Format

Send to

Choose Destination
Crit Rev Biochem Mol Biol. 2015;50(4):269-83. doi: 10.3109/10409238.2015.1051505. Epub 2015 Jun 3.

Protein-DNA binding in high-resolution.

Author information

1
a Department of Biochemistry & Molecular Biology , Center for Eukaryotic Gene Regulation, The Pennsylvania State University , University Park , PA , USA.

Abstract

Recent advances in experimental and computational methodologies are enabling ultra-high resolution genome-wide profiles of protein-DNA binding events. For example, the ChIP-exo protocol precisely characterizes protein-DNA cross-linking patterns by combining chromatin immunoprecipitation (ChIP) with 5' → 3' exonuclease digestion. Similarly, deeply sequenced chromatin accessibility assays (e.g. DNase-seq and ATAC-seq) enable the detection of protected footprints at protein-DNA binding sites. With these techniques and others, we have the potential to characterize the individual nucleotides that interact with transcription factors, nucleosomes, RNA polymerases and other regulatory proteins in a particular cellular context. In this review, we explain the experimental assays and computational analysis methods that enable high-resolution profiling of protein-DNA binding events. We discuss the challenges and opportunities associated with such approaches.

KEYWORDS:

ChIP-exo; ChIP-seq; DNase-seq; high-resolution; protein–DNA binding; transcription factor binding

PMID:
26038153
PMCID:
PMC4580520
DOI:
10.3109/10409238.2015.1051505
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Taylor & Francis Icon for PubMed Central
Loading ...
Support Center