{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T18:58:51Z","timestamp":1785437931207,"version":"3.56.0"},"reference-count":46,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2026,4,19]],"date-time":"2026-04-19T00:00:00Z","timestamp":1776556800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"crossref","award":["22-74-10053-P"],"award-info":[{"award-number":["22-74-10053-P"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"crossref"}]},{"award":["22-74-10053-P"],"award-info":[{"award-number":["22-74-10053-P"]}],"id":[{"id":"https:\/\/ror.org\/03y2gwe85","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Long non-coding RNAs (lncRNAs) interact with chromatin and recruit epigenetic complexes to specific genomic loci, yet their relationship with super-enhancers (SEs), key regulatory elements frequently reprogrammed in cancer, remains unexplored. We developed an integrative pipeline that combines RNA\u2013chromatin contact data (RNA-Chrom), histone modification\u2013lncRNA expression correlation profiles (HiMoRNA peaks), and super-enhancer annotations (SEdb 3.0) to map lncRNA\u2013SE regulatory axes. Applying this framework to SNHG1 in HCT116 colorectal cancer cells, we identified 21 SNHG1-reactive super-enhancers (\u03a8-SEs) among 184 cancer-specific SEs, at which SNHG1 physical contacts co-occur with SNHG1-correlated histone modifications (HiMoRNA peaks), predominantly H3K4me1 (permutation p = 0.001, fold enrichment = 2.03). Comparison with 4145 lncRNAs demonstrated that epigenetic correlations alone do not distinguish SNHG1; instead, the addition of the contact layer is required to delineate the \u03a8-SE set. Differential expression (DESeq2) and co-expression analyses in 471 TCGA-COAD tumor samples identified 12 \u03a8-SE target genes (including CDC20, PDP1, and TOP1) consistently upregulated in both HCT116 cells and patient tumors and positively correlated with SNHG1, with the co-expression signal robust to tumor purity correction. The proposed \u03a8\/\u03a9 classification provides a generalizable framework for prioritizing super-enhancers at which lncRNA\u2013chromatin interactions may shape the local epigenetic environment across cancer types.<\/jats:p>","DOI":"10.3390\/ijms27083642","type":"journal-article","created":{"date-parts":[[2026,4,20]],"date-time":"2026-04-20T08:24:23Z","timestamp":1776673463000},"page":"3642","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrative Mapping of SNHG1 RNA\u2013Chromatin Contacts onto the Cancer-Specific Super-Enhancer Landscape in HCT116 Colorectal Cancer Cells"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2225-156X","authenticated-orcid":false,"given":"Grigory K.","family":"Ryabykh","sequence":"first","affiliation":[{"name":"Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina St., 119991 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ekaterina D.","family":"Osintseva","sequence":"additional","affiliation":[{"name":"Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4140-0652","authenticated-orcid":false,"given":"German A.","family":"Ashniev","sequence":"additional","affiliation":[{"name":"Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia"},{"name":"Central University, 7 Gasheka St., 123056 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yulia V.","family":"Makus","sequence":"additional","affiliation":[{"name":"Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia"},{"name":"Central University, 7 Gasheka St., 123056 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7408-3927","authenticated-orcid":false,"given":"Alexey V.","family":"Orlov","sequence":"additional","affiliation":[{"name":"Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia"},{"name":"Central University, 7 Gasheka St., 123056 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1573-5512","authenticated-orcid":false,"given":"Petr I.","family":"Nikitin","sequence":"additional","affiliation":[{"name":"Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalia N.","family":"Orlova","sequence":"additional","affiliation":[{"name":"Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,4,19]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/j.cell.2013.03.035","article-title":"Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes","volume":"153","author":"Whyte","year":"2013","journal-title":"Cell"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1016\/j.cell.2013.03.036","article-title":"Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers","volume":"153","author":"Hoke","year":"2013","journal-title":"Cell"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"934","DOI":"10.1016\/j.cell.2013.09.053","article-title":"Super-Enhancers in the Control of Cell Identity and Disease","volume":"155","author":"Hnisz","year":"2013","journal-title":"Cell"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1186\/s12943-024-02066-z","article-title":"Super-Enhancer Omics in Stem Cell","volume":"23","author":"Ma","year":"2024","journal-title":"Mol. 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