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However, existing methods for cis-regulatory network reconstruction using single-cell chromatin accessibility data were only designed for cells belonging to one cell type, and resulting networks may be incomparable directly due to diverse cell numbers of different cell types. Here, we adopt a computational method to jointly reconstruct cis-regulatory interaction maps (JRIM) of multiple cell populations based on patterns of co-accessibility in single-cell data. We applied JRIM to explore common and specific regulatory interactions across multiple tissues from single-cell ATAC-seq dataset containing ~80\u00a0000 cells across 13 mouse tissues. Reconstructed common interactions among 13 tissues indeed relate to basic biological functions, and individual cis-regulatory networks show strong tissue specificity and functional relevance. More importantly, tissue-specific regulatory interactions are mediated by coordination of histone modifications and tissue-related TFs, and many of them may reveal novel regulatory mechanisms.<\/jats:p>","DOI":"10.1093\/bib\/bbaa120","type":"journal-article","created":{"date-parts":[[2020,5,23]],"date-time":"2020-05-23T15:10:17Z","timestamp":1590246617000},"source":"Crossref","is-referenced-by-count":11,"title":["Joint reconstruction of\n                    <i>cis<\/i>\n                    -regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data"],"prefix":"10.1093","volume":"22","author":[{"given":"Kangning","family":"Dong","sequence":"first","affiliation":[{"name":"Academy of Mathematics and Systems Science, Chinese Academy of Sciences"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shihua","family":"Zhang","sequence":"additional","affiliation":[{"name":"Academy of Mathematics and Systems Science, Chinese Academy of Sciences"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,6,24]]},"reference":[{"key":"2021052110032824000_ref1","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nrg3095","article-title":"Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence","volume":"13","author":"Wittkopp","year":"2012","journal-title":"Nat Rev Genet"},{"key":"2021052110032824000_ref2","doi-asserted-by":"crossref","first-page":"12380","DOI":"10.1093\/nar\/gku923","article-title":"Profiling the transcription factor regulatory networks of human cell types","volume":"42","author":"Zhang","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2021052110032824000_ref3","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/nmeth.1906","article-title":"ChromHMM: automating chromatin-state discovery and characterization","volume":"9","author":"Ernst","year":"2012","journal-title":"Nat Methods"},{"key":"2021052110032824000_ref4","doi-asserted-by":"crossref","first-page":"9230","DOI":"10.1093\/nar\/gkt712","article-title":"Discovery of cell-type specific regulatory elements in the human genome using differential chromatin modification analysis","volume":"41","author":"Chen","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2021052110032824000_ref5","doi-asserted-by":"crossref","first-page":"4374","DOI":"10.1093\/hmg\/ddv172","article-title":"Systematic DNA methylation analysis of multiple cell lines reveals common and specific patterns within and across tissues of origin","volume":"24","author":"Yang","year":"2015","journal-title":"Hum Mol Genet"},{"key":"2021052110032824000_ref6","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1093\/jmcb\/mjx058","article-title":"Large-scale determination and characterization of cell type-specific regulatory elements in the human genome","volume":"9","author":"Wang","year":"2017","journal-title":"J Mol Cell Biol"},{"key":"2021052110032824000_ref7","doi-asserted-by":"crossref","first-page":"2583","DOI":"10.1101\/gad.1026202","article-title":"The RNA polymerase II core promoter: a key component in the regulation of gene expression","volume":"16","author":"Butler","year":"2002","journal-title":"Genes Dev"},{"key":"2021052110032824000_ref8","doi-asserted-by":"crossref","first-page":"1291","DOI":"10.1083\/jcb.141.6.1291","article-title":"Different cis-regulatory DNA elements mediate developmental stage-and tissue-specific expression of the human COL2A1 gene in transgenic mice. 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