Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Grapotte, M, Saraswat, M, Bessière, C et al. (487 more authors) (2021) Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature Communications, 12. 3297. ISSN 2041-1723

Abstract

Metadata

Authors/Creators:
  • Grapotte, M
  • Saraswat, M
  • Bessière, C
  • Menichelli, C
  • Ramilowski, JA
  • Severin, J
  • Hayashizaki, Y
  • Itoh, M
  • Tagami, M
  • Murata, M
  • Kojima-Ishiyama, M
  • Noma, S
  • Noguchi, S
  • Kasukawa, T
  • Hasegawa, A
  • Suzuki, H
  • Nishiyori-Sueki, H
  • Frith, MC
  • Abugessaisa, I
  • Aitken, S
  • Aken, BL
  • Alam, I
  • Alam, T
  • Alasiri, R
  • Alhendi, AMN
  • Alinejad-Rokny, H
  • Alvarez, MJ
  • Andersson, R
  • Arakawa, T
  • Araki, M
  • Arbel, T
  • Archer, J
  • Archibald, AL
  • Arner, E
  • Arner, P
  • Asai, K
  • Ashoor, H
  • Astrom, G
  • Babina, M
  • Baillie, JK
  • Bajic, VB
  • Bajpai, A
  • Baker, S
  • Baldarelli, RM
  • Balic, A
  • Bansal, M
  • Batagov, AO
  • Batzoglou, S
  • Beckhouse, AG
  • Beltrami, AP
  • Beltrami, CA
  • Bertin, N
  • Bhattacharya, S
  • Bickel, PJ
  • Blake, JA
  • Blanchette, M
  • Bodega, B
  • Bonetti, A
  • Bono, H
  • Bornholdt, J
  • Bttcher, M
  • Bougouffa, S
  • Boyd, M
  • Breda, J
  • Brombacher, F
  • Brown, JB
  • Bult, CJ
  • Burroughs, AM
  • Burt, DW
  • Busch, A
  • Caglio, G
  • Califano, A
  • Cameron, CJ
  • Cannistraci, CV
  • Carbone, A
  • Carlisle, AJ
  • Carninci, P
  • Carter, KW
  • Cesselli, D
  • Chang, J-C
  • Chen, JC
  • Chen, Y
  • Chierici, M
  • Christodoulou, J
  • Ciani, Y
  • Clark, EL
  • Coskun, M
  • Dalby, M
  • Dalla, E
  • Daub, CO
  • Davis, CA
  • de Hoon, MJL
  • de Rie, D
  • Denisenko, E
  • Deplancke, B
  • Detmar, M
  • Deviatiiarov, R
  • Di Bernardo, D
  • Diehl, AD
  • Dieterich, LC
  • Dimont, E
  • Djebali, S
  • Dohi, T
  • Dostie, J
  • Drablos, F
  • Edge, ASB
  • Edinger, M
  • Ehrlund, A
  • Ekwall, K
  • Elofsson, A
  • Endoh, M
  • Enomoto, H
  • Enomoto, S
  • Faghihi, M
  • Fagiolini, M
  • Farach-Carson, MC
  • Faulkner, GJ
  • Favorov, A
  • Fernandes, AM
  • Ferrai, C
  • Forrest, ARR
  • Forrester, LM
  • Forsberg, M
  • Fort, A
  • Francescatto, M
  • Freeman, TC
  • Frith, M
  • Fukuda, S
  • Funayama, M
  • Furlanello, C
  • Furuno, M
  • Furusawa, C
  • Gao, H
  • Gazova, I
  • Gebhard, C
  • Geier, F
  • Geijtenbeek, TBH
  • Ghosh, S
  • Ghosheh, Y
  • Gingeras, TR
  • Gojobori, T
  • Goldberg, T
  • Goldowitz, D
  • Gough, J
  • Greco, D
  • Gruber, AJ
  • Guhl, S
  • Guigo, R
  • Guler, R
  • Gusev, O
  • Gustincich, S
  • Ha, TJ
  • Haberle, V
  • Hale, P
  • Hallstrom, BM
  • Hamada, M
  • Handoko, L
  • Hara, M
  • Harbers, M
  • Harrow, J
  • Harshbarger, J
  • Hase, T
  • Hasegawa, A
  • Hashimoto, K
  • Hatano, T
  • Hattori, N
  • Hayashi, R
  • Hayashizaki, Y
  • Herlyn, M
  • Heutink, P
  • Hide, W
  • Hitchens, KJ
  • Sui, SH
  • ’t Hoen, PAC
