Back to Search Start Over

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

Authors :
Grapotte M.
Saraswat M.
Bessiere C.
Menichelli C.
Ramilowski J. A.
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 M. C.
Abugessaisa I.
Aitken S.
Aken B. L.
Alam I.
Alam T.
Alasiri R.
Alhendi A. M. N.
Alinejad-Rokny H.
Alvarez M. J.
Andersson R.
Arakawa T.
Araki M.
Arbel T.
Archer J.
Archibald A. L.
Arner E.
Arner P.
Asai K.
Ashoor H.
Astrom G.
Babina M.
Baillie J. K.
Bajic V. B.
Bajpai A.
Baker S.
Baldarelli R. M.
Balic A.
Bansal M.
Batagov A. O.
Batzoglou S.
Beckhouse A. G.
Beltrami A. P.
Beltrami C. A.
Bertin N.
Bhattacharya S.
Bickel P. J.
Blake J. A.
Blanchette M.
Bodega B.
Bonetti A.
Bono H.
Bornholdt J.
Bttcher M.
Bougouffa S.
Boyd M.
Breda J.
Brombacher F.
Brown J. B.
Bult C. J.
Burroughs A. M.
Burt D. W.
Busch A.
Caglio G.
Califano A.
Cameron C. J.
Cannistraci C. V.
Carbone A.
Carlisle A. J.
Carninci P.
Carter K. W.
Cesselli D.
Chang J. -C.
Chen J. C.
Chen Y.
Chierici M.
Christodoulou J.
Ciani Y.
Clark E. L.
Coskun M.
Dalby M.
Dalla E.
Daub C. O.
Davis C. A.
de Hoon M. J. L.
de Rie D.
Denisenko E.
Deplancke B.
Detmar M.
Deviatiiarov R.
Di Bernardo D.
Diehl A. D.
Dieterich L. C.
Dimont E.
Djebali S.
Dohi T.
Dostie J.
Drablos F.
Edge A. S. B.
Edinger M.
Ehrlund A.
Ekwall K.
Elofsson A.
Endoh M.
Enomoto H.
Enomoto S.
Faghihi M.
Fagiolini M.
Farach-Carson M. C.
Faulkner G. J.
Favorov A.
Fernandes A. M.
Ferrai C.
Forrest A. R. R.
Forrester L. M.
Forsberg M.
Fort A.
Francescatto M.
Freeman T. C.
Frith M.
Fukuda S.
Funayama M.
Furlanello C.
Furuno M.
Furusawa C.
Gao H.
Gazova I.
Gebhard C.
Geier F.
Geijtenbeek T. B. H.
Ghosh S.
Ghosheh Y.
Gingeras T. R.
Gojobori T.
Goldberg T.
Goldowitz D.
Gough J.
Greco D.
Gruber A. J.
Guhl S.
Guigo R.
Guler R.
Gusev O.
Gustincich S.
Ha T. J.
Haberle V.
Hale P.
Hallstrom B. M.
Hamada M.
Handoko L.
Hara M.
Harbers M.
Harrow J.
Harshbarger J.
Hase T.
Hashimoto K.
Hatano T.
Hattori N.
Hayashi R.
Herlyn M.
Hettne K.
Heutink P.
Hide W.
Hitchens K. J.
Sui S. H.
't Hoen P. A. C.
Hon C. C.
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.
Ivshina A. V.
Jankovic B. R.
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 A. S.
Katayama T.
Kato S.
Kawaguchi S.
Kawai J.
Kawaji H.
Kawamoto H.
Kawamura Y. I.
Kawasaki S.
Kawashima T.
Kempfle J. S.
Kenna T. J.
Kere J.
Khachigian L.
Kiryu H.
Kishima M.
Kitajima H.
Kitamura T.
Kitano H.
Klaric E.
Klepper K.
Klinken S. P.
Kloppmann E.
Knox A. J.
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 V. A.
Kwon T. J.
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 G. K.
Makeev V.
Manabe R.
Mandai M.
Mar J.
Maruyama K.
Maruyama T.
Mason E.
Mathelier A.
Matsuda H.
Medvedeva Y. A.
Meehan T. F.
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 A. K.
Mummery C. L.
Mungall C. J.
Murakawa Y.
Muramatsu M.
