Nature Communications (Jun 2021)
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
- Mathys Grapotte,
- Manu Saraswat,
- Chloé Bessière,
- Christophe Menichelli,
- Jordan A. Ramilowski,
- Jessica Severin,
- Yoshihide Hayashizaki,
- Masayoshi Itoh,
- Michihira Tagami,
- Mitsuyoshi Murata,
- Miki Kojima-Ishiyama,
- Shohei Noma,
- Shuhei Noguchi,
- Takeya Kasukawa,
- Akira Hasegawa,
- Harukazu Suzuki,
- Hiromi Nishiyori-Sueki,
- Martin C. Frith,
- FANTOM consortium,
- Clément Chatelain,
- Piero Carninci,
- Michiel J. L. de Hoon,
- Wyeth W. Wasserman,
- Laurent Bréhélin,
- Charles-Henri Lecellier
Affiliations
- Mathys Grapotte
- Institut de Biologie Computationnelle
- Manu Saraswat
- Institut de Biologie Computationnelle
- Chloé Bessière
- Institut de Biologie Computationnelle
- Christophe Menichelli
- Institut de Biologie Computationnelle
- Jordan A. Ramilowski
- RIKEN Center for Integrative Medical Sciences
- Jessica Severin
- RIKEN Center for Integrative Medical Sciences
- Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program
- Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program
- Michihira Tagami
- RIKEN Center for Integrative Medical Sciences
- Mitsuyoshi Murata
- RIKEN Center for Integrative Medical Sciences
- Miki Kojima-Ishiyama
- RIKEN Center for Integrative Medical Sciences
- Shohei Noma
- RIKEN Center for Integrative Medical Sciences
- Shuhei Noguchi
- RIKEN Center for Integrative Medical Sciences
- Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences
- Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences
- Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences
- Hiromi Nishiyori-Sueki
- RIKEN Center for Integrative Medical Sciences
- Martin C. Frith
- Artificial Intelligence Research Center, AIST
- FANTOM consortium
- Clément Chatelain
- SANOFI R&D, Translational Sciences
- Piero Carninci
- RIKEN Center for Integrative Medical Sciences
- Michiel J. L. de Hoon
- RIKEN Center for Integrative Medical Sciences
- Wyeth W. Wasserman
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia
- Laurent Bréhélin
- Institut de Biologie Computationnelle
- Charles-Henri Lecellier
- Institut de Biologie Computationnelle
- DOI
- https://doi.org/10.1038/s41467-021-23143-7
- Journal volume & issue
-
Vol. 12,
no. 1
pp. 1 – 18
Abstract
Mammalian genomes are scattered with repetitive sequences, but their biology remains largely elusive. Here, the authors show that transcription can initiate from short tandem repetitive sequences, and that genetic variants linked to human diseases are preferentially found at repeats with high transcription initiation level.
