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

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.

Authors:
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Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Contributing Org.:
FANTOM Consortium
OSTI Identifier:
1826558
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; genomics; machine learning; transcriptomics

Citation Formats

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., Abugessaisa, Imad, Aitken, Stuart, Aken, Bronwen L., Alam, Intikhab, Alam, Tanvir, Alasiri, Rami, Alhendi, Ahmad N., Alinejad-Rokny, Hamid, Alvarez, Mariano J., Andersson, Robin, Arakawa, Takahiro, Araki, Marito, Arbel, Taly, Archer, John, Archibald, Alan L., Arner, Erik, Arner, Peter, Asai, Kiyoshi, Ashoor, Haitham, Astrom, Gaby, Babina, Magda, Baillie, J. Kenneth, Bajic, Vladimir B., Bajpai, Archana, Baker, Sarah, Baldarelli, Richard M., Balic, Adam, Bansal, Mukesh, Batagov, Arsen O., Batzoglou, Serafim, Beckhouse, Anthony G., Beltrami, Antonio P., Beltrami, Carlo A., Bertin, Nicolas, Bhattacharya, Sharmodeep, Bickel, Peter J., Blake, Judith A., Blanchette, Mathieu, Bodega, Beatrice, Bonetti, Alessandro, Bono, Hidemasa, Bornholdt, Jette, Bttcher, Michael, Bougouffa, Salim, Boyd, Mette, Breda, Jeremie, Brombacher, Frank, Brown, James B., Bult, Carol J., Burroughs, A. Maxwell, Burt, Dave W., Busch, Annika, Caglio, Giulia, Califano, Andrea, Cameron, Christopher J., Cannistraci, Carlo V., Carbone, Alessandra, Carlisle, Ailsa J., Carninci, Piero, Carter, Kim W., Cesselli, Daniela, Chang, Jen-Chien, Chen, Julie C., Chen, Yun, Chierici, Marco, Christodoulou, John, Ciani, Yari, Clark, Emily L., Coskun, Mehmet, Dalby, Maria, Dalla, Emiliano, Daub, Carsten O., Davis, Carrie A., de Hoon, Michiel L., de Rie, Derek, Denisenko, Elena, Deplancke, Bart, Detmar, Michael, Deviatiiarov, Ruslan, Di Bernardo, Diego, Diehl, Alexander D., Dieterich, Lothar C., Dimont, Emmanuel, Djebali, Sarah, Dohi, Taeko, Dostie, Jose, Drablos, Finn, Edge, Albert B., Edinger, Matthias, Ehrlund, Anna, Ekwall, Karl, Elofsson, Arne, Endoh, Mitsuhiro, Enomoto, Hideki, Enomoto, Saaya, Faghihi, Mohammad, Fagiolini, Michela, Farach-Carson, Mary C., Faulkner, Geoffrey J., Favorov, Alexander, Fernandes, Ana Miguel, Ferrai, Carmelo, Forrest, Alistair R., Forrester, Lesley M., Forsberg, Mattias, Fort, Alexandre, Francescatto, Margherita, Freeman, Tom C., Frith, Martin, Fukuda, Shinji, Funayama, Manabu, Furlanello, Cesare, Furuno, Masaaki, Furusawa, Chikara, Gao, Hui, Gazova, Iveta, Gebhard, Claudia, Geier, Florian, Geijtenbeek, Teunis H., Ghosh, Samik, Ghosheh, Yanal, Gingeras, Thomas R., Gojobori, Takashi, Goldberg, Tatyana, Goldowitz, Daniel, Gough, Julian, Greco, Dario, Gruber, Andreas J., Guhl, Sven, Guigo, Roderic, Guler, Reto, Gusev, Oleg, Gustincich, Stefano, Ha, Thomas J., Haberle, Vanja, Hale, Paul, Hallstrom, Bjrn M., Hamada, Michiaki, Handoko, Lusy, Hara, Mitsuko, Harbers, Matthias, Harrow, Jennifer, Harshbarger, Jayson, Hase, Takeshi, Hasegawa, Akira, Hashimoto, Kosuke, Hatano, Taku, Hattori, Nobutaka, Hayashi, Ryuhei, Hayashizaki, Yoshihide, Herlyn, Meenhard, Hettne, Kristina, Heutink, Peter, Hide, Winston, Hitchens, Kelly J., Sui, Shannon Ho, ’t Hoen, Peter C., Hon, Chung Chau, Hori, Fumi, Horie, Masafumi, Horimoto, Katsuhisa, Horton, Paul, Hou, Rui, Huang, Edward, Huang, Yi, Hugues, Richard, Hume, David, Ienasescu, Hans, Iida, Kei, Ikawa, Tomokatsu, Ikemura, Toshimichi, Ikeo, Kazuho, Inoue, Norihiko, Ishizu, Yuri, Ito, Yosuke, Itoh, Masayoshi, Ivshina, Anna V., Jankovic, Boris R., Jenjaroenpun, Piroon, Johnson, Rory, Jorgensen, Mette, Jorjani, Hadi, Joshi, Anagha, Jurman, Giuseppe, Kaczkowski, Bogumil, Kai, Chieko, Kaida, Kaoru, Kajiyama, Kazuhiro, Kaliyaperumal, Rajaram, Kaminuma, Eli, Kanaya, Takashi, Kaneda, Hiroshi, Kapranov, Philip, Kasianov, Artem S., Kasukawa, Takeya, Katayama, Toshiaki, Kato, Sachi, Kawaguchi, Shuji, Kawai, Jun, Kawaji, Hideya, Kawamoto, Hiroshi, Kawamura, Yuki I., Kawasaki, Satoshi, Kawashima, Tsugumi, Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon, Kiryu, Hisanori, Kishima, Mami, Kitajima, Hiroyuki, Kitamura, Toshio, Kitano, Hiroaki, Klaric, Enio, Klepper, Kjetil, Klinken, S. Peter, Kloppmann, Edda, Knox, Alan J., Kodama, Yuichi, Kogo, Yasushi, Kojima, Miki, Kojima, Soichi, Komatsu, Norio, Komiyama, Hiromitsu, Kono, Tsukasa, Koseki, Haruhiko, Koyasu, Shigeo, Kratz, Anton, Kukalev, Alexander, Kulakovskiy, Ivan, Kundaje, Anshul, Kunikata, Hiroshi, Kuo, Richard, Kuo, Tony, Kuraku, Shigehiro, Kuznetsov, Vladimir