TREND-DB—a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation
| العنوان: | TREND-DB—a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation |
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| المؤلفون: | Denise Scherzinger, Federico Marini, Sven Danckwardt |
| المصدر: | Nucleic Acids Research |
| بيانات النشر: | Oxford University Press (OUP), 2020. |
| سنة النشر: | 2020 |
| مصطلحات موضوعية: | Transcription, Genetic, Polyadenylation, AcademicSubjects/SCI00010, education, MiRNA binding, RNA-binding protein, Computational biology, Biology, Transcriptome, User-Computer Interface, 03 medical and health sciences, 0302 clinical medicine, RNA interference, Transcription (biology), Databases, Genetic, Genetics, Humans, Database Issue, 3' Untranslated Regions, Gene, 030304 developmental biology, Regulation of gene expression, Internet, 0303 health sciences, Cleavage And Polyadenylation Specificity Factor, RNA, Gene Expression Regulation, 030217 neurology & neurosurgery |
| الوصف: | 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’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’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 >170 proteins involved in various facets of transcriptional, co- and posttranscriptional gene regulation, epigenetic modifications, and further processes. TREND-DB visualizes the dynamics of transcriptome 3’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, RNA-binding proteins). TREND-DB thereby fosters disentangling the role of APA for various biological programs, including potential disease mechanisms, and helps to identify their diagnostic and therapeutic potential. |
| تدمد: | 1362-4962 0305-1048 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::471d581a55640b6372894c9278c11cc6 https://doi.org/10.1093/nar/gkaa722 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....471d581a55640b6372894c9278c11cc6 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 13624962 03051048 |
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