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Thanks to its rather simple protocol, assay for transposase-accessible chromatin using sequencing (ATAC)-seq has been rapidly adopted as a major tool for chromatin-accessible profiling at both bulk and single-cell levels; however, to picture the arrangement of nucleosomes per se remains a challenge with ATAC-seq. In the present work, we introduce a novel ATAC-seq analysis toolkit, named decoding nucleosome organization profile based on ATAC-seq data (deNOPA), to predict nucleosome positions. Assessments showed that deNOPA outperformed state-of-the-art tools with ultra-sparse ATAC-seq data, e.g. no more than 0.5 fragment per base pair. The remarkable performance of deNOPA was fueled by the short fragment reads, which compose nearly half of sequenced reads in the ATAC-seq libraries and are commonly discarded by state-of-the-art nucleosome positioning tools. However, we found that the short fragment reads enrich information on nucleosome positions and that the linker regions were predicted by reads from both short and long fragments using Gaussian smoothing. Last, using deNOPA, we showed that the dynamics of nucleosome organization may not directly couple with chromatin accessibility in the cis-regulatory regions when human cells respond to heat shock stimulation. Our deNOPA provides a powerful tool with which to analyze the dynamics of chromatin at nucleosome position level with ultra-sparse ATAC-seq data.<\/jats:p>","DOI":"10.1093\/bib\/bbab469","type":"journal-article","created":{"date-parts":[[2021,10,16]],"date-time":"2021-10-16T03:54:31Z","timestamp":1634356471000},"source":"Crossref","is-referenced-by-count":7,"title":["DeNOPA: decoding nucleosome positions sensitively with sparse ATAC-seq data"],"prefix":"10.1093","volume":"23","author":[{"given":"Bingxiang","family":"Xu","sequence":"first","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China"},{"name":"School of Life Science, University of Chinese Academy of Sciences, Beijing, P.R. China"},{"name":"School of Kinesiology, Shanghai University of Sport, Shanghai, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoli","family":"Li","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China"},{"name":"School of Life Science, University of Chinese Academy of Sciences, Beijing, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaomeng","family":"Gao","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China"},{"name":"School of Life Science, University of Chinese Academy of Sciences, Beijing, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yan","family":"Jia","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jing","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Feifei","family":"Li","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7706-9247","authenticated-orcid":false,"given":"Zhihua","family":"Zhang","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China"},{"name":"School of Life Science, University of Chinese Academy of Sciences, Beijing, P.R. China"},{"name":"School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, P.R. 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