Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions.

Abstract:

:Transcription factors canonically bind nucleosome-free DNA, making the positioning of nucleosomes within regulatory regions crucial to the regulation of gene expression. Using the assay of transposase accessible chromatin (ATAC-seq), we observe a highly structured pattern of DNA fragment lengths and positions around nucleosomes in Saccharomyces cerevisiae, and use this distinctive two-dimensional nucleosomal "fingerprint" as the basis for a new nucleosome-positioning algorithm called NucleoATAC. We show that NucleoATAC can identify the rotational and translational positions of nucleosomes with up to base-pair resolution and provide quantitative measures of nucleosome occupancy in S. cerevisiae, Schizosaccharomyces pombe, and human cells. We demonstrate the application of NucleoATAC to a number of outstanding problems in chromatin biology, including analysis of sequence features underlying nucleosome positioning, promoter chromatin architecture across species, identification of transient changes in nucleosome occupancy and positioning during a dynamic cellular response, and integrated analysis of nucleosome occupancy and transcription factor binding.

journal_name

Genome Res

journal_title

Genome research

authors

Schep AN,Buenrostro JD,Denny SK,Schwartz K,Sherlock G,Greenleaf WJ

doi

10.1101/gr.192294.115

subject

Has Abstract

pub_date

2015-11-01 00:00:00

pages

1757-70

issue

11

eissn

1088-9051

issn

1549-5469

pii

gr.192294.115

journal_volume

25

pub_type

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