{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T17:50:33Z","timestamp":1760205033400,"version":"3.40.4"},"reference-count":55,"publisher":"S. Karger AG","issue":"1","license":[{"start":{"date-parts":[[2019,1,1]],"date-time":"2019-01-01T00:00:00Z","timestamp":1546300800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/karger.com\/pages\/terms-and-conditions"},{"start":{"date-parts":[[2019,1,1]],"date-time":"2019-01-01T00:00:00Z","timestamp":1546300800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/karger.com\/pages\/terms-and-conditions"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cytogenet Genome Res"],"published-print":{"date-parts":[[2019]]},"abstract":"<jats:p>The switch\/sucrose non-fermenting (SWI\/SNF) complex is an ATP-dependent chromatin remodeller that regulates the spacing of nucleosomes and thereby controls gene expression. Heterozygous mutations in genes encoding subunits of the SWI\/SNF complex have been reported in individuals with Coffin-Siris syndrome (CSS), with the majority of the mutations in ARID1B. CSS is a rare congenital disorder characterized by facial dysmorphisms, digital anomalies, and variable intellectual disability. We hypothesized that mutations in genes encoding subunits of the ubiquitously expressed SWI\/SNF complex may lead to alterations of the nucleosome profiles in different cell types. We performed the first study on CSS-patient samples and investigated the nucleosome landscapes of cell-free DNA (cfDNA) isolated from blood plasma by whole-genome sequencing. In addition, we studied the nucleosome landscapes of CD14+ monocytes from CSS-affected individuals by nucleosome occupancy and methylome-sequencing (NOMe-seq) as well as their expression profiles. In cfDNA of CSS-affected individuals with heterozygous ARID1B mutations, we did not observe major changes in the nucleosome profile around transcription start sites. In CD14+ monocytes, we found few genomic regions with different nucleosome occupancy when compared to controls. RNA-seq analysis of CD14+ monocytes of these individuals detected only few differentially expressed genes, which were not in proximity to any of the identified differential nucleosome-depleted regions. In conclusion, we show that heterozygous mutations in the human SWI\/SNF subunit ARID1B do not have a major impact on the nucleosome landscape or gene expression in blood cells. This might be due to functional redundancy, cell-type specificity, or alternative functions of ARID1B.<\/jats:p>","DOI":"10.1159\/000503266","type":"journal-article","created":{"date-parts":[[2019,10,28]],"date-time":"2019-10-28T22:00:33Z","timestamp":1572300033000},"page":"1-11","source":"Crossref","is-referenced-by-count":5,"title":["Genome-Wide Analysis of the Nucleosome Landscape in Individuals with Coffin-Siris Syndrome"],"prefix":"10.1159","volume":"159","author":[{"given":"Alexander","family":"Kalmbach","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher","family":"Schr\u00f6der","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ludger","family":"Klein-Hitpass","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karl","family":"Nordstr\u00f6m","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Ulz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ellen","family":"Heitzer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael R.","family":"Speicher","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sven","family":"Rahmann","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dagmar","family":"Wieczorek","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bernhard","family":"Horsthemke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nuria C.","family":"Bramswig","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"127","published-online":{"date-parts":[[2019,10,26]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu638"},{"key":"ref2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-07193-y"},{"key":"ref3","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1495"},{"key":"ref4","doi-asserted-by":"publisher","DOI":"10.1159\/000321577"},{"key":"ref5","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb1030"},{"key":"ref6","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/21.3.751"},{"key":"ref7","doi-asserted-by":"publisher","DOI":"10.1038\/nature08450"},{"key":"ref8","doi-asserted-by":"publisher","DOI":"10.1038\/nature00876"},{"key":"ref9","doi-asserted-by":"publisher","DOI":"10.1001\/archpedi.1970.02100050435009"},{"key":"ref