@article{Schep01112015,
author = {Schep, Alicia N. and Buenrostro, Jason D. and Denny, Sarah K. and Schwartz, Katja and Sherlock, Gavin and Greenleaf, William J.}, 
title = {Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions},
volume = {25}, 
number = {11}, 
pages = {1757-1770}, 
year = {2015}, 
doi = {10.1101/gr.192294.115}, 
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.}, 
URL = {http://genome.cshlp.org/content/25/11/1757.abstract}, 
eprint = {http://genome.cshlp.org/content/25/11/1757.full.pdf+html}, 
journal = {Genome Research} 
}