title: Mapping accessible chromatin regions using Sono-Seq.
abstract: 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.
authors.affiliation: Program in Computational Biology, Yale University, New Haven, CT 06520, USA.
authors.forename: Raymond K
authors.initials: RK
authors.lastname: Auerbach
authors.forename: Ghia
authors.initials: G
authors.lastname: Euskirchen
authors.forename: Joel
authors.initials: J
authors.lastname: Rozowsky
authors.forename: Nathan
authors.initials: N
authors.lastname: Lamarre-Vincent
authors.forename: Zarmik
authors.initials: Z
authors.lastname: Moqtaderi
authors.forename: Philippe
authors.initials: P
authors.lastname: Lefrançois
authors.forename: Kevin
authors.initials: K
authors.lastname: Struhl
authors.forename: Mark
authors.initials: M
authors.lastname: Gerstein
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
mesh_terms: D000818:Animals; D001483:Base Sequence; D002843:Chromatin; D002874:Chromosome Mapping / Q000379:methods*; D015870:Gene Expression; D005819:Genetic Markers; D006367:HeLa Cells; D006657:Histones / Q000378:metabolism; D006801:Humans; D008745:Methylation; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D002843:Chromatin; D005819:Genetic Markers; D006657:Histones
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