  • Hon, CC
  • Hori, F
  • Horie, M
  • Horimoto, K
  • Horton, P
  • Hou, R
  • Huang, E
  • Huang, Y
  • Hugues, R
  • Hume, D
  • Ienasescu, H
  • Iida, K
  • Ikawa, T
  • Ikemura, T
  • Ikeo, K
  • Inoue, N
  • Ishizu, Y
  • Ito, Y
  • Itoh, M
  • Ivshina, AV
  • Jankovic, BR
  • Jenjaroenpun, P
  • Johnson, R
  • Jorgensen, M
  • Jorjani, H
  • Joshi, A
  • Jurman, G
  • Kaczkowski, B
  • Kai, C
  • Kaida, K
  • Kajiyama, K
  • Kaliyaperumal, R
  • Kaminuma, E
  • Kanaya, T
  • Kaneda, H
  • Kapranov, P
  • Kasianov, AS
  • Kasukawa, T
  • Katayama, T
  • Kato, S
  • Kawaguchi, S
  • Kawai, J
  • Kawaji, H
  • Kawamoto, H
  • Kawamura, YI
  • Kawasaki, S
  • Kawashima, T
  • Kempfle, JS
  • Kenna, TJ
  • Kere, J
  • Khachigian, L
  • Kiryu, H
  • Kishima, M
  • Kitajima, H
  • Kitamura, T
  • Kitano, H
  • Klaric, E
  • Klepper, K
  • Klinken, SP
  • Kloppmann, E
  • Knox, AJ
  • Kodama, Y
  • Kogo, Y
  • Kojima, M
  • Kojima, S
  • Komatsu, N
  • Komiyama, H
  • Kono, T
  • Koseki, H
  • Koyasu, S
  • Kratz, A
  • Kukalev, A
  • Kulakovskiy, I
  • Kundaje, A
  • Kunikata, H
  • Kuo, R
  • Kuo, T
  • Kuraku, S
  • Kuznetsov, VA
  • Kwon, TJ
  • Larouche, M
  • Lassmann, T
  • Law, A
  • Le-Cao, K-A
  • Lecellier, C-H
  • Lee, W
  • Lenhard, B
  • Lennartsson, A
  • Li, K
  • Li, R
  • Lilje, B
  • Lipovich, L
  • Lizio, M
  • Lopez, G
  • Magi, S
  • Mak, GK
  • Makeev, V
  • Manabe, R
  • Mandai, M
  • Mar, J
  • Maruyama, K
  • Maruyama, T
  • Mason, E
  • Mathelier, A
  • Matsuda, H
  • Medvedeva, YA
  • Meehan, TF
  • Mejhert, N
  • Meynert, A
  • Mikami, N
  • Minoda, A
  • Miura, H
  • Miyagi, Y
  • Miyawaki, A
  • Mizuno, Y
  • Morikawa, H
  • Morimoto, M
  • Morioka, M
  • Morishita, S
  • Moro, K
  • Motakis, E
  • Motohashi, H
  • Mukarram, AK
  • Mummery, CL
  • Mungall, CJ
  • Murakawa, Y
  • Muramatsu, M
  • Murata, M
  • Nagasaka, K
  • Nagase, T
  • Nakachi, Y
  • Nakahara, F
  • Nakai, K
  • Nakamura, K
  • Nakamura, Y
  • Nakamura, Y
  • Nakazawa, T
  • Nason, GP
  • Nepal, C
  • Nguyen, QH
  • Nielsen, LK
  • Nishida, K
  • Nishiguchi, KM
  • Nishiyori, H
  • Nitta, K
  • Noguchi, S
  • Noma, S
  • Notredame, C
  • Ogishima, S
  • Ohkura, N
  • Ohno, H
  • Ohshima, M
  • Ohtsu, T
  • Okada, Y
  • Okada-Hatakeyama, M
  • Okazaki, Y
  • Oksvold, P
  • Orlando, V
  • Ow, GS
  • Ozturk, M
  • Pachkov, M
  • Paparountas, T
  • Parihar, SP
  • Park, S-J
  • Pascarella, G
  • Passier, R
  • Persson, H
  • Philippens, IH
  • Piazza, S
  • Plessy, C
  • Pombo, A
  • Ponten, F
  • Poulain, S
  • Poulsen, TM
  • Pradhan, S
  • Prezioso, C
  • Pridans, C
  • Qin, X-Y
  • Quackenbush, J
  • Rackham, O
  • Ramilowski, J
  • Ravasi, T
  • Rehli, M
  • Rennie, S
  • Rito, T
  • Rizzu, P
  • Robert, C
  • Roos, M
  • Rost, B
  • Roudnicky, F
  • Roy, R
  • Rye, MB
  • Sachenkova, O
  • Saetrom, P
  • Sai, H
  • Saiki, S
  • Saito, M
  • Saito, A
