Abstract

Disruptions in local chromatin structure often indicate features of biological interest such as regulatory regions. We find that sonication of crosslinked chromatin when combined with a size selection step and massively parallel sequencing can be used as a method (Sono-Seq) to map locations of high chromatin accessibility in promoter regions. Sono-Seq sites frequently correspond to actively transcribed promoter regions as evidenced by their co-association with RNA Polymerase II ChIP regions, transcription start sites, histone H3 lysine 4 trimethylation (H3K4me3) marks, and CpG islands. The pattern of breakage by Sono-Seq overlaps with, but is distinct from, that observed for FAIRE and DNase hypersensitive sites. Our results demonstrate that Sono-Seq can be a useful and simple method for mapping many local alterations in chromatin structure. Furthermore, our results provide insights into the mapping of binding sites using ChIP-Seq experiments and the value of reference samples that should be used in such experiments.