{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,24]],"date-time":"2026-04-24T18:37:25Z","timestamp":1777055845124,"version":"3.51.4"},"reference-count":57,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2023,5,23]],"date-time":"2023-05-23T00:00:00Z","timestamp":1684800000000},"content-version":"vor","delay-in-days":142,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Every year there is more and more evidence that non-coding RNAs play an important role in biological processes affecting various levels of organization of living systems: from the cellular (regulation of gene expression, remodeling and maintenance of chromatin structure, co-transcriptional suppression of transposons, splicing, post-transcriptional RNA modifications, etc.) to cell populations and even organismal ones (development, aging, cancer, cardiovascular and many other diseases). The development and creation of mutually complementary databases that will aggregate, unify and structure different types of data can help to reach the system level of studying non-coding RNAs. Here we present the RNA-Chrom manually curated analytical database, which contains the coordinates of billions of contacts of thousands of human and mouse RNAs with chromatin. Through the user-friendly web interface (https:\/\/rnachrom2.bioinf.fbb.msu.ru\/), two approaches to the analysis of the RNA\u2013chromatin interactome were implemented. Firstly, to find out whether the RNA of interest to a user contacts with chromatin, and if so, with which genes or DNA loci? Secondly, to find out which RNAs are in contact with the DNA locus of interest to a user (and probably participate in its regulation), and if there are such, what is the nature of their interaction? For a more detailed study of contact maps and their comparison with other data, the web interface allows a user to view them in the UCSC Genome Browser.<\/jats:p>\n                  <jats:p>Database URL https:\/\/rnachrom2.bioinf.fbb.msu.ru\/<\/jats:p>","DOI":"10.1093\/database\/baad025","type":"journal-article","created":{"date-parts":[[2023,5,23]],"date-time":"2023-05-23T19:59:00Z","timestamp":1684871940000},"source":"Crossref","is-referenced-by-count":16,"title":["RNA-Chrom: a manually curated analytical database of RNA\u2013chromatin interactome"],"prefix":"10.1093","volume":"2023","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2225-156X","authenticated-orcid":false,"given":"G K","family":"Ryabykh","sequence":"first","affiliation":[{"name":"Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University , Leninskiye Gory, Moscow 119234, Russia"},{"name":"Kharkevich Institute for Information Transmission Problems RAS , Bolshoy Karetny per., Moscow 127051, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S V","family":"Kuznetsov","sequence":"additional","affiliation":[{"name":"Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University , Leninskiye Gory, Moscow 119234, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Y D","family":"Korostelev","sequence":"additional","affiliation":[{"name":"Kharkevich Institute for Information Transmission Problems RAS , Bolshoy Karetny per., Moscow 127051, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"A I","family":"Sigorskikh","sequence":"additional","affiliation":[{"name":"Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University , Leninskiye Gory, Moscow 119234, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"A A","family":"Zharikova","sequence":"additional","affiliation":[{"name":"Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University , Leninskiye Gory, Moscow 119234, Russia"},{"name":"Kharkevich Institute for Information Transmission Problems RAS , Bolshoy Karetny per., Moscow 127051, Russia"},{"name":"National Medical Research Center for Therapy and Preventive Medicine , Petroverigsky per., Moscow, 101000, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"A A","family":"Mironov","sequence":"additional","affiliation":[{"name":"Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University , Leninskiye Gory, Moscow 119234, Russia"},{"name":"Kharkevich Institute for Information Transmission Problems RAS , Bolshoy Karetny per., Moscow 127051, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,4,24]]},"reference":[{"key":"2023101317175387800_R1","doi-asserted-by":"crossref","first-page":"1379","DOI":"10.1073\/pnas.57.5.1379","article-title":"Molecular complementarity between nuclear DNA and organ-specific chromosomal RNA","volume":"57","author":"Bonner","year":"1967","journal-title":"PNAS"},{"key":"2023101317175387800_R2","doi-asserted-by":"crossref","first-page":"960","DOI":"10.1073\/pnas.54.3.960","article-title":"Histone-bound RNA, a component of native nucleohistone","volume":"54","author":"Huang","year":"1965","journal-title":"PNAS"},{"key":"2023101317175387800_R3","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1016\/0092-8674(92)90519-I","article-title":"The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus","volume":"71","author":"Brockdorff","year":"1992","journal-title":"Cell"},{"key":"2023101317175387800_R4","doi-asserted-by":"crossref","first-page":"7855","DOI":"10.1128\/MCB.24.18.7855-7862.2004","article-title":"An antisense RNA regulates the bidirectional silencing property of the Kcnq1 imprinting control region","volume":"24","author":"Thakur","year":"2004","journal-title":"Mol. 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