Transcriptional regulatory code of a eukaryotic genome.
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.
Harbison
Christopher T
CT
Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA.
Gordon
D Benjamin
DB
Lee
Tong Ihn
TI
Rinaldi
Nicola J
NJ
Macisaac
Kenzie D
KD
Danford
Timothy W
TW
Hannett
Nancy M
NM
Tagne
Jean-Bosco
JB
Reynolds
David B
DB
Yoo
Jane
J
Jennings
Ezra G
EG
Zeitlinger
Julia
J
Pokholok
Dmitry K
DK
Kellis
Manolis
M
Rolfe
P Alex
PA
Takusagawa
Ken T
KT
Lander
Eric S
ES
Gifford
David K
DK
Fraenkel
Ernest
E
Young
Richard A
RA
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*
D014157:Transcription Factors