A., Kwon, Tae Jun, Larouche, Matt, Lassmann, Timo, Law, Andy, Le-Cao, Kim-Anh, Lecellier, Charles-Henri, Lee, Weonju, Lenhard, Boris, Lennartsson, Andreas, Li, Kang, Li, Ruohan, Lilje, Berit, Lipovich, Leonard, Lizio, Marina, Lopez, Gonzalo, Magi, Shigeyuki, Mak, Gloria K., Makeev, Vsevolod, Manabe, Riichiro, Mandai, Michiko, Mar, Jessica, Maruyama, Kazuichi, Maruyama, Taeko, Mason, Elizabeth, Mathelier, Anthony, Matsuda, Hideo, Medvedeva, Yulia A., Meehan, Terrence F., Mejhert, Niklas, Meynert, Alison, Mikami, Norihisa, Minoda, Akiko, Miura, Hisashi, Miyagi, Yohei, Miyawaki, Atsushi, Mizuno, Yosuke, Morikawa, Hiromasa, Morimoto, Mitsuru, Morioka, Masaki, Morishita, Soji, Moro, Kazuyo, Motakis, Efthymios, Motohashi, Hozumi, Mukarram, Abdul Kadir, Mummery, Christine L., Mungall, Christopher J., Murakawa, Yasuhiro, Muramatsu, Masami, Murata, Mitsuyoshi, Nagasaka, Kazunori, Nagase, Takahide, Nakachi, Yutaka, Nakahara, Fumio, Nakai, Kenta, Nakamura, Kumi, Nakamura, Yasukazu, Nakamura, Yukio, Nakazawa, Toru, Nason, Guy P., Nepal, Chirag, Nguyen, Quan Hoang, Nielsen, Lars K., Nishida, Kohji, Nishiguchi, Koji M., Nishiyori, Hiromi, Nitta, Kazuhiro, Noguchi, Shuhei, Noma, Shohei, Notredame, Cedric, Ogishima, Soichi, Ohkura, Naganari, Ohno, Hiroshi, Ohshima, Mitsuhiro, Ohtsu, Takashi, Okada, Yukinori, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Oksvold, Per, Orlando, Valerio, Ow, Ghim Sion, Ozturk, Mumin, Pachkov, Mikhail, Paparountas, Triantafyllos, Parihar, Suraj P., Park, Sung-Joon, Pascarella, Giovanni, Passier, Robert, Persson, Helena, Philippens, Ingrid H., Piazza, Silvano, Plessy, Charles, Pombo, Ana, Ponten, Fredrik, Poulain, Stéphane, Poulsen, Thomas M., Pradhan, Swati, Prezioso, Carolina, Pridans, Clare, Qin, Xiang-Yang, Quackenbush, John, Rackham, Owen, Ramilowski, Jordan, Ravasi, Timothy, Rehli, Michael, Rennie, Sarah, Rito, Tiago, Rizzu, Patrizia, Robert, Christelle, Roos, Marco, Rost, Burkhard, Roudnicky, Filip, Roy, Riti, Rye, Morten B., Sachenkova, Oxana, Saetrom, Pal, Sai, Hyonmi, Saiki, Shinji, Saito, Mitsue, Saito, Akira, Sakaguchi, Shimon, Sakai, Mizuho, Sakaue, Saori, Sakaue-Sawano, Asako, Sandelin, Albin, Sano, Hiromi, Sasamoto, Yuzuru, Sato, Hiroki, Saxena, Alka, Saya, Hideyuki, Schafferhans, Andrea, Schmeier, Sebastian, Schmidl, Christian, Schmocker, Daniel, Schneider, Claudio, Schueler, Marcus, Schultes, Erik A., Schulze-Tanzil, Gundula, Semple, Colin A., Seno, Shigeto, Seo, Wooseok, Sese, Jun, Severin, Jessica, Sheng, Guojun, Shi, Jiantao, Shimoni, Yishai, Shin, Jay W., SimonSanchez, Javier, Sivertsson, Asa, Sjostedt, Evelina, Soderhall, Cilla, Laurent, Georges St, Stoiber, Marcus H., Sugiyama, Daisuke, Summers, Kim M., Suzuki, Ana Maria, Suzuki, Harukazu, Suzuki, Kenji, Suzuki, Mikiko, Suzuki, Naoko, Suzuki, Takahiro, Swanson, Douglas J., Swoboda, Rolf K., Tagami, Michihira, Taguchi, Ayumi, Takahashi, Hazuki, Takahashi, Masayo, Takamochi, Kazuya, Takeda, Satoru, Takenaka, Yoichi, Tam, Kin Tung, Tanaka, Hiroshi, Tanaka, Rica, Tanaka, Yuji, Tang, Dave, Taniuchi, Ichiro, Tanzer, Andrea, Tarui, Hiroshi, Taylor, Martin S., Terada, Aika, Terao, Yasuhisa, Testa, Alison C., Thomas, Mark, Thongjuea, Supat, Tomii, Kentaro, Triglia, Elena Torlai, Toyoda, Hiroo, Tsang, H. Gwen, Tsujikawa, Motokazu, Uhlén, Mathias, Valen, Eivind, van de Wetering, Marc, van Nimwegen, Erik, Velmeshev, Dmitry, Verardo, Roberto, Vitezic, Morana, Vitting-Seerup, Kristoffer, von Feilitzen, Kalle, Voolstra, Christian R., Vorontsov, Ilya E., Wahlestedt, Claes, Wasserman, Wyeth W., Watanabe, Kazuhide, Watanabe, Shoko, Wells, Christine A., Winteringham, Louise N., Wolvetang, Ernst, Yabukami, Haruka, Yagi, Ken, Yamada, Takuji, Yamaguchi, Yoko, Yamamoto, Masayuki, Yamamoto, Yasutomo, Yamamoto, Yumiko, Yamanaka, Yasunari, Yano, Kojiro, Yasuzawa, Kayoko, Yatsuka, Yukiko, Yo, Masahiro, Yokokura, Shunji, Yoneda, Misako, Yoshida, Emiko, Yoshida, Yuki, Yoshihara, Masahito, Young, Rachel, Young, Robert S., Yu, Nancy Y., Yumoto, Noriko, Zabierowski, Susan E., Zhang, Peter G., Zucchelli, Silvia, Zwahlen, Martin, Chatelain, Clément, Carninci, Piero, de Hoon, Michiel L., Wasserman, Wyeth W., Bréhélin, Laurent, and Lecellier, Charles-Henri. Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. United States: N. p., 2021. Web. doi:10.1038/s41467-021-23143-7.
