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

Genome Res. 2015 Nov;25(11):1757-70. doi: 10.1101/gr.192294.115. Epub 2015 Aug 27.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Cell Line
  • Chromatin / chemistry*
  • Chromatin Assembly and Disassembly
  • Chromosome Mapping*
  • DNA, Fungal / genetics
  • Databases, Genetic
  • Gene Rearrangement
  • Humans
  • Nucleosomes / genetics*
  • Nucleosomes / metabolism
  • Promoter Regions, Genetic
  • Regulatory Sequences, Nucleic Acid*
  • Saccharomyces cerevisiae / genetics*
  • Schizosaccharomyces / genetics
  • Sequence Analysis, DNA
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Transcription, Genetic

Substances

  • Chromatin
  • DNA, Fungal
  • Nucleosomes
  • Transcription Factors

Associated data

  • GEO/GSE66386