  • Sakaguchi, S
  • Sakai, M
  • Sakaue, S
  • Sakaue-Sawano, A
  • Sandelin, A
  • Sano, H
  • Sasamoto, Y
  • Sato, H
  • Saxena, A
  • Saya, H
  • Schafferhans, A
  • Schmeier, S
  • Schmidl, C
  • Schmocker, D
  • Schneider, C
  • Schueler, M
  • Schultes, EA
  • Schulze-Tanzil, G
  • Semple, CA
  • Seno, S
  • Seo, W
  • Sese, J
  • Severin, J
  • Sheng, G
  • Shi, J
  • Shimoni, Y
  • Shin, JW
  • SimonSanchez, J
  • Sivertsson, A
  • Sjostedt, E
  • Soderhall, C
  • Laurent, GS
  • Stoiber, MH
  • Sugiyama, D
  • Summers, KM
  • Suzuki, AM
  • Suzuki, H
  • Suzuki, K
  • Suzuki, M
  • Suzuki, N
  • Suzuki, T
  • Swanson, DJ
  • Swoboda, RK
  • Tagami, M
  • Taguchi, A
  • Takahashi, H
  • Takahashi, M
  • Takamochi, K
  • Takeda, S
  • Takenaka, Y
  • Tam, KT
  • Tanaka, H
  • Tanaka, R
  • Tanaka, Y
  • Tang, D
  • Taniuchi, I
  • Tanzer, A
  • Tarui, H
  • Taylor, MS
  • Terada, A
  • Terao, Y
  • Testa, AC
  • Thomas, M
  • Thongjuea, S
  • Tomii, K
  • Triglia, ET
  • Toyoda, H
  • Tsang, HG
  • Tsujikawa, M
  • Uhlén, M
  • Valen, E
  • van de Wetering, M
  • van Nimwegen, E
  • Velmeshev, D
  • Verardo, R
  • Vitezic, M
  • Vitting-Seerup, K
  • von Feilitzen, K
  • Voolstra, CR
  • Vorontsov, IE
  • Wahlestedt, C
  • Wasserman, WW
  • Watanabe, K
  • Watanabe, S
  • Wells, CA
  • Winteringham, LN
  • Wolvetang, E
  • Yabukami, H
  • Yagi, K
  • Yamada, T
  • Yamaguchi, Y
  • Yamamoto, M
  • Yamamoto, Y
  • Yamamoto, Y
  • Yamanaka, Y
  • Yano, K
  • Yasuzawa, K
  • Yatsuka, Y
  • Yo, M
  • Yokokura, S
  • Yoneda, M
  • Yoshida, E
  • Yoshida, Y
  • Yoshihara, M
  • Young, R
  • Young, RS
  • Yu, NY
  • Yumoto, N
  • Zabierowski, SE
  • Zhang, PG
  • Zucchelli, S
  • Zwahlen, M
  • Chatelain, C
  • Carninci, P
  • de Hoon, MJL
  • Wasserman, WW
  • Bréhélin, L
  • Lecellier, C-H
Copyright, Publisher and Additional Information: © The Author(s) 2021. Open Access: This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
Keywords: A549 Cells; Animals; Base Sequence; Computational Biology; Deep Learning; Enhancer Elements, Genetic; Genome, Human; High-Throughput Nucleotide Sequencing; Humans; Mice; Microsatellite Repeats; Neural Networks, Computer; Neurodegenerative Diseases; Polymorphism, Genetic; Promoter Regions, Genetic; Transcription Initiation Site; Transcription Initiation, Genetic
Dates:
  • Accepted: 13 April 2021
  • Published (online): 2 June 2021
  • Published: 2 June 2021
Institution: The University of Sheffield
Academic Units: The University of Sheffield > Faculty of Medicine, Dentistry and Health (Sheffield) > Department of Neuroscience (Sheffield)
Depositing User: Symplectic Sheffield
Date Deposited: 07 Mar 2022 14:55
Last Modified: 07 Mar 2022 14:55
Status: Published
Publisher: Nature Research (part of Springer Nature)
Refereed: Yes
Identification Number: https://doi.org/10.1038/s41467-021-23143-7
Related URLs:

Share / Export

Statistics