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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., Abugessaisa, Imad, Aitken, Stuart, Aken, Bronwen L., Alam, Intikhab, Alam, Tanvir, Alasiri, Rami, Alhendi, Ahmad N., Alinejad-Rokny, Hamid, Alvarez, Mariano J., Andersson, Robin, Arakawa, Takahiro, Araki, Marito, Arbel, Taly, Archer, John, Archibald, Alan L., Arner, Erik, Arner, Peter, Asai, Kiyoshi, Ashoor, Haitham, Astrom, Gaby, Babina, Magda, Baillie, J. Kenneth, Bajic, Vladimir B., Bajpai, Archana, Baker, Sarah, Baldarelli, Richard M., Balic, Adam, Bansal, Mukesh, Batagov, Arsen O., Batzoglou, Serafim, Beckhouse, Anthony G., Beltrami, Antonio P., Beltrami, Carlo A., Bertin, Nicolas, Bhattacharya, Sharmodeep, Bickel, Peter J., Blake, Judith A., Blanchette, Mathieu, Bodega, Beatrice, Bonetti, Alessandro, Bono, Hidemasa, Bornholdt, Jette, Bttcher, Michael, Bougouffa, Salim, Boyd, Mette, Breda, Jeremie, Brombacher, Frank, Brown, James B., Bult, Carol J., Burroughs, A. Maxwell, Burt, Dave W., Busch, Annika, Caglio, Giulia, Califano, Andrea, Cameron, Christopher J., Cannistraci, Carlo V., Carbone, Alessandra, Carlisle, Ailsa J., Carninci, Piero, Carter, Kim W., Cesselli, Daniela, Chang, Jen-Chien, Chen, Julie C., Chen, Yun, Chierici, Marco, Christodoulou, John, Ciani, Yari, Clark, Emily L., Coskun, Mehmet, Dalby, Maria, Dalla, Emiliano, Daub, Carsten O., Davis, Carrie A., de Hoon, Michiel L., de Rie, Derek, Denisenko, Elena, Deplancke, Bart, Detmar, Michael, Deviatiiarov, Ruslan, Di Bernardo, Diego, Diehl, Alexander D., Dieterich, Lothar C., Dimont, Emmanuel, Djebali, Sarah, Dohi, Taeko, Dostie, Jose, Drablos, Finn, Edge, Albert B., Edinger, Matthias, Ehrlund, Anna, Ekwall, Karl, Elofsson, Arne, Endoh, Mitsuhiro, Enomoto, Hideki, Enomoto, Saaya, Faghihi, Mohammad, Fagiolini, Michela, Farach-Carson, Mary C., Faulkner, Geoffrey J., Favorov, Alexander, Fernandes, Ana Miguel, Ferrai, Carmelo, Forrest, Alistair R., Forrester, Lesley M., Forsberg, Mattias, Fort, Alexandre, Francescatto, Margherita, Freeman, Tom C., Frith, Martin, Fukuda, Shinji, Funayama, Manabu, Furlanello, Cesare, Furuno, Masaaki, Furusawa, Chikara, Gao, Hui, Gazova, Iveta, Gebhard, Claudia, Geier, Florian, Geijtenbeek, Teunis H., Ghosh, Samik, Ghosheh, Yanal, Gingeras, Thomas R., Gojobori, Takashi, Goldberg, Tatyana, Goldowitz, Daniel, Gough, Julian, Greco, Dario, Gruber, Andreas J., Guhl, Sven, Guigo, Roderic, Guler, Reto, Gusev, Oleg, Gustincich, Stefano, Ha, Thomas J., Haberle, Vanja, Hale, Paul, Hallstrom, Bjrn M., Hamada, Michiaki, Handoko, Lusy, Hara, Mitsuko, Harbers, Matthias, Harrow, Jennifer, Harshbarger, Jayson, Hase, Takeshi, Hasegawa, Akira, Hashimoto, Kosuke, Hatano, Taku, Hattori, Nobutaka, Hayashi, Ryuhei, Hayashizaki, Yoshihide, Herlyn, Meenhard, Hettne, Kristina, Heutink, Peter, Hide, Winston, Hitchens, Kelly J., Sui, Shannon Ho, ’t Hoen, Peter C., Hon, Chung Chau, Hori, Fumi, Horie, Masafumi, Horimoto, Katsuhisa, Horton, Paul, Hou, Rui, Huang, Edward, Huang, Yi, Hugues, Richard, Hume, David, Ienasescu, Hans, Iida, Kei, Ikawa, Tomokatsu, Ikemura, Toshimichi, Ikeo, Kazuho, Inoue, Norihiko, Ishizu, Yuri, Ito, Yosuke, Itoh, Masayoshi, Ivshina, Anna V., Jankovic, Boris R., Jenjaroenpun, Piroon, Johnson, Rory, Jorgensen, Mette, Jorjani, Hadi, Joshi, Anagha, Jurman, Giuseppe, Kaczkowski, Bogumil, Kai, Chieko, Kaida, Kaoru, Kajiyama, Kazuhiro, Kaliyaperumal, Rajaram, Kaminuma, Eli, Kanaya, Takashi, Kaneda, Hiroshi, Kapranov, Philip, Kasianov, Artem S., Kasukawa, Takeya, Katayama, Toshiaki, Kato, Sachi, Kawaguchi, Shuji, Kawai, Jun, Kawaji, Hideya, Kawamoto, Hiroshi, Kawamura, Yuki I., Kawasaki, Satoshi, Kawashima, Tsugumi, Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon, Kiryu, Hisanori, Kishima, Mami, Kitajima, Hiroyuki, Kitamura, Toshio, Kitano, Hiroaki, Klaric, Enio, Klepper, Kjetil, Klinken, S. Peter, Kloppmann, Edda, Knox, Alan J., Kodama, Yuichi, Kogo, Yasushi, Kojima, Miki, Kojima, Soichi, Komatsu, Norio, Komiyama, Hiromitsu, Kono, Tsukasa, Koseki, Haruhiko, Koyasu, Shigeo, Kratz, Anton, Kukalev, Alexander, Kulakovskiy, Ivan, Kundaje, Anshul, Kunikata, Hiroshi, Kuo, Richard, Kuo, Tony, Kuraku, Shigehiro, Kuznetsov, Vladimir