10","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts635"},{"key":"ref11","doi-asserted-by":"publisher","DOI":"10.1016\/j.tig.2013.05.010"},{"key":"ref12","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3157"},{"key":"ref13","doi-asserted-by":"publisher","DOI":"10.1002\/1096-8628(20010215)99:1<1::aid-ajmg1127>3.0.co;2-a"},{"key":"ref14","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20030714"},{"key":"ref15","doi-asserted-by":"publisher","DOI":"10.1186\/gm434"},{"key":"ref16","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0812888106"},{"key":"ref17","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2012.02.007"},{"key":"ref18","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn923"},{"key":"ref19","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2008.211"},{"key":"ref20","doi-asserted-by":"publisher","DOI":"10.1038\/370481a0"},{"key":"ref21","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M205961200"},{"key":"ref22","doi-asserted-by":"publisher","DOI":"10.1042\/BJ20101358"},{"key":"ref23","doi-asserted-by":"publisher","DOI":"10.1101\/gr.196394.115"},{"key":"ref24","doi-asserted-by":"publisher","DOI":"10.1101\/gr.143008.112"},{"key":"ref25","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.30506"},{"key":"ref26","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1405528111"},{"key":"ref27","doi-asserted-by":"publisher","DOI":"10.1038\/370477a0"},{"key":"ref28","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-7774-1_19"},{"key":"ref29","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2007.06.019"},{"key":"ref30","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp324"},{"key":"ref31","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"ref32","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3080"},{"key":"ref33","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8"},{"key":"ref34","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2018.09.032"},{"key":"ref35","doi-asserted-by":"publisher","DOI":"10.1101\/gad.992102"},{"key":"ref36","doi-asserted-by":"publisher","DOI":"10.1101\/gad.1391006"},{"key":"ref37","doi-asserted-by":"publisher","DOI":"10.1101\/021592"},{"key":"ref38","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1005748"},{"key":"ref39","doi-asserted-by":"publisher","DOI":"10.1093\/emboj\/17.23.6979"},{"key":"ref40","doi-asserted-by":"publisher","DOI":"10.1038\/nature14248"},{"key":"ref41","doi-asserted-by":"publisher","DOI":"10.1038\/ng.2217"},{"key":"ref42","doi-asserted-by":"publisher","DOI":"10.1002\/humu.22394"},{"key":"ref43","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3735"},{"key":"ref44","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv770"},{"key":"ref45","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1302209110"},{"key":"ref46","doi-asserted-by":"publisher","DOI":"10.1038\/ng.2219"},{"key":"ref47","doi-asserted-by":"publisher","DOI":"10.1111\/cge.12225"},{"key":"ref48","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3648"},{"key":"ref49","doi-asserted-by":"publisher","DOI":"10.1038\/nn.3359"},{"key":"ref50","doi-asserted-by":"publisher","DOI":"10.1186\/s13072-016-0079-z"},{"key":"ref51","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddt366"},{"key":"ref52","doi-asserted-by":"publisher","DOI":"10.1161\/CIRCRESAHA.112.265587"},{"key":"ref53","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2007.08.021"},{"key":"ref54","doi-asserted-by":"publisher","DOI":"10.1126\/science.1112178"},{"key":"ref55","doi-asserted-by":"publisher","DOI":"10.1093\/database\/bav119"}],"container-title":["Cytogenetic and Genome Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/karger.com\/cgr\/article-pdf\/159\/1\/1\/3926763\/000503266.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/karger.com\/cgr\/article-pdf\/159\/1\/1\/3926763\/000503266.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,4,23]],"date-time":"2025-04-23T15:59:11Z","timestamp":1745423951000},"score":1,"resource":{"primary":{"URL":"https:\/\/karger.com\/article\/doi\/10.1159\/000503266"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019]]},"references-count":55,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2019,11,14]]},"published-print":{"date-parts":[[2019,1,1]]}},"URL":"https:\/\/doi.org\/10.1159\/000503266","archive":["Portico"],"relation":{},"ISSN":["1424-8581","1424-859X"],"issn-type":[{"type":"print","value":"1424-8581"},{"type":"electronic","value":"1424-859X"}],"subject":[],"published":{"date-parts":[[2019]]}}}