Nagasaka K.
Nagase T.
Nakachi Y.
Nakahara F.
Nakai K.
Nakamura K.
Nakamura Y.
Nakazawa T.
Nason G. P.
Nepal C.
Nguyen Q. H.
Nielsen L. K.
Nishida K.
Nishiguchi K. M.
Nishiyori H.
Nitta K.
Notredame C.
Ogishima S.
Ohkura N.
Ohno H.
Ohshima M.
Ohtsu T.
Okada Y.
Okada-Hatakeyama M.
Okazaki Y.
Oksvold P.
Orlando V.
Ow G. S.
Ozturk M.
Pachkov M.
Paparountas T.
Parihar S. P.
Park S. -J.
Pascarella G.
Passier R.
Persson H.
Philippens I. H.
Piazza S.
Plessy C.
Pombo A.
Ponten F.
Poulain S.
Poulsen T. M.
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 M. B.
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 E. A.
Schulze-Tanzil G.
Semple C. A.
Seno S.
Seo W.
Sese J.
Sheng G.
Shi J.
Shimoni Y.
Shin J. W.
SimonSanchez J.
Sivertsson A.
Sjostedt E.
Soderhall C.
Laurent G. S.
Stoiber M. H.
Sugiyama D.
Summers K. M.
Suzuki A. M.
Suzuki K.
Suzuki M.
Suzuki N.
Suzuki T.
Swanson D. J.
Swoboda R. K.
Taguchi A.
Takahashi H.
Takahashi M.
Takamochi K.
Takeda S.
Takenaka Y.
Tam K. T.
Tanaka H.
Tanaka R.
Tanaka Y.
Tang D.
Taniuchi I.
Tanzer A.
Tarui H.
Taylor M. S.
Terada A.
Terao Y.
Testa A. C.
Thomas M.
Thongjuea S.
Tomii K.
Triglia E. T.
Toyoda H.
Tsang H. G.
Tsujikawa M.
Uhlen M.
Valen E.
van de Wetering M.
van Nimwegen E.
Velmeshev D.
Verardo R.
Vitezic M.
Vitting-Seerup K.
von Feilitzen K.
Voolstra C. R.
Vorontsov I. E.
Wahlestedt C.
Wasserman W. W.
Watanabe K.
Watanabe S.
Wells C. A.
Winteringham L. N.
Wolvetang E.
Yabukami H.
Yagi K.
Yamada T.
Yamaguchi Y.
Yamamoto M.
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 R. S.
Yu N. Y.
Yumoto N.
Zabierowski S. E.
Zhang P. G.
Zucchelli S.
Zwahlen M.
Chatelain C.
Brehelin L.
Grapotte, M.
Saraswat, M.
Bessiere, C.
Menichelli, C.
Ramilowski, J. A.
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, M. C.
Abugessaisa, I.
Aitken, S.
Aken, B. L.
Alam, I.
Alam, T.
Alasiri, R.
Alhendi, A. M. N.
Alinejad-Rokny, H.
Alvarez, M. J.
Andersson, R.
Arakawa, T.
Araki, M.
Arbel, T.
Archer, J.
Archibald, A. L.
Arner, E.
Arner, P.
Asai, K.
Ashoor, H.
Astrom, G.
Babina, M.
Baillie, J. K.
Bajic, V. B.
Bajpai, A.
Baker, S.
Baldarelli, R. M.
Balic, A.
Bansal, M.
Batagov, A. O.
Batzoglou, S.
Beckhouse, A. G.
Beltrami, A. P.
Beltrami, C. A.
Bertin, N.
Bhattacharya, S.
Bickel, P. J.
Blake, J. A.
Blanchette, M.
Bodega, B.
Bonetti, A.
Bono, H.
Bornholdt, J.
Bttcher, M.
Bougouffa, S.
Boyd, M.
Breda, J.
Brombacher, F.
Brown, J. B.
Bult, C. J.
Burroughs, A. M.
Burt, D. W.
Busch, A.
Caglio, G.
Califano, A.
Cameron, C. J.
Cannistraci, C. V.
Carbone, A.
Carlisle, A. J.
Carninci, P.
Carter, K. W.
Cesselli, D.
Chang, J. -C.
Chen, J. C.
Chen, Y.
Chierici, M.
Christodoulou, J.