A., Kwon, Tae Jun, Larouche, Matt, Lassmann, Timo, Law, Andy, Le-Cao, Kim-Anh, Lecellier, Charles-Henri, Lee, Weonju, Lenhard, Boris, Lennartsson, Andreas, Li, Kang, Li, Ruohan, Lilje, Berit, Lipovich, Leonard, Lizio, Marina, Lopez, Gonzalo, Magi, Shigeyuki, Mak, Gloria K., Makeev, Vsevolod, Manabe, Riichiro, Mandai, Michiko, Mar, Jessica, Maruyama, Kazuichi, Maruyama, Taeko, Mason, Elizabeth, Mathelier, Anthony, Matsuda, Hideo, Medvedeva, Yulia A., Meehan, Terrence F., Mejhert, Niklas, Meynert, Alison, Mikami, Norihisa, Minoda, Akiko, Miura, Hisashi, Miyagi, Yohei, Miyawaki, Atsushi, Mizuno, Yosuke, Morikawa, Hiromasa, Morimoto, Mitsuru, Morioka, Masaki, Morishita, Soji, Moro, Kazuyo, Motakis, Efthymios, Motohashi, Hozumi, Mukarram, Abdul Kadir, Mummery, Christine L., Mungall, Christopher J., Murakawa, Yasuhiro, Muramatsu, Masami, Murata, Mitsuyoshi, Nagasaka, Kazunori, Nagase, Takahide, Nakachi, Yutaka, Nakahara, Fumio, Nakai, Kenta, Nakamura, Kumi, Nakamura, Yasukazu, Nakamura, Yukio, Nakazawa, Toru, Nason, Guy P., Nepal, Chirag, Nguyen, Quan Hoang, Nielsen, Lars K., Nishida, Kohji, Nishiguchi, Koji M., Nishiyori, Hiromi, Nitta, Kazuhiro, Noguchi, Shuhei, Noma, Shohei, Notredame, Cedric, Ogishima, Soichi, Ohkura, Naganari, Ohno, Hiroshi, Ohshima, Mitsuhiro, Ohtsu, Takashi, Okada, Yukinori, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Oksvold, Per, Orlando, Valerio, Ow, Ghim Sion, Ozturk, Mumin, Pachkov, Mikhail, Paparountas, Triantafyllos, Parihar, Suraj P., Park, Sung-Joon, Pascarella, Giovanni, Passier, Robert, Persson, Helena, Philippens, Ingrid H., Piazza, Silvano, Plessy, Charles, Pombo, Ana, Ponten, Fredrik, Poulain, Stéphane, Poulsen, Thomas M., Pradhan, Swati, Prezioso, Carolina, Pridans, Clare, Qin, Xiang-Yang, Quackenbush, John, Rackham, Owen, Ramilowski, Jordan, Ravasi, Timothy, Rehli, Michael, Rennie, Sarah, Rito, Tiago, Rizzu, Patrizia, Robert, Christelle, Roos, Marco, Rost, Burkhard, Roudnicky, Filip, Roy, Riti, Rye, Morten B., Sachenkova, Oxana, Saetrom, Pal, Sai, Hyonmi, Saiki, Shinji, Saito, Mitsue, Saito, Akira, Sakaguchi, Shimon, Sakai, Mizuho, Sakaue, Saori, Sakaue-Sawano, Asako, Sandelin, Albin, Sano, Hiromi, Sasamoto, Yuzuru, Sato, Hiroki, Saxena, Alka, Saya, Hideyuki, Schafferhans, Andrea, Schmeier, Sebastian, Schmidl, Christian, Schmocker, Daniel, Schneider, Claudio, Schueler, Marcus, Schultes, Erik A., Schulze-Tanzil, Gundula, Semple, Colin A., Seno, Shigeto, Seo, Wooseok, Sese, Jun, Severin, Jessica, Sheng, Guojun, Shi, Jiantao, Shimoni, Yishai, Shin, Jay W., SimonSanchez, Javier, Sivertsson, Asa, Sjostedt, Evelina, Soderhall, Cilla, Laurent, Georges St, Stoiber, Marcus H., Sugiyama, Daisuke, Summers, Kim M., Suzuki, Ana Maria, Suzuki, Harukazu, Suzuki, Kenji, Suzuki, Mikiko, Suzuki, Naoko, Suzuki, Takahiro, Swanson, Douglas J., Swoboda, Rolf K., Tagami, Michihira, Taguchi, Ayumi, Takahashi, Hazuki, Takahashi, Masayo, Takamochi, Kazuya, Takeda, Satoru, Takenaka, Yoichi, Tam, Kin Tung, Tanaka, Hiroshi, Tanaka, Rica, Tanaka, Yuji, Tang, Dave, Taniuchi, Ichiro, Tanzer, Andrea, Tarui, Hiroshi, Taylor, Martin S., Terada, Aika, Terao, Yasuhisa, Testa, Alison C., Thomas, Mark, Thongjuea, Supat, Tomii, Kentaro, Triglia, Elena Torlai, Toyoda, Hiroo, Tsang, H. Gwen, Tsujikawa, Motokazu, Uhlén, Mathias, Valen, Eivind, van de Wetering, Marc, van Nimwegen, Erik, Velmeshev, Dmitry, Verardo, Roberto, Vitezic, Morana, Vitting-Seerup, Kristoffer, von Feilitzen, Kalle, Voolstra, Christian R., Vorontsov, Ilya E., Wahlestedt, Claes, Wasserman, Wyeth W., Watanabe, Kazuhide, Watanabe, Shoko, Wells, Christine A., Winteringham, Louise N., Wolvetang, Ernst, Yabukami, Haruka, Yagi, Ken, Yamada, Takuji, Yamaguchi, Yoko, Yamamoto, Masayuki, Yamamoto, Yasutomo, Yamamoto, Yumiko, Yamanaka, Yasunari, Yano, Kojiro, Yasuzawa, Kayoko, Yatsuka, Yukiko, Yo, Masahiro, Yokokura, Shunji, Yoneda, Misako, Yoshida, Emiko, Yoshida, Yuki, Yoshihara, Masahito, Young, Rachel, Young, Robert S., Yu, Nancy Y., Yumoto, Noriko, Zabierowski, Susan E., Zhang, Peter G., Zucchelli, Silvia, Zwahlen, Martin, Chatelain, Clément, Carninci, Piero, de Hoon, Michiel L., Wasserman, Wyeth W., Bréhélin, Laurent, & Lecellier, Charles-Henri. Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. United States. https://doi.org/10.1038/s41467-021-23143-7
