Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

Abstract

SUMMARY Chromatin immunoprecipitation (ChIP-chip and ChIP-seq) assays identify where proteins bind throughout a genome. However, DNA contamination and DNA fragmentation heterogeneity produce false positives (erroneous calls) and imprecision in mapping. Consequently, stringent data filtering produces false negatives (missed calls). Here we describe ChIP-exo, where an exonuclease trims ChIP DNA to a precise distance from the crosslinking site. Bound locations are detectable as peak-pairs by deep sequencing. Contaminating DNA is degraded or fails to form complementary peak-pairs. With the single bp accuracy provided by ChIP-exo, we show an unprecedented view into genome-wide binding of the yeast transcription factors Reb1, Gal4, Phd1, Rap1, and human CTCF. Each of these factors was chosen to address potential limitations of ChIP-exo. We found that binding sites become unambiguous and reveal diverse tendencies governing in vivo DNA binding specificity that include sequence variants, functionally distinct motifs, motif clustering, secondary interactions, and combinatorial modules within a compound motif.

Role of CCCTC binding factor (CTCF) and cohesin in the generation of single-cell diversity of Protocadherin-α gene expression

“…S1). These flanking sequences are similar to motifs that have been identified flanking CTCF sites genome-wide, which are thought to be additional sites of contact between DNA and CTCF (18,19).…”

Genome-wide identification of Bacillus subtilis CodY-binding sites at single-nucleotide resolution

“…Another single-nucleotide approach, ChIP-exo, has been described to analyze protein-DNA interactions in vivo (35). We predict that our approach can be used to identify precisely the DNA-binding sites of other proteins and can be especially useful for analysis of global regulators.…”

Uniform, optimal signal processing of mapped deep-sequencing data

“…Importantly, DFilter extends seamlessly to optimal integrative analysis of multiple data sets, as we demonstrated by combining DNase-seq and FAIRE-seq data to detect open chromatin. DFilter should also be applicable to other signal detection problems, such as Sono-seq, CLIP-seq and ChIP-exo 1, 45,46 .…”