title: General transcription factor specified global gene regulation in archaea.
abstract: Cells responding to dramatic environmental changes or undergoing a developmental switch typically change the expression of numerous genes. In bacteria, sigma factors regulate much of this process, whereas in eukaryotes, four RNA polymerases and a multiplicity of generalized transcription factors (GTFs) are required. Here, by using a systems approach, we provide experimental evidence (including protein-coimmunoprecipitation, ChIP-Chip, GTF perturbation and knockout, and measurement of transcriptional changes in these genetically perturbed strains) for how archaea likely accomplish similar large-scale transcriptional segregation and modulation of physiological functions. We are able to associate GTFs to nearly half of all putative promoters and show evidence for at least 7 of the possible 42 functional GTF pairs. This report represents a significant contribution toward closing the gap in our understanding of gene regulation by GTFs for all three domains of life and provides an example for how to use various experimental techniques to rapidly learn significant portions of a global gene regulatory network of organisms for which little has been previously known.
authors.affiliation: Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98121, USA.
authors.forename: Marc T
authors.initials: MT
authors.lastname: Facciotti
authors.forename: David J
authors.initials: DJ
authors.lastname: Reiss
authors.forename: Min
authors.initials: M
authors.lastname: Pan
authors.forename: Amardeep
authors.initials: A
authors.lastname: Kaur
authors.forename: Madhavi
authors.initials: M
authors.lastname: Vuthoori
authors.forename: Richard
authors.initials: R
authors.lastname: Bonneau
authors.forename: Paul
authors.initials: P
authors.lastname: Shannon
authors.forename: Alok
authors.initials: A
authors.lastname: Srivastava
authors.forename: Samuel M
authors.initials: SM
authors.lastname: Donohoe
authors.forename: Leroy E
authors.initials: LE
authors.lastname: Hood
authors.forename: Nitin S
authors.initials: NS
authors.lastname: Baliga
mesh_terms: D000818:Animals; D001105:Archaea; D047369:Chromatin Immunoprecipitation; D019143:Evolution, Molecular; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D005821:Genetic Techniques; D008954:Models, Biological; D010802:Phylogeny; D010957:Plasmids / Q000378:metabolism; D011401:Promoter Regions, Genetic; D025941:Protein Interaction Mapping; D012333:RNA, Messenger / Q000378:metabolism; D035165:Transcription Factors, General / Q000096:biosynthesis*; D014158:Transcription, Genetic
chemical_list: D012333:RNA, Messenger; D035165:Transcription Factors, General