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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., Abugessaisa, Imad, Aitken, Stuart, Aken, Bronwen L., Alam, Intikhab, Alam, Tanvir, Alasiri, Rami, Alhendi, Ahmad N., Alinejad-Rokny, Hamid, Alvarez, Mariano J., Andersson, Robin, Arakawa, Takahiro, Araki, Marito, Arbel, Taly, Archer, John, Archibald, Alan L., Arner, Erik, Arner, Peter, Asai, Kiyoshi, Ashoor, Haitham, Astrom, Gaby, Babina, Magda, Baillie, J. Kenneth, Bajic, Vladimir B., Bajpai, Archana, Baker, Sarah, Baldarelli, Richard M., Balic, Adam, Bansal, Mukesh, Batagov, Arsen O., Batzoglou, Serafim, Beckhouse, Anthony G., Beltrami, Antonio P., Beltrami, Carlo A., Bertin, Nicolas, Bhattacharya, Sharmodeep, Bickel, Peter J., Blake, Judith A., Blanchette, Mathieu, Bodega, Beatrice, Bonetti, Alessandro, Bono, Hidemasa, Bornholdt, Jette, Bttcher, Michael, Bougouffa, Salim, Boyd, Mette, Breda, Jeremie, Brombacher, Frank, Brown, James B., Bult, Carol J., Burroughs, A. Maxwell, Burt, Dave W., Busch, Annika, Caglio, Giulia, Califano, Andrea, Cameron, Christopher J., Cannistraci, Carlo V., Carbone, Alessandra, Carlisle, Ailsa J., Carninci, Piero, Carter, Kim W., Cesselli, Daniela, Chang, Jen-Chien, Chen, Julie C., Chen, Yun, Chierici, Marco, Christodoulou, John, Ciani, Yari, Clark, Emily L., Coskun, Mehmet, Dalby, Maria, Dalla, Emiliano, Daub, Carsten O., Davis, Carrie A., de Hoon, Michiel L., de Rie, Derek, Denisenko, Elena, Deplancke, Bart, Detmar, Michael, Deviatiiarov, Ruslan, Di Bernardo, Diego, Diehl, Alexander D., Dieterich, Lothar C., Dimont, Emmanuel, Djebali, Sarah, Dohi, Taeko, Dostie, Jose, Drablos, Finn, Edge, Albert B., Edinger, Matthias, Ehrlund, Anna, Ekwall, Karl, Elofsson, Arne, Endoh, Mitsuhiro, Enomoto, Hideki, Enomoto, Saaya, Faghihi, Mohammad, Fagiolini, Michela, Farach-Carson, Mary C., Faulkner, Geoffrey J., Favorov, Alexander, Fernandes, Ana Miguel, Ferrai, Carmelo, Forrest, Alistair R., Forrester, Lesley M., Forsberg, Mattias, Fort, Alexandre, Francescatto, Margherita, Freeman, Tom C., Frith, Martin, Fukuda, Shinji, Funayama, Manabu, Furlanello, Cesare, Furuno, Masaaki, Furusawa, Chikara, Gao, Hui, Gazova, Iveta, Gebhard, Claudia, Geier, Florian, Geijtenbeek, Teunis H., Ghosh, Samik, Ghosheh, Yanal, Gingeras, Thomas R., Gojobori, Takashi, Goldberg, Tatyana, Goldowitz, Daniel, Gough, Julian, Greco, Dario, Gruber, Andreas J., Guhl, Sven, Guigo, Roderic, Guler, Reto, Gusev, Oleg, Gustincich, Stefano, Ha, Thomas J., Haberle, Vanja, Hale, Paul, Hallstrom, Bjrn M., Hamada, Michiaki, Handoko, Lusy, Hara, Mitsuko, Harbers, Matthias, Harrow, Jennifer, Harshbarger, Jayson, Hase, Takeshi, Hasegawa, Akira, Hashimoto, Kosuke, Hatano, Taku, Hattori, Nobutaka, Hayashi, Ryuhei, Hayashizaki, Yoshihide, Herlyn, Meenhard, Hettne, Kristina, Heutink, Peter, Hide, Winston, Hitchens, Kelly J., Sui, Shannon Ho, ’t Hoen, Peter C., Hon, Chung Chau, Hori, Fumi, Horie, Masafumi, Horimoto, Katsuhisa, Horton, Paul, Hou, Rui, Huang, Edward, Huang, Yi, Hugues, Richard, Hume, David, Ienasescu, Hans, Iida, Kei, Ikawa, Tomokatsu, Ikemura, Toshimichi, Ikeo, Kazuho, Inoue, Norihiko, Ishizu, Yuri, Ito, Yosuke, Itoh, Masayoshi, Ivshina, Anna V., Jankovic, Boris R., Jenjaroenpun, Piroon, Johnson, Rory, Jorgensen, Mette, Jorjani, Hadi, Joshi, Anagha, Jurman, Giuseppe, Kaczkowski, Bogumil, Kai, Chieko, Kaida, Kaoru, Kajiyama, Kazuhiro, Kaliyaperumal, Rajaram, Kaminuma, Eli, Kanaya, Takashi, Kaneda, Hiroshi, Kapranov, Philip, Kasianov, Artem S., Kasukawa, Takeya, Katayama, Toshiaki, Kato, Sachi, Kawaguchi, Shuji, Kawai, Jun, Kawaji, Hideya, Kawamoto, Hiroshi, Kawamura, Yuki I., Kawasaki, Satoshi, Kawashima, Tsugumi, Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon, Kiryu, Hisanori, Kishima, Mami, Kitajima, Hiroyuki, Kitamura, Toshio, Kitano, Hiroaki, Klaric, Enio, Klepper, Kjetil, Klinken, S. Peter, Kloppmann, Edda, Knox, Alan