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LIBRIS Formathandbok  (Information om MARC21)
FältnamnIndikatorerMetadata
00004595naa a2200529 4500
001oai:DiVA.org:kth-309717
003SwePub
008220309s2021 | |||||||||||000 ||eng|
009oai:DiVA.org:su-211977
0247 a https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-3097172 URI
0247 a https://doi.org/10.1038/s41467-021-23143-72 DOI
0247 a https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-2119772 URI
040 a (SwePub)kthd (SwePub)su
041 a engb eng
042 9 SwePub
072 7a ref2 swepub-contenttype
072 7a art2 swepub-publicationtype
1001 a Grapotte, Mathys4 aut
2451 0a Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
264 c 2021-06-02
264 1b Springer Science and Business Media LLC,c 2021
338 a print2 rdacarrier
500 a QC 20220309Correction in: Nature Communications, Volume 13, Issue 1, Article Number 1200, DOI 10.1038/s41467-022-28758-y, WOS:000771136200018
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
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 7a NATURVETENSKAPx Biologix Biokemi och molekylärbiologi0 (SwePub)106022 hsv//swe
650 7a NATURAL SCIENCESx Biological Sciencesx Biochemistry and Molecular Biology0 (SwePub)106022 hsv//eng
650 7a NATURVETENSKAPx Biologi0 (SwePub)1062 hsv//swe
650 7a NATURAL SCIENCESx Biological Sciences0 (SwePub)1062 hsv//eng
7001 a Forsberg, Mattiasu KTH,Systembiologi4 aut0 (Swepub:kth)u1l9h7ku
7001 a Oksvold, Peru KTH,Science for Life Laboratory, SciLifeLab4 aut0 (Swepub:kth)u1qey3lv
7001 a Sivertsson, Åsau KTH,Science for Life Laboratory, SciLifeLab,Systembiologi4 aut0 (Swepub:kth)u195d5b0
7001 a Sjöstedt, Evelinau KTH,Science for Life Laboratory, SciLifeLab,Proteinvetenskap4 aut0 (Swepub:kth)u12iezpl
7001 a Uhlén, Mathiasu KTH,Science for Life Laboratory, SciLifeLab,Albanova VinnExcellence Center for Protein Technology, ProNova,Systembiologi4 aut0 (Swepub:kth)u1dulvmw
7001 a von Feilitzen, Kalleu KTH,Systembiologi,Proteinteknologi,Science for Life Laboratory, SciLifeLab4 aut0 (Swepub:kth)u1dbmi38
7001 a Zwahlen, Martinu KTH,Science for Life Laboratory, SciLifeLab,Systembiologi4 aut0 (Swepub:kth)u1fcjpxe
7001 a Elofsson, Arne,d 1966-u Stockholms universitet,Institutionen för biokemi och biofysik4 aut0 (Swepub:su)aelof
7001 a Sachenkova, Oxanau Stockholms universitet,Institutionen för biokemi och biofysik4 aut0 (Swepub:su)osach
7001 a Bréhélin, Laurent4 aut
7001 a Lecellier, Charles-Henri4 aut
7102 a KTHb Systembiologi4 org
7730 t Nature Communicationsd : Springer Science and Business Media LLCx 2041-1723
8564 u https://doi.org/10.1038/s41467-021-23143-7y Fulltext
8564 u https://www.nature.com/articles/s41467-021-23143-7.pdf
8564 8u https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-309717
8564 8u https://doi.org/10.1038/s41467-021-23143-7
8564 8u https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-211977

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