Genome-wide mapping of in vivo protein-DNA interactions.
In vivo protein-DNA interactions connect each transcription factor with its direct targets to form a gene network scaffold. To map these protein-DNA interactions comprehensively across entire mammalian genomes, we developed a large-scale chromatin immunoprecipitation assay (ChIPSeq) based on direct ultrahigh-throughput DNA sequencing. This sequence census method was then used to map in vivo binding of the neuron-restrictive silencer factor (NRSF; also known as REST, for repressor element-1 silencing transcription factor) to 1946 locations in the human genome. The data display sharp resolution of binding position [+/-50 base pairs (bp)], which facilitated our finding motifs and allowed us to identify noncanonical NRSF-binding motifs. These ChIPSeq data also have high sensitivity and specificity [ROC (receiver operator characteristic) area >/= 0.96] and statistical confidence (P <10(-4)), properties that were important for inferring new candidate interactions. These include key transcription factors in the gene network that regulates pancreatic islet cell development.
Johnson
David S
DS
Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305-5120, USA.
Mortazavi
Ali
A
Myers
Richard M
RM
Wold
Barbara
B
D000465:Algorithms; D020816:Amino Acid Motifs; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D053263:Gene Regulatory Networks; D015894:Genome, Human; D006801:Humans; D050417:Insulin-Secreting Cells / Q000166:cytology / Q000502:physiology; D035683:MicroRNAs / Q000235:genetics; D009474:Neurons / Q000502:physiology; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D012097:Repressor Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D009435:Synaptic Transmission; D013601:T-Lymphocytes / Q000378:metabolism; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic; D016335:Zinc Fingers; D000099229:RE1-Silencing Transcription Factor
D004247:DNA; D004268:DNA-Binding Proteins; D035683:MicroRNAs; D012097:Repressor Proteins; D014157:Transcription Factors; D000099229:RE1-Silencing Transcription Factor