J., Kodama, Yuichi, Kogo, Yasushi, Kojima, Miki, Kojima, Soichi, Komatsu, Norio, Komiyama, Hiromitsu, Kono, Tsukasa, Koseki, Haruhiko, Koyasu, Shigeo, Kratz, Anton, Kukalev, Alexander, Kulakovskiy, Ivan, Kundaje, Anshul, Kunikata, Hiroshi, Kuo, Richard, Kuo, Tony, Kuraku, Shigehiro, Kuznetsov, Vladimir A., Kwon, Tae Jun, Larouche, Matt, Lassmann, Timo, Law, Andy, Le-Cao, Kim-Anh, Lecellier, Charles-Henri, Lee, Weonju, Lenhard, Boris, Lennartsson, Andreas, Li, Kang, Li, Ruohan, Lilje, Berit, Lipovich, Leonard, Lizio, Marina, Lopez, Gonzalo, Magi, Shigeyuki, Mak, Gloria K., Makeev, Vsevolod, Manabe, Riichiro, Mandai, Michiko, Mar, Jessica, Maruyama, Kazuichi, Maruyama, Taeko, Mason, Elizabeth, Mathelier, Anthony, Matsuda, Hideo, Medvedeva, Yulia A., Meehan, Terrence F., Mejhert, Niklas, Meynert, Alison, Mikami, Norihisa, Minoda, Akiko, Miura, Hisashi, Miyagi, Yohei, Miyawaki, Atsushi, Mizuno, Yosuke, Morikawa, Hiromasa, Morimoto, Mitsuru, Morioka, Masaki, Morishita, Soji, Moro, Kazuyo, Motakis, Efthymios, Motohashi, Hozumi, Mukarram, Abdul Kadir, Mummery, Christine L., Mungall, Christopher J., Murakawa, Yasuhiro, Muramatsu, Masami, Murata, Mitsuyoshi, Nagasaka, Kazunori, Nagase, Takahide, Nakachi, Yutaka, Nakahara, Fumio, Nakai, Kenta, Nakamura, Kumi, Nakamura, Yasukazu, Nakamura, Yukio, Nakazawa, Toru, Nason, Guy P., Nepal, Chirag, Nguyen, Quan Hoang, Nielsen, Lars K., Nishida, Kohji, Nishiguchi, Koji M., Nishiyori, Hiromi, Nitta, Kazuhiro, Noguchi, Shuhei, Noma, Shohei, Notredame, Cedric, Ogishima, Soichi, Ohkura, Naganari, Ohno, Hiroshi, Ohshima, Mitsuhiro, Ohtsu, Takashi, Okada, Yukinori, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Oksvold, Per, Orlando, Valerio, Ow, Ghim Sion, Ozturk, Mumin, Pachkov, Mikhail, Paparountas, Triantafyllos, Parihar, Suraj P., Park, Sung-Joon, Pascarella, Giovanni, Passier, Robert, Persson, Helena, Philippens, Ingrid H., Piazza, Silvano, Plessy, Charles, Pombo, Ana, Ponten, Fredrik, Poulain, Stéphane, Poulsen, Thomas M., Pradhan, Swati, Prezioso, Carolina, Pridans, Clare, Qin, Xiang-Yang, Quackenbush, John, Rackham, Owen, Ramilowski, Jordan, Ravasi, Timothy, Rehli, Michael, Rennie, Sarah, Rito, Tiago, Rizzu, Patrizia, Robert, Christelle, Roos, Marco, Rost, Burkhard, Roudnicky, Filip, Roy, Riti, Rye, Morten B., Sachenkova, Oxana, Saetrom, Pal, Sai, Hyonmi, Saiki, Shinji, Saito, Mitsue, Saito, Akira, Sakaguchi, Shimon, Sakai, Mizuho, Sakaue, Saori, Sakaue-Sawano, Asako, Sandelin, Albin, Sano, Hiromi, Sasamoto, Yuzuru, Sato, Hiroki, Saxena, Alka, Saya, Hideyuki, Schafferhans, Andrea, Schmeier, Sebastian, Schmidl, Christian, Schmocker, Daniel, Schneider, Claudio, Schueler, Marcus, Schultes, Erik A., Schulze-Tanzil, Gundula, Semple, Colin A., Seno, Shigeto, Seo, Wooseok, Sese, Jun, Severin, Jessica, Sheng, Guojun, Shi, Jiantao, Shimoni, Yishai, Shin, Jay W., SimonSanchez, Javier, Sivertsson, Asa, Sjostedt, Evelina, Soderhall, Cilla, Laurent, Georges St, Stoiber, Marcus H., Sugiyama, Daisuke, Summers, Kim M., Suzuki, Ana Maria, Suzuki, Harukazu, Suzuki, Kenji, Suzuki, Mikiko, Suzuki, Naoko, Suzuki, Takahiro, Swanson, Douglas J., Swoboda, Rolf K., Tagami, Michihira, Taguchi, Ayumi, Takahashi, Hazuki, Takahashi, Masayo, Takamochi, Kazuya, Takeda, Satoru, Takenaka, Yoichi, Tam, Kin Tung, Tanaka, Hiroshi, Tanaka, Rica, Tanaka, Yuji, Tang, Dave, Taniuchi, Ichiro, Tanzer, Andrea, Tarui, Hiroshi, Taylor, Martin S., Terada, Aika, Terao, Yasuhisa, Testa, Alison C., Thomas, Mark, Thongjuea, Supat, Tomii, Kentaro, Triglia, Elena Torlai, Toyoda, Hiroo, Tsang, H. Gwen, Tsujikawa, Motokazu, Uhlén, Mathias, Valen, Eivind, van de Wetering, Marc, van Nimwegen, Erik, Velmeshev, Dmitry, Verardo, Roberto, Vitezic, Morana, Vitting-Seerup, Kristoffer, von Feilitzen, Kalle, Voolstra, Christian R., Vorontsov, Ilya E., Wahlestedt, Claes, Wasserman, Wyeth W., Watanabe, Kazuhide, Watanabe, Shoko, Wells, Christine A., Winteringham, Louise