Mapping accessible chromatin regions using Sono-Seq

被引:136
作者
Auerbach, Raymond K. [1 ]
Euskirchen, Ghia [2 ]
Rozowsky, Joel [3 ]
Lamarre-Vincent, Nathan [4 ]
Moqtaderi, Zarmik [4 ]
Lefrancois, Philippe [2 ]
Struhl, Kevin [4 ]
Gerstein, Mark [1 ,3 ]
Snyder, Michael [1 ,2 ]
机构
[1] Yale Univ, Program Computat Biol, New Haven, CT 06520 USA
[2] Yale Univ, Dept Mol Cellular & Dev Biol, New Haven, CT 06520 USA
[3] Yale Univ, Dept Mol Biophys & Biochem, New Haven, CT 06520 USA
[4] Harvard Univ, Sch Med, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA
基金
美国国家卫生研究院;
关键词
ChIP-Seq; ENCODE; formaldehyde cross-linking; sonication; DNA sequencing; GENOME-WIDE ANALYSIS; BINDING-SITES; TRANSCRIPTION; CHIP; EXPRESSION;
D O I
10.1073/pnas.0905443106
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
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.
引用
收藏
页码:14926 / 14931
页数:6
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