title: 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.
authors: Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA;
authors: Alicia N
authors: AN
authors: Schep
authors: Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA;
authors: Jason D
authors: JD
authors: Buenrostro
authors: Biophysics Program, Stanford University School of Medicine, Stanford, California 94305, USA;
authors: Sarah K
authors: SK
authors: Denny
authors: Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA;
authors: Katja
authors: K
authors: Schwartz
authors: Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA;
authors: Gavin
authors: G
authors: Sherlock
authors: Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Applied Physics, Stanford University, Stanford, California 94305, USA.
authors: William J
authors: WJ
authors: Greenleaf
mesh_terms: D002460:Cell Line; D002843:Chromatin / Q000737:chemistry*; D042002:Chromatin Assembly and Disassembly; D002874:Chromosome Mapping; D004271:DNA, Fungal / Q000235:genetics; D030541:Databases, Genetic; D015321:Gene Rearrangement; D006801:Humans; D009707:Nucleosomes / Q000235:genetics* / Q000378:metabolism; D011401:Promoter Regions, Genetic; D012045:Regulatory Sequences, Nucleic Acid; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D012568:Schizosaccharomyces / Q000235:genetics; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D004271:DNA, Fungal; D009707:Nucleosomes; D014157:Transcription Factors