title: Transcriptional regulatory code of a eukaryotic genome.
abstract: DNA-binding transcriptional regulators interpret the genome's regulatory code by binding to specific sequences to induce or repress gene expression. Comparative genomics has recently been used to identify potential cis-regulatory sequences within the yeast genome on the basis of phylogenetic conservation, but this information alone does not reveal if or when transcriptional regulators occupy these binding sites. We have constructed an initial map of yeast's transcriptional regulatory code by identifying the sequence elements that are bound by regulators under various conditions and that are conserved among Saccharomyces species. The organization of regulatory elements in promoters and the environment-dependent use of these elements by regulators are discussed. We find that environment-specific use of regulatory elements predicts mechanistic models for the function of a large population of yeast's transcriptional regulators.
authors.affiliation: Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA.
authors.forename: Christopher T
authors.initials: CT
authors.lastname: Harbison
authors.forename: D Benjamin
authors.initials: DB
authors.lastname: Gordon
authors.forename: Tong Ihn
authors.initials: TI
authors.lastname: Lee
authors.forename: Nicola J
authors.initials: NJ
authors.lastname: Rinaldi
authors.forename: Kenzie D
authors.initials: KD
authors.lastname: Macisaac
authors.forename: Timothy W
authors.initials: TW
authors.lastname: Danford
authors.forename: Nancy M
authors.initials: NM
authors.lastname: Hannett
authors.forename: Jean-Bosco
authors.initials: JB
authors.lastname: Tagne
authors.forename: David B
authors.initials: DB
authors.lastname: Reynolds
authors.forename: Jane
authors.initials: J
authors.lastname: Yoo
authors.forename: Ezra G
authors.initials: EG
authors.lastname: Jennings
authors.forename: Julia
authors.initials: J
authors.lastname: Zeitlinger
authors.forename: Dmitry K
authors.initials: DK
authors.lastname: Pokholok
authors.forename: Manolis
authors.initials: M
authors.lastname: Kellis
authors.forename: P Alex
authors.initials: PA
authors.lastname: Rolfe
authors.forename: Ken T
authors.initials: KT
authors.lastname: Takusagawa
authors.forename: Eric S
authors.initials: ES
authors.lastname: Lander
authors.forename: David K
authors.initials: DK
authors.lastname: Gifford
authors.forename: Ernest
authors.initials: E
authors.lastname: Fraenkel
authors.forename: Richard A
authors.initials: RA
authors.lastname: Young
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D017124:Conserved Sequence / Q000235:genetics; D005057:Eukaryotic Cells / Q000378:metabolism; D016681:Genome, Fungal; D011401:Promoter Regions, Genetic / Q000235:genetics; D020218:Response Elements / Q000235:genetics*; D012440:Saccharomyces / Q000145:classification / Q000235:genetics*; D013379:Substrate Specificity; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D014157:Transcription Factors