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These models unveil the importance of STR surrounding sequen"],"journal":["Nature communications"],"pubmed_title":["Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network."],"pmcid":["PMC8172540"],"funding_grant_id":["P30 CA008748","106954/Z/15/Z","U01 CA151118"],"pubmed_authors":["Bessiere C","Bickel PJ","Sese J","Saito M","Kaminuma E","Kawaguchi S","Matsuda H","Winteringham LN","Yumoto N","Forrester LM","Watanabe K","Beltrami CA","Kajiyama K","Rost B","Iida K","Busch A","Lilje B","Kawai J","Ohshima M","Zucchelli S","Brombacher F","Kawamura YI","Kuznetsov VA","Frith MC","Ikeo K","Young R","Yu NY","Farach-Carson MC","Saito A","Faghihi M","Seno S","Herlyn M","Bult CJ","Freeman TC","Bajic VB","Ivshina AV","Hugues R","Ponten F","Motakis E","Lopez G","Horie M","Rehli M","Hashimoto K","Hale P","Sakaue S","Kratz A","Lipovich L","Soderhall C","Mungall CJ","Coskun M","Minoda A","Funayama M","Kitano H","Testa AC","Endoh M","Bansal 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P","Okada Y","Kitamura T","Hattori N","Jurman G","Motohashi H","Schmidl C","Orlando V"],"additional_accession":[]},"is_claimable":false,"name":"Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.","description":"Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequen","dates":{"release":"2021-01-01T00:00:00Z","publication":"2021 Jun","modification":"2026-05-08T01:23:32.057Z","creation":"2022-02-10T14:11:36.014Z"},"accession":"S-EPMC8172540","cross_references":{"pubmed":["34078885"],"doi":["10.1038/s41467-021-23143-7"]}}