Ciani, Y.
Clark, E. L.
Coskun, M.
Dalby, M.
Dalla, E.
Daub, C. O.
Davis, C. A.
de Hoon, M. J. L.
de Rie, D.
Denisenko, E.
Deplancke, B.
Detmar, M.
Deviatiiarov, R.
Di Bernardo, D.
Diehl, A. D.
Dieterich, L. C.
Dimont, E.
Djebali, S.
Dohi, T.
Dostie, J.
Drablos, F.
Edge, A. S. B.
Edinger, M.
Ehrlund, A.
Ekwall, K.
Elofsson, A.
Endoh, M.
Enomoto, H.
Enomoto, S.
Faghihi, M.
Fagiolini, M.
Farach-Carson, M. C.
Faulkner, G. J.
Favorov, A.
Fernandes, A. M.
Ferrai, C.
Forrest, A. R. R.
Forrester, L. M.
Forsberg, M.
Fort, A.
Francescatto, M.
Freeman, T. C.
Frith, M.
Fukuda, S.
Funayama, M.
Furlanello, C.
Furuno, M.
Furusawa, C.
Gao, H.
Gazova, I.
Gebhard, C.
Geier, F.
Geijtenbeek, T. B. H.
Ghosh, S.
Ghosheh, Y.
Gingeras, T. R.
Gojobori, T.
Goldberg, T.
Goldowitz, D.
Gough, J.
Greco, D.
Gruber, A. J.
Guhl, S.
Guigo, R.
Guler, R.
Gusev, O.
Gustincich, S.
Ha, T. J.
Haberle, V.
Hale, P.
Hallstrom, B. M.
Hamada, M.
Handoko, L.
Hara, M.
Harbers, M.
Harrow, J.
Harshbarger, J.
Hase, T.
Hashimoto, K.
Hatano, T.
Hattori, N.
Hayashi, R.
Herlyn, M.
Hettne, K.
Heutink, P.
Hide, W.
Hitchens, K. J.
Sui, S. H.
't Hoen, P. A. C.
Hon, C. C.
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.
Ivshina, A. V.
Jankovic, B. R.
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, A. S.
Katayama, T.
Kato, S.
Kawaguchi, S.
Kawai, J.
Kawaji, H.
Kawamoto, H.
Kawamura, Y. I.
Kawasaki, S.
Kawashima, T.
Kempfle, J. S.
Kenna, T. J.
Kere, J.
Khachigian, L.
Kiryu, H.
Kishima, M.
Kitajima, H.
Kitamura, T.
Kitano, H.
Klaric, E.
Klepper, K.
Klinken, S. P.
Kloppmann, E.
Knox, A. J.
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, V. A.
Kwon, T. J.
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, G. K.
Makeev, V.
Manabe, R.
Mandai, M.
Mar, J.
Maruyama, K.
Maruyama, T.
Mason, E.
Mathelier, A.
Matsuda, H.
Medvedeva, Y. A.
Meehan, T. F.
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, A. K.
Mummery, C. L.
Mungall, C. J.
Murakawa, Y.
Muramatsu, M.
Nagasaka, K.
Nagase, T.
Nakachi, Y.
Nakahara, F.
Nakai, K.
Nakamura, K.
Nakamura, Y.
Nakazawa, T.
Nason, G. P.
Nepal, C.
Nguyen, Q. H.
Nielsen, L. K.
Nishida, K.
Nishiguchi, K. M.
Nishiyori, H.
Nitta, K.
Notredame, C.
Ogishima, S.
Ohkura, N.
Ohno, H.
Ohshima, M.
Ohtsu, T.
Okada, Y.
Okada-Hatakeyama, M.
Okazaki, Y.
Oksvold, P.
Orlando, V.
Ow, G. S.
Ozturk, M.
Pachkov, M.
Paparountas, T.
Parihar, S. P.
Park, S. -J.
Pascarella, G.
Passier, R.
Persson, H.
Philippens, I. H.
Piazza, S.
Plessy, C.
Pombo, A.
Ponten, F.
Poulain, S.
Poulsen, T. M.
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, M. B.
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, E. A.
Schulze-Tanzil, G.
Semple, C. A.
Seno, S.
Seo, W.
Sese, J.
Sheng, G.
Shi, J.
