Genome-wide mapping of in vivo protein-DNA interactions

Science. 2007 Jun 8;316(5830):1497-502. doi: 10.1126/science.1141319. Epub 2007 May 31.

Abstract

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Motifs
  • Binding Sites
  • Chromatin Immunoprecipitation*
  • DNA / metabolism*
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism*
  • Gene Regulatory Networks
  • Genome, Human*
  • Humans
  • Insulin-Secreting Cells / cytology
  • Insulin-Secreting Cells / physiology
  • MicroRNAs / genetics
  • Neurons / physiology
  • Promoter Regions, Genetic
  • Protein Binding
  • Repressor Proteins / chemistry
  • Repressor Proteins / genetics
  • Repressor Proteins / metabolism*
  • Sensitivity and Specificity
  • Sequence Analysis, DNA*
  • Synaptic Transmission
  • T-Lymphocytes / metabolism
  • Transcription Factors / chemistry
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*
  • Transcription, Genetic
  • Zinc Fingers

Substances

  • DNA-Binding Proteins
  • MicroRNAs
  • RE1-silencing transcription factor
  • Repressor Proteins
  • Transcription Factors
  • DNA