N., Wolvetang, Ernst, Yabukami, Haruka, Yagi, Ken, Yamada, Takuji, Yamaguchi, Yoko, Yamamoto, Masayuki, Yamamoto, Yasutomo, Yamamoto, Yumiko, Yamanaka, Yasunari, Yano, Kojiro, Yasuzawa, Kayoko, Yatsuka, Yukiko, Yo, Masahiro, Yokokura, Shunji, Yoneda, Misako, Yoshida, Emiko, Yoshida, Yuki, Yoshihara, Masahito, Young, Rachel, Young, Robert S., Yu, Nancy Y., Yumoto, Noriko, Zabierowski, Susan E., Zhang, Peter G., Zucchelli, Silvia, Zwahlen, Martin, Chatelain, Clément, Carninci, Piero, de Hoon, Michiel L., Wasserman, Wyeth W., Bréhélin, Laurent, and Lecellier, Charles-Henri. Wed . "Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network". United States. https://doi.org/10.1038/s41467-021-23143-7. https://www.osti.gov/servlets/purl/1826558.
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@article{osti_1826558,
title = {Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network},
author = {Grapotte, Mathys and Saraswat, Manu and Bessière, Chloé and Menichelli, Christophe and Ramilowski, Jordan A. and Severin, Jessica and Hayashizaki, Yoshihide and Itoh, Masayoshi and Tagami, Michihira and Murata, Mitsuyoshi and Kojima-Ishiyama, Miki and Noma, Shohei and Noguchi, Shuhei and Kasukawa, Takeya and Hasegawa, Akira and Suzuki, Harukazu and Nishiyori-Sueki, Hiromi and Frith, Martin C. and Abugessaisa, Imad and Aitken, Stuart and Aken, Bronwen L. and Alam, Intikhab and Alam, Tanvir and Alasiri, Rami and Alhendi, Ahmad N. and Alinejad-Rokny, Hamid and Alvarez, Mariano J. and Andersson, Robin and Arakawa, Takahiro and Araki, Marito and Arbel, Taly and Archer, John and Archibald, Alan L. and Arner, Erik and Arner, Peter and Asai, Kiyoshi and Ashoor, Haitham and Astrom, Gaby and Babina, Magda and Baillie, J. Kenneth and Bajic, Vladimir B. and Bajpai, Archana and Baker, Sarah and Baldarelli, Richard M. and Balic, Adam and Bansal, Mukesh and Batagov, Arsen O. and Batzoglou, Serafim and Beckhouse, Anthony G. and Beltrami, Antonio P. and Beltrami, Carlo A. and Bertin, Nicolas and Bhattacharya, Sharmodeep and Bickel, Peter J. and Blake, Judith A. and Blanchette, Mathieu and Bodega, Beatrice and Bonetti, Alessandro and Bono, Hidemasa and Bornholdt, Jette and Bttcher, Michael and Bougouffa, Salim and Boyd, Mette and Breda, Jeremie and Brombacher, Frank and Brown, James B. and Bult, Carol J. and Burroughs, A. Maxwell and Burt, Dave W. and Busch, Annika and Caglio, Giulia and Califano, Andrea and Cameron, Christopher J. and Cannistraci, Carlo V. and Carbone, Alessandra and Carlisle, Ailsa J. and Carninci, Piero and Carter, Kim W. and Cesselli, Daniela and Chang, Jen-Chien and Chen, Julie C. and Chen, Yun and Chierici, Marco and Christodoulou, John and Ciani, Yari and Clark, Emily L. and Coskun, Mehmet and Dalby, Maria and Dalla, Emiliano and Daub, Carsten O. and Davis, Carrie A. and de Hoon, Michiel L. and de Rie, Derek and Denisenko, Elena and Deplancke, Bart and Detmar, Michael and Deviatiiarov, Ruslan and Di Bernardo, Diego and Diehl, Alexander D. and Dieterich, Lothar C. and Dimont, Emmanuel and Djebali, Sarah and Dohi, Taeko and Dostie, Jose and Drablos, Finn and Edge, Albert B. and Edinger, Matthias and Ehrlund, Anna and Ekwall, Karl and Elofsson, Arne and Endoh, Mitsuhiro and Enomoto, Hideki and Enomoto, Saaya and Faghihi, Mohammad and Fagiolini, Michela and Farach-Carson, Mary C. and Faulkner, Geoffrey J. and Favorov, Alexander and Fernandes, Ana Miguel and Ferrai, Carmelo and Forrest, Alistair R. and Forrester, Lesley M. and Forsberg, Mattias and Fort, Alexandre and Francescatto, Margherita and Freeman, Tom C. and Frith, Martin and Fukuda, Shinji and Funayama, Manabu and Furlanello, Cesare and Furuno, Masaaki and Furusawa, Chikara and Gao, Hui and Gazova, Iveta and Gebhard, Claudia and Geier, Florian and Geijtenbeek, Teunis H. and Ghosh, Samik and Ghosheh, Yanal and Gingeras, Thomas R. and Gojobori, Takashi and Goldberg, Tatyana and Goldowitz, Daniel and Gough, Julian and Greco, Dario and Gruber, Andreas J. and Guhl, Sven and Guigo, Roderic and Guler, Reto and Gusev, Oleg and Gustincich, Stefano and Ha, Thomas J. and Haberle, Vanja and Hale, Paul and Hallstrom, Bjrn M. and Hamada, Michiaki and Handoko, Lusy and Hara, Mitsuko