Shimoni, Y.
Shin, J. W.
Simonsanchez, J.
Sivertsson, A.
Sjostedt, E.
Soderhall, C.
Laurent, G. S.
Stoiber, M. H.
Sugiyama, D.
Summers, K. M.
Suzuki, A. M.
Suzuki, K.
Suzuki, M.
Suzuki, N.
Suzuki, T.
Swanson, D. J.
Swoboda, R. K.
Taguchi, A.
Takahashi, H.
Takahashi, M.
Takamochi, K.
Takeda, S.
Takenaka, Y.
Tam, K. T.
Tanaka, H.
Tanaka, R.
Tanaka, Y.
Tang, D.
Taniuchi, I.
Tanzer, A.
Tarui, H.
Taylor, M. S.
Terada, A.
Terao, Y.
Testa, A. C.
Thomas, M.
Thongjuea, S.
Tomii, K.
Triglia, E. T.
Toyoda, H.
Tsang, H. G.
Tsujikawa, M.
Uhlen, M.
Valen, E.
van de Wetering, M.
van Nimwegen, E.
Velmeshev, D.
Verardo, R.
Vitezic, M.
Vitting-Seerup, K.
von Feilitzen, K.
Voolstra, C. R.
Vorontsov, I. E.
Wahlestedt, C.
Wasserman, W. W.
Watanabe, K.
Watanabe, S.
Wells, C. A.
Winteringham, L. N.
Wolvetang, E.
Yabukami, H.
Yagi, K.
Yamada, T.
Yamaguchi, Y.
Yamamoto, M.
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, R. S.
Yu, N. Y.
Yumoto, N.
Zabierowski, S. E.
Zhang, P. G.
Zucchelli, S.
Zwahlen, M.
Chatelain, C.
Brehelin, L.
Institute of Biotechnology
Biosciences
Institut de Génétique Moléculaire de Montpellier (IGMM)
Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Institut de Biologie Computationnelle (IBC)
Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Méthodes et Algorithmes pour la Bioinformatique (MAB)
Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM)
Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
RIKEN Center for Integrative Medical Sciences [Yokohama] (RIKEN IMS)
RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN)
National Institute of Advanced Industrial Science and Technology (AIST)
SANOFI Recherche
University of British Columbia (UBC)
Experimental Immunology
Infectious diseases
AII - Infectious diseases
Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)
Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)
Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)
Source :
Nature communications, vol 12, iss 1, Nature Communications, Nature Communications, 2021, 12, pp.1-18/3297. ⟨10.1038/s41467-021-23143-7⟩, Nature communications, 12(1):3297. Nature Publishing Group, Nature Communications, Nature Publishing Group, 2021, 12, pp.1-18. ⟨10.1038/s41467-021-23143-7⟩, Nature Communications, Vol 12, Iss 1, Pp 1-18 (2021), Grapotte, M, Saraswat, M, Bessière, C, Menichelli, C, Ramilowski, J A, 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, M C, Abugessaisa, I, Aitken, S, Aken, B L, Alam, I, Alam, T, Alasiri, R, Alhendi, A M N, Alinejad-Rokny, H, Alvarez, M J, Andersson, R, Arakawa, T, Araki, M, Arbel, T, Bornholdt, J, Boyd, M, Chen, Y, Coskun, M, Dalby, M, Ienasescu, H, Jørgensen, M, Kaczkowski, B, Kere, J, Li, K, Lilje, B, Nepal, C, Nguyen, Q H, Nielsen, L K, Rennie, S, Sandelin, A, Valen, E, Vitezic, M, Vitting-Seerup, K & FANTOM Consortium 2021, ' Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network ', Nature Communications, vol. 12, 3297 . https://doi.org/10.1038/s41467-021-23143-7, Grapotte, Mathys; Saraswat, Manu; Bessière, Chloé; Menichelli, Christophe; Ramilowski, Jordan A; Severin, Jessica; Hayashizaki, Yoshihide; Itoh, Masayoshi; Tagami, Michihira; Murata, Mitsuyoshi; Kojima-Ishiyama, Miki; Noma, Shohei; Noguchi, Shuhei; Kasukawa, Takeya; Hasegawa, Akira; Suzuki, Harukazu; Nishiyori-Sueki, Hiromi; Frith, Martin C; Chatelain, Clément; Carninci, Piero; ... (2021). Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature communications, 12(1), p. 3297. Nature Publishing Group 10.1038/s41467-021-23143-7 , Grapotte, M, Saraswat, M, Bessière, C, Menichelli, C, Ramilowski, J A, 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, M, Abugessaisa, I, Aitken, S, Aken, B L, Alam, I, Alam, T, Alasiri, R, Alhendi, A M N, Alinejad-rokny, H, Alvarez, M J, Andersson, R, Arakawa, T, Araki, M, Arbel, T, Archer, J, Archibald, A L, Arner, E, Arner, P, Asai, K, Ashoor, H, Astrom, G, Babina, M, Baillie, J K, Bajic, V B, Bajpai, A, Baker, S, Baldarelli, R M, Balic, A, Bansal, M, Batagov, A O, Batzoglou, S, Beckhouse, A G, Beltrami, A P, Beltrami, C A, Bertin, N, Bhattacharya, S, Bickel, P J, Blake, J A, Blanchette, M, Bodega, B, Bonetti, A, Bono, H, Bornholdt, J, Bttcher, M, Bougouffa, S, Boyd, M, Breda, J, Brombacher, F, Brown, J B, Bult, C J, Burroughs, A M, Burt, D W, Busch, A, Caglio, G, Califano, A, Cameron, C J, Cannistraci, C V, Carbone, A, Carlisle, A J, Carninci, P, Carter, K W, Cesselli, D, Chang, J, Chen, J C, Chen, Y, Chierici, M, Christodoulou, J, Ciani, Y, Clark, E L, Coskun, M, Dalby, M, Dalla, E, Daub, C O, Davis, C A, De Hoon, M J L, De Rie, D, Denisenko, E, Deplancke, B, Detmar, M, Deviatiiarov, R, Di Bernardo, D, Diehl, A D, Dieterich, L C, Dimont, E, Djebali, S, Dohi, T, Dostie, J, Drablos, F, Edge, A S B, Edinger, M, Ehrlund, A, Ekwall, K, Elofsson, A, Endoh, M, Enomoto, H, Enomoto, S, Faghihi, M, Fagiolini, M, Farach-carson, M C, Faulkner, G J, Favorov, A, Fernandes, A M, Ferrai, C, Forrest, A R R, Forrester, L M, Forsberg, M, Fort, A, Francescatto, M, Freeman, T C, Frith, M, Fukuda, S, Funayama, M, Furlanello, C, Furuno, M, Furusawa, C, Gao, H, Gazova, I, Gebhard, C, Geier, F, Geijtenbeek, T B H, Ghosh, S, Ghosheh, Y, Gingeras, T R, Gojobori, T, Goldberg, T, Goldowitz, D, Gough, J, Greco, D, Gruber, A J, Guhl, S, Guigo, R, Guler, R, Gusev, O, Gustincich, S, Ha, T J, Haberle, V, Hale, P, Hallstrom, B M, 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, Hettne, K, Heutink, P, Hide, W, Hitchens, K J, Sui, S H, ’t Hoen, P A C, Hon, C C, 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, A V, Jankovic, B R, 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, A S, Kasukawa, T, Katayama, T, Kato, S, Kawaguchi, S, Kawai, J, Kawaji, H, Kawamoto, H, Kawamura, Y I, Kawasaki, S, Kawashima, T, Kempfle, J S, Kenna, T J, Kere, J, Khachigian, L, Kiryu, H, Kishima, M, Kitajima, H, Kitamura, T, Kitano, H, Klaric, E, Klepper, K, Klinken, S P, Kloppmann, E, Knox, A J, 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, V A, Kwon, T J, Larouche, M, Lassmann, T, Law, A, Le-cao, K, Lecellier, C, Lee, W, Lenhard, B, Lennartsson, A, Li, K, Li, R, Lilje, B, Lipovich, L, Lizio, M, Lopez, G, Magi, S, Mak, G K, Makeev, V, Manabe, R, Mandai, M, Mar, J, Maruyama, K, Maruyama, T, Mason, E, Mathelier, A, Matsuda, H, Medvedeva, Y A, Meehan, T F, 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, A K, Mummery, C L, Mungall, C J, 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, G P, Nepal, C, Nguyen, Q H, Nielsen, L K, Nishida, K, Nishiguchi, K M, 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, G S, Ozturk, M, Pachkov, M, Paparountas, T, Parihar, S P, Park, S, Pascarella, G, Passier, R, Persson, H, Philippens, I H, Piazza, S, Plessy, C, Pombo, A, Ponten, F, Poulain, S, Poulsen, T M, Pradhan, S, Prezioso, C, Pridans, C, Qin, X, 