Protein-DNA binding in high-resolution

Shaun Mahony, B. Franklin Pugh

Research output: Contribution to journalReview articlepeer-review

34 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)269-283
Number of pages15
JournalCritical Reviews in Biochemistry and Molecular Biology
Issue number4
StatePublished - Jul 4 2015

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology


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