and Harbers, Matthias and Harrow, Jennifer and Harshbarger, Jayson and Hase, Takeshi and Hasegawa, Akira and Hashimoto, Kosuke and Hatano, Taku and Hattori, Nobutaka and Hayashi, Ryuhei and Hayashizaki, Yoshihide and Herlyn, Meenhard and Hettne, Kristina and Heutink, Peter and Hide, Winston and Hitchens, Kelly J. and Sui, Shannon Ho and ’t Hoen, Peter C. and Hon, Chung Chau and Hori, Fumi and Horie, Masafumi and Horimoto, Katsuhisa and Horton, Paul and Hou, Rui and Huang, Edward and Huang, Yi and Hugues, Richard and Hume, David and Ienasescu, Hans and Iida, Kei and Ikawa, Tomokatsu and Ikemura, Toshimichi and Ikeo, Kazuho and Inoue, Norihiko and Ishizu, Yuri and Ito, Yosuke and Itoh, Masayoshi and Ivshina, Anna V. and Jankovic, Boris R. and Jenjaroenpun, Piroon and Johnson, Rory and Jorgensen, Mette and Jorjani, Hadi and Joshi, Anagha and Jurman, Giuseppe and Kaczkowski, Bogumil and Kai, Chieko and Kaida, Kaoru and Kajiyama, Kazuhiro and Kaliyaperumal, Rajaram and Kaminuma, Eli and Kanaya, Takashi and Kaneda, Hiroshi and Kapranov, Philip and Kasianov, Artem S. and Kasukawa, Takeya and Katayama, Toshiaki and Kato, Sachi and Kawaguchi, Shuji and Kawai, Jun and Kawaji, Hideya and Kawamoto, Hiroshi and Kawamura, Yuki I. and Kawasaki, Satoshi and Kawashima, Tsugumi and Kempfle, Judith S. and Kenna, Tony J. and Kere, Juha and Khachigian, Levon and Kiryu, Hisanori and Kishima, Mami and Kitajima, Hiroyuki and Kitamura, Toshio and Kitano, Hiroaki and Klaric, Enio and Klepper, Kjetil and Klinken, S. Peter and Kloppmann, Edda and Knox, Alan J. and Kodama, Yuichi and Kogo, Yasushi and Kojima, Miki and Kojima, Soichi and Komatsu, Norio and Komiyama, Hiromitsu and Kono, Tsukasa and Koseki, Haruhiko and Koyasu, Shigeo and Kratz, Anton and Kukalev, Alexander and Kulakovskiy, Ivan and Kundaje, Anshul and Kunikata, Hiroshi and Kuo, Richard and Kuo, Tony and Kuraku, Shigehiro and Kuznetsov, Vladimir A. and Kwon, Tae Jun and Larouche, Matt and Lassmann, Timo and Law, Andy and Le-Cao, Kim-Anh and Lecellier, Charles-Henri and Lee, Weonju and Lenhard, Boris and Lennartsson, Andreas and Li, Kang and Li, Ruohan and Lilje, Berit and Lipovich, Leonard and Lizio, Marina and Lopez, Gonzalo and Magi, Shigeyuki and Mak, Gloria K. and Makeev, Vsevolod and Manabe, Riichiro and Mandai, Michiko and Mar, Jessica and Maruyama, Kazuichi and Maruyama, Taeko and Mason, Elizabeth and Mathelier, Anthony and Matsuda, Hideo and Medvedeva, Yulia A. and Meehan, Terrence F. and Mejhert, Niklas and Meynert, Alison and Mikami, Norihisa and Minoda, Akiko and Miura, Hisashi and Miyagi, Yohei and Miyawaki, Atsushi and Mizuno, Yosuke and Morikawa, Hiromasa and Morimoto, Mitsuru and Morioka, Masaki and Morishita, Soji and Moro, Kazuyo and Motakis, Efthymios and Motohashi, Hozumi and Mukarram, Abdul Kadir and Mummery, Christine L. and Mungall, Christopher J. and Murakawa, Yasuhiro and Muramatsu, Masami and Murata, Mitsuyoshi and Nagasaka, Kazunori and Nagase, Takahide and Nakachi, Yutaka and Nakahara, Fumio and Nakai, Kenta and Nakamura, Kumi and Nakamura, Yasukazu and Nakamura, Yukio and Nakazawa, Toru and Nason, Guy P. and Nepal, Chirag and Nguyen, Quan Hoang and Nielsen, Lars K. and Nishida, Kohji and Nishiguchi, Koji M. and Nishiyori, Hiromi and Nitta, Kazuhiro and Noguchi, Shuhei and Noma, Shohei and Notredame, Cedric and Ogishima, Soichi and Ohkura, Naganari and Ohno, Hiroshi and Ohshima, Mitsuhiro and Ohtsu, Takashi and Okada, Yukinori and Okada-Hatakeyama, Mariko and Okazaki, Yasushi and Oksvold, Per and Orlando, Valerio and Ow, Ghim Sion and Ozturk, Mumin and Pachkov, Mikhail and Paparountas, Triantafyllos and Parihar, Suraj P. and Park, Sung-Joon and Pascarella, Giovanni and Passier, Robert and Persson, Helena and Philippens, Ingrid H. and Piazza, Silvano and Plessy, Charles and Pombo, Ana and Ponten, Fredrik and Poulain, Stéphane and Poulsen, Thomas M. and Pradhan, Swati and Prezioso, Carolina and Pridans, Clare and Qin, Xiang-Yang and Quackenbush, John and Rackham, Owen and Ramilowski, Jordan and Ravasi, Timothy and Rehli, Michael and Rennie, Sarah and Rito, Tiago and