{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:41:19Z","timestamp":1772138479813,"version":"3.50.1"},"reference-count":98,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2020,9,25]],"date-time":"2020-09-25T00:00:00Z","timestamp":1600992000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004807","name":"DFG","doi-asserted-by":"publisher","award":["DA 1189\/2-1"],"award-info":[{"award-number":["DA 1189\/2-1"]}],"id":[{"id":"10.13039\/100004807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004807","name":"DFG","doi-asserted-by":"publisher","award":["GRK 1591"],"award-info":[{"award-number":["GRK 1591"]}],"id":[{"id":"10.13039\/100004807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004807","name":"DFG","doi-asserted-by":"publisher","award":["SPP 1935"],"award-info":[{"award-number":["SPP 1935"]}],"id":[{"id":"10.13039\/100004807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"Federal Ministry of Education and Research","doi-asserted-by":"publisher","award":["BMBF 01EO1003"],"award-info":[{"award-number":["BMBF 01EO1003"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005859","name":"Dr. Hella B\u00fchler Stiftung","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005859","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Alternative polyadenylation (APA) profoundly expands the transcriptome complexity. Perturbations of APA can disrupt biological processes, ultimately resulting in devastating disorders. A major challenge in identifying mechanisms and consequences of APA (and its perturbations) lies in the complexity of RNA 3\u2032 end processing, involving poorly conserved RNA motifs and multi-component complexes consisting of far more than 50 proteins. This is further complicated in that RNA 3\u2032 end maturation is closely linked to transcription, RNA processing and even epigenetic (histone\/DNA\/RNA) modifications. Here, we present TREND-DB (http:\/\/shiny.imbei.uni-mainz.de:3838\/trend-db), a resource cataloging the dynamic landscape of APA after depletion of &amp;gt;170 proteins involved in various facets of transcriptional, co- and post-transcriptional gene regulation, epigenetic modifications and further processes. TREND-DB visualizes the dynamics of transcriptome 3\u2032 end diversification (TREND) in a highly interactive manner; it provides a global APA network map and allows interrogating genes affected by specific APA-regulators and vice versa. It also permits condition-specific functional enrichment analyses of APA-affected genes, which suggest wide biological and clinical relevance across all RNAi conditions. The implementation of the UCSC Genome Browser provides additional customizable layers of gene regulation accounting for individual transcript isoforms (e.g. epigenetics, miRNA-binding sites and RNA-binding proteins). TREND-DB thereby fosters disentangling the role of APA for various biological programs, including potential disease mechanisms, and helps identify their diagnostic and therapeutic potential.<\/jats:p>","DOI":"10.1093\/nar\/gkaa722","type":"journal-article","created":{"date-parts":[[2020,8,25]],"date-time":"2020-08-25T07:12:08Z","timestamp":1598339528000},"page":"D243-D253","source":"Crossref","is-referenced-by-count":33,"title":["TREND-DB\u2014a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation"],"prefix":"10.1093","volume":"49","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3252-7758","authenticated-orcid":false,"given":"Federico","family":"Marini","sequence":"first","affiliation":[{"name":"Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center Mainz, 55131 Mainz, Germany"},{"name":"Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, 55131 Mainz,\u00a0Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Denise","family":"Scherzinger","sequence":"additional","affiliation":[{"name":"Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center Mainz, 55131 Mainz, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3176-2265","authenticated-orcid":false,"given":"Sven","family":"Danckwardt","sequence":"additional","affiliation":[{"name":"Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, 55131 Mainz,\u00a0Germany"},{"name":"Posttranscriptional Gene Regulation, Cancer Research and Experimental Hemostasis, University Medical Center Mainz, 55131 Mainz, Germany"},{"name":"Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, 55131 Mainz, Germany"},{"name":"German Center for Cardiovascular Research (DZHK), Rhine-Main, 55131 Mainz, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,9,25]]},"reference":[{"key":"2021010313112758800_B1","doi-asserted-by":"crossref","first-page":"1559","DOI":"10.1126\/science.1112014","article-title":"The transcriptional landscape of the mammalian genome","volume":"309","author":"Carninci","year":"2005","journal-title":"Science"},{"key":"2021010313112758800_B2","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1038\/nature07509","article-title":"Alternative isoform regulation in human tissue transcriptomes","volume":"456","author":"Wang","year":"2008","journal-title":"Nature"},{"key":"2021010313112758800_B3","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1093\/nar\/gkx1165","article-title":"Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues","volume":"46","author":"Reyes","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2021010313112758800_B4","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1038\/nrg3482","article-title":"Alternative cleavage and polyadenylation: extent, regulation and function","volume":"14","author":"Elkon","year":"2013","journal-title":"Nat. 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