Genomics

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Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position


ABSTRACT: We describe an assay for transposase-accessible chromatin using sequencing (ATAC-seq), based on direct in vitro transposition of sequencing adaptors into native chromatin, as a rapid and sensitive method for integrative epigenomic analysis. ATAC-seq captures open chromatin sites using a simple two-step protocol with 500–50,000 cells and reveals the interplay between genomic locations of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution. We discovered classes of DNA-binding factors that strictly avoided, could tolerate or tended to overlap with the nucleosome. Using ATAC-seq maps of human CD4+ T cells from a proband obtained on consecutive days, we demonstrated the feasibility of analyzing an individual’s epigenome on a timescale compatible with clinical decision-making. We examined chromatin structure using ATAC-seq in 2 cell types (GM12878 cell line, purified CD4+ T cells).

ORGANISM(S): Homo sapiens  

SUBMITTER: Jason D Buenrostro   Lisa C Zaba  Howard Y Chang  Paul G Giresi  William J Greenleaf 

PROVIDER: E-GEOD-47753 | ArrayExpress | 2013-10-01

SECONDARY ACCESSION(S): GSE47753SRP024293PRJNA207663

REPOSITORIES: GEO, ArrayExpress, ENA

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