{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:13Z","timestamp":1740185113140,"version":"3.37.3"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2018,12,10]],"date-time":"2018-12-10T00:00:00Z","timestamp":1544400000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","award":["310030-153099"],"award-info":[{"award-number":["310030-153099"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ticino Foundation for Cancer Research and Fidinam"},{"name":"Ceresio Foundation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Long non-coding RNAs (lncRNAs) have gained increasing relevance in epigenetic regulation and nuclear functional organization. High-throughput sequencing approaches have revealed frequent non-coding transcription in promoter-proximal regions. However, a comprehensive catalogue of promoter-associated RNAs (paRNAs) and an analysis of the possible interactions with neighboring genes and genomic regulatory elements are missing.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Integrating data from multiple cell types and experimental platforms we identified thousands of paRNAs in the human genome. paRNAs are transcribed in both sense and antisense orientation, are mostly non-polyadenylated and retained in the cell nucleus. Transcriptional regulators, epigenetic effectors and activating chromatin marks are enriched in paRNA-positive promoters. Furthermore, paRNA-positive promoters exhibit chromatin signatures of both active promoters and enhancers. Promoters with paRNAs reside preferentially at chromatin loop boundaries, suggesting an involvement in anchor site recognition and chromatin looping. Importantly, these features are independent of the transcriptional state of neighboring genes. Thus, paRNAs may act as cis-regulatory modules with an impact on local recruitment of transcription factors, epigenetic state and chromatin loop organization. This study provides a comprehensive analysis of the promoter-proximal transcriptome and offers novel insights into the roles of paRNAs in epigenetic processes and human diseases.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Genomic coordinates of predicted paRNAs are available at https:\/\/figshare.com: https:\/\/doi.org\/10.6084\/m9.figshare.7392791.v1 and https:\/\/doi.org\/10.6084\/m9.figshare.4856630.v2.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty981","type":"journal-article","created":{"date-parts":[[2018,12,7]],"date-time":"2018-12-07T20:15:50Z","timestamp":1544213750000},"page":"2529-2534","source":"Crossref","is-referenced-by-count":2,"title":["Deciphering the complexity of human non-coding promoter-proximal transcriptome"],"prefix":"10.1093","volume":"35","author":[{"given":"Sarah N","family":"Mapelli","sequence":"first","affiliation":[{"name":"Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), Universit\u00e0 della Svizzera Italiana (USI), Bellinzona, Switzerland"},{"name":"Institute of Computational Science, Universit\u00e0 della Svizzera Italiana (USI), Lugano, Switzerland"},{"name":"Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sara","family":"Napoli","sequence":"additional","affiliation":[{"name":"Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), Universit\u00e0 della Svizzera Italiana (USI), Bellinzona, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giuseppina","family":"Pisignano","sequence":"additional","affiliation":[{"name":"Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), Universit\u00e0 della Svizzera Italiana (USI), Bellinzona, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ramon","family":"Garcia-Escudero","sequence":"additional","affiliation":[{"name":"Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), Universit\u00e0 della Svizzera Italiana (USI), Bellinzona, Switzerland"},{"name":"Molecular Oncology Unit-CIEMAT and Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giuseppina M","family":"Carbone","sequence":"additional","affiliation":[{"name":"Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), Universit\u00e0 della Svizzera Italiana (USI), Bellinzona, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carlo V","family":"Catapano","sequence":"additional","affiliation":[{"name":"Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), Universit\u00e0 della Svizzera Italiana (USI), Bellinzona, Switzerland"},{"name":"Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland"},{"name":"Department of Oncology, Faculty of Biology and Medicine, University of Lausanne, Lausanne1066, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,12,10]]},"reference":[{"key":"2023062713055565100_bty981-B1","doi-asserted-by":"crossref","first-page":"e02200","DOI":"10.7554\/eLife.02200","article-title":"Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms","volume":"3","author":"Allen","year":"2014","journal-title":"Elife"},{"key":"2023062713055565100_bty981-B2","doi-asserted-by":"crossref","first-page":"772.","DOI":"10.1038\/nrg.2016.147","article-title":"Organization and function of the 3D genome","volume":"17","author":"Bonev","year":"2016","journal-title":"Nat. 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