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, M B, 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, E A, Schulze-tanzil, G, Semple, C A, Seno, S, Seo, W, Sese, J, Severin, J, Sheng, G, Shi, J, Shimoni, Y, Shin, J W, Simonsanchez, J, Sivertsson, A, Sjostedt, E, Soderhall, C, Laurent, G S, Stoiber, M H, Sugiyama, D, Summers, K M, Suzuki, A M, Suzuki, H, Suzuki, K, Suzuki, M, Suzuki, N, Suzuki, T, Swanson, D J, Swoboda, R K, Tagami, M, Taguchi, A, Takahashi, H, Takahashi, M, Takamochi, K, Takeda, S, Takenaka, Y, Tam, K T, Tanaka, H, Tanaka, R, Tanaka, Y, Tang, D, Taniuchi, I, Tanzer, A, Tarui, H, Taylor, M S, Terada, A, Terao, Y, Testa, A C, Thomas, M, Thongjuea, S, Tomii, K, Triglia, E T, Toyoda, H, Tsang, H G, 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, C R, Vorontsov, I E, Wahlestedt, C, Wasserman, W W, Watanabe, K, Watanabe, S, Wells, C A, Winteringham, L N, 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, R S, Yu, N Y, Yumoto, N, Zabierowski, S E, Zhang, P G, Zucchelli, S, Zwahlen, M, Chatelain, C, Carninci, P, De Hoon, M J L, Wasserman, W W, Bréhélin, L & Lecellier, C 2021, ' Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network ', Nature Communications, vol. 12, no. 1 . https://doi.org/10.1038/s41467-021-23143-7, Nature Communications, Nature Publishing Group, 2021, 12 (1), ⟨10.1038/s41467-021-23143-7⟩, Nature Communications, 12 (1)
Publication Year :
2020

Abstract

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.<br />Nature Communications, 12 (1)<br />ISSN:2041-1723

Subjects

Subjects :
0301 basic medicine
General Physics and Astronomy
Genome
Mice
0302 clinical medicine
Transcription (biology)
Promoter Regions, Genetic
Transcription Initiation, Genetic
0303 health sciences
Multidisciplinary
1184 Genetics, developmental biology, physiology
High-Throughput Nucleotide Sequencing
Neurodegenerative Diseases
222 Other engineering and technologies
Genomics
[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
humanities
Enhancer Elements, Genetic
Microsatellite Repeat
Transcription Initiation Site
Sequence motif
Transcription Initiation
Human
Enhancer Elements
Neural Networks
Science
610 Medicine & health
Computational biology
Biology
Article
General Biochemistry, Genetics and Molecular Biology
Promoter Regions
03 medical and health sciences
Computer
Deep Learning
Tandem repeat
Genetic
Clinical Research
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN]
Machine learning
Genetics
Animals
Humans
Polymorphism
Enhancer
Transcriptomics
Gene
A549 Cell
030304 developmental biology
Polymorphism, Genetic
Neurodegenerative Disease
Base Sequence
Animal
Genome, Human
Human Genome
Computational Biology
Promoter
General Chemistry
113 Computer and information sciences
Cap analysis gene expression
030104 developmental biology
[SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics
Cardiovascular and Metabolic Diseases
A549 Cells
Minion
Generic health relevance
3111 Biomedicine
Neural Networks, Computer
610 Medizin und Gesundheit
030217 neurology & neurosurgery
FANTOM consortium
Microsatellite Repeats

Details

ISSN :
20411723
Volume :
12
Issue :
1
Database :
OpenAIRE
Journal :
Nature communications
Accession number :
edsair.doi.dedup.....071cc9b35fa8ab5830f24ee8cb404eaf
Full Text :
https://doi.org/10.1038/s41467-021-23143-7⟩
Full Text Access
View/download PDF

Tools

Authors Abstract Subjects Details