Journal
NATURE METHODS
Volume 10, Issue 12, Pages 1213-+Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/NMETH.2688
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Funding
- US National Institutes of Health [RC4NS073015, U01DK089532, U19AI057229]
- Scleroderma Research Foundation
- California Institute for Regenerative Medicine
- Howard Hughes Medical Institute
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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 nucleosomes. 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.
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