Mapping accessible chromatin regions using Sono-Seq

Raymond K. Auerbach

doi:10.1073/pnas.0905443106

Mapping accessible chromatin regions using Sono-Seq

2009-09-01

185

OA

AI

Nathan Lamarre-Vincent

DOI：10.1073/pnas.0905443106

原文链接

查看原文

摘要

En 中文

Disruptions in local chromatin structure often indicate features of biological interest such as regulatory regions. We find that sonication of cross-linked chromatin, when combined with a size-selection step and massively parallel short-read 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; signals over other sites, such as those bound by the CTCF insulator, are also observed. The pattern of breakage by Sono-Seq overlaps with, but is distinct from, that observed for FAIRE and DNase I hypersensitive sites. Our results demonstrate that Sono-Seq can be a useful and simple method by which to map many local alterations in chromatin structure. Furthermore, our results provide insights into the mapping of binding sites by using ChIP-Seq experiments and the value of reference samples that should be used in such experiments.

Keyword:

ChIP-Seq

ENCODE

formaldehyde cross-linking

sonication

DNA sequencing

Mapping accessible chromatin regions using Sono-Seq

摘要

AI总结

期刊

机构