Genome-Wide Mapping of in Vivo Protein-DNA Interactions

TLDR

In vivo protein‑DNA interactions link each transcription factor to its direct targets, forming a gene‑network scaffold. The authors developed a large‑scale ChIP‑Seq assay using direct ultrahigh‑throughput DNA sequencing to comprehensively map protein‑DNA interactions across mammalian genomes. Using this method, they mapped NRSF binding to 1,946 sites in the human genome with ±50‑bp resolution, identified canonical and noncanonical motifs, achieved ROC ≥ 0.96 and P < 10⁻⁴, and revealed key transcription factors involved in pancreatic islet cell development.

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 &lt;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.