Sökning: WFRF:(Sjöstedt Evelina) > Discovery of widesp...
Fältnamn | Indikatorer | Metadata |
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000 | 05643naa a2200805 4500 | |
001 | oai:prod.swepub.kib.ki.se:146825299 | |
003 | SwePub | |
008 | 240701s2021 | |||||||||||000 ||eng| | |
009 | oai:DiVA.org:su-211977 | |
009 | oai:DiVA.org:kth-309717 | |
024 | 7 | a http://kipublications.ki.se/Default.aspx?queryparsed=id:1468252992 URI |
024 | 7 | a https://doi.org/10.1038/s41467-021-23143-72 DOI |
024 | 7 | a https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-2119772 URI |
024 | 7 | a https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-3097172 URI |
040 | a (SwePub)kid (SwePub)sud (SwePub)kth | |
041 | a engb eng | |
042 | 9 SwePub | |
072 | 7 | a ref2 swepub-contenttype |
072 | 7 | a art2 swepub-publicationtype |
100 | 1 | a Grapotte, M4 aut |
245 | 1 0 | a Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network |
264 | c 2021-06-02 | |
264 | 1 | b Springer Science and Business Media LLC,c 2021 |
500 | a For correction, see: Grapotte, M., Saraswat, M., Bessière, C. et al. Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nat Commun 13, 1200 (2022). DOI: 10.1038/s41467-022-28758-y | |
500 | a QC 20220309Correction in: Nature Communications, Volume 13, Issue 1, Article Number 1200, DOI 10.1038/s41467-022-28758-y, WOS:000771136200018 | |
520 | a 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 sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism. | |
650 | 7 | a MEDICIN OCH HÄLSOVETENSKAPx Medicinska och farmaceutiska grundvetenskaperx Medicinsk genetik0 (SwePub)301072 hsv//swe |
650 | 7 | a MEDICAL AND HEALTH SCIENCESx Basic Medicinex Medical Genetics0 (SwePub)301072 hsv//eng |
650 | 7 | a NATURVETENSKAPx Biologix Biokemi och molekylärbiologi0 (SwePub)106022 hsv//swe |
650 | 7 | a NATURAL SCIENCESx Biological Sciencesx Biochemistry and Molecular Biology0 (SwePub)106022 hsv//eng |
700 | 1 | a Saraswat, M4 aut |
700 | 1 | a Bessiere, C4 aut |
700 | 1 | a Menichelli, C4 aut |
700 | 1 | a Ramilowski, JA4 aut |
700 | 1 | a Severin, J4 aut |
700 | 1 | a Hayashizaki, Y4 aut |
700 | 1 | a Itoh, M4 aut |
700 | 1 | a Tagami, M4 aut |
700 | 1 | a Murata, M4 aut |
700 | 1 | a Kojima-Ishiyamas, M4 aut |
700 | 1 | a Noma, S4 aut |
700 | 1 | a Noguchi, S4 aut |
700 | 1 | a Kasukawa, T4 aut |
700 | 1 | a Hasegawa, A4 aut |
700 | 1 | a Suzuki, H4 aut |
700 | 1 | a Nishiyori-Sueki, H4 aut |
700 | 1 | a Frith, MC4 aut |
700 | 1 | a Chatelain, C4 aut |
700 | 1 | a Carninci, P4 aut |
700 | 1 | a de Hoom, MJL4 aut |
700 | 1 | a Wasserman, WW4 aut |
700 | 1 | a Brehelin, L4 aut |
700 | 1 | a Lecellieree, CH4 aut |
700 | 1 | a Elofsson, Arne,d 1966-u Stockholms universitet,Institutionen för biokemi och biofysik4 aut0 (Swepub:su)aelof |
700 | 1 | a Sachenkova, Oxanau Stockholms universitet,Institutionen för biokemi och biofysik4 aut0 (Swepub:su)osach |
700 | 1 | a Forsberg, Mattiasu KTH,Systembiologi4 aut0 (Swepub:kth)u1l9h7ku |
700 | 1 | a Oksvold, Peru KTH,Science for Life Laboratory, SciLifeLab4 aut0 (Swepub:kth)u1qey3lv |
700 | 1 | a Sivertsson, Åsau KTH,Science for Life Laboratory, SciLifeLab,Systembiologi4 aut0 (Swepub:kth)u195d5b0 |
700 | 1 | a Sjöstedt, Evelinau KTH,Science for Life Laboratory, SciLifeLab,Proteinvetenskap4 aut0 (Swepub:kth)u12iezpl |
700 | 1 | a Uhlén, Mathiasu KTH,Science for Life Laboratory, SciLifeLab,Albanova VinnExcellence Center for Protein Technology, ProNova,Systembiologi4 aut0 (Swepub:kth)u1dulvmw |
700 | 1 | a von Feilitzen, Kalleu KTH,Systembiologi,Proteinteknologi,Science for Life Laboratory, SciLifeLab4 aut0 (Swepub:kth)u1dbmi38 |
700 | 1 | a Zwahlen, Martinu KTH,Science for Life Laboratory, SciLifeLab,Systembiologi4 aut0 (Swepub:kth)u1fcjpxe |
710 | 2 | a Stockholms universitetb Institutionen för biokemi och biofysik4 org |
773 | 0 | t Nature communicationsd : Springer Science and Business Media LLCg 12:1, s. 3297-q 12:1<3297-x 2041-1723 |
856 | 4 | u https://www.nature.com/articles/s41467-021-23143-7.pdf |
856 | 4 | u https://doi.org/10.1038/s41467-021-23143-7y Fulltext |
856 | 4 8 | u http://kipublications.ki.se/Default.aspx?queryparsed=id:146825299 |
856 | 4 8 | u https://doi.org/10.1038/s41467-021-23143-7 |
856 | 4 8 | u https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-211977 |
856 | 4 8 | u https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-309717 |
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