authors.initials: SR
authors.lastname: Bates
authors.affiliation: Department of Applied Physics, Stanford University, Stanford, California, United States of America; Department of Bioengineering and HHMI, Stanford University, Stanford, California, United States of America.
authors.forename: Stephen R
authors.initials: SR
authors.lastname: Quake
mesh_terms: D012321:DNA-Directed RNA Polymerases / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D046210:Microfluidic Analytical Techniques; D058977:Molecular Sequence Annotation; D025941:Protein Interaction Mapping; D060066:Protein Interaction Maps; D021122:Protein Subunits / Q000235:genetics / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D029968:Escherichia coli Proteins; D021122:Protein Subunits; D014157:Transcription Factors; D012321:DNA-Directed RNA Polymerases