Search: (WFRF:(Kasukawa T.)) srt2:(2020-2024) >
Discovery of widesp...
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
-
Grapotte, M (author)
-
Saraswat, M (author)
-
Bessiere, C (author)
-
show more...
-
Menichelli, C (author)
-
Ramilowski, JA (author)
-
Severin, J (author)
-
Hayashizaki, Y (author)
-
Itoh, M (author)
-
Tagami, M (author)
-
Murata, M (author)
-
Kojima-Ishiyamas, M (author)
-
Noma, S (author)
-
Noguchi, S (author)
-
Kasukawa, T (author)
-
Hasegawa, A (author)
-
Suzuki, H (author)
-
Nishiyori-Sueki, H (author)
-
Frith, MC (author)
-
Chatelain, C (author)
-
Carninci, P (author)
-
de Hoom, MJL (author)
-
Wasserman, WW (author)
-
Brehelin, L (author)
-
Lecellieree, CH (author)
-
- Elofsson, Arne, 1966- (author)
- Stockholms universitet,Institutionen för biokemi och biofysik
-
- Sachenkova, Oxana (author)
- Stockholms universitet,Institutionen för biokemi och biofysik
-
- Forsberg, Mattias (author)
- KTH,Systembiologi
-
- Oksvold, Per (author)
- KTH,Science for Life Laboratory, SciLifeLab
-
- Sivertsson, Åsa (author)
- KTH,Science for Life Laboratory, SciLifeLab,Systembiologi
-
- Sjöstedt, Evelina (author)
- KTH,Science for Life Laboratory, SciLifeLab,Proteinvetenskap
-
- Uhlén, Mathias (author)
- KTH,Science for Life Laboratory, SciLifeLab,Albanova VinnExcellence Center for Protein Technology, ProNova,Systembiologi
-
- von Feilitzen, Kalle (author)
- KTH,Systembiologi,Proteinteknologi,Science for Life Laboratory, SciLifeLab
-
- Zwahlen, Martin (author)
- KTH,Science for Life Laboratory, SciLifeLab,Systembiologi
-
show less...
-
(creator_code:org_t)
- 2021-06-02
- 2021
- English.
-
In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1, s. 3297-
- Related links:
-
https://www.nature.c...
-
show more...
-
https://doi.org/10.1...
-
http://kipublication...
-
https://doi.org/10.1...
-
https://urn.kb.se/re...
-
https://urn.kb.se/re...
-
show less...
Abstract
Subject headings
Close
- 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.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)
Publication and Content Type
- ref (subject category)
- art (subject category)
Find in a library
To the university's database
- By the author/editor
-
Grapotte, M
-
Saraswat, M
-
Bessiere, C
-
Menichelli, C
-
Ramilowski, JA
-
Severin, J
-
show more...
-
Hayashizaki, Y
-
Itoh, M
-
Tagami, M
-
Murata, M
-
Kojima-Ishiyamas ...
-
Noma, S
-
Noguchi, S
-
Kasukawa, T
-
Hasegawa, A
-
Suzuki, H
-
Nishiyori-Sueki, ...
-
Frith, MC
-
Chatelain, C
-
Carninci, P
-
de Hoom, MJL
-
Wasserman, WW
-
Brehelin, L
-
Lecellieree, CH
-
Elofsson, Arne, ...
-
Sachenkova, Oxan ...
-
Forsberg, Mattia ...
-
Oksvold, Per
-
Sivertsson, Åsa
-
Sjöstedt, Evelin ...
-
Uhlén, Mathias
-
von Feilitzen, K ...
-
Zwahlen, Martin
-
show less...
- About the subject
-
- MEDICAL AND HEALTH SCIENCES
-
MEDICAL AND HEAL ...
-
and Basic Medicine
-
and Medical Genetics
-
- NATURAL SCIENCES
-
NATURAL SCIENCES
-
and Biological Scien ...
-
and Biochemistry and ...
- Articles in the publication
-
Nature communica ...
- By the university
-
Karolinska Institutet
-
Stockholm University
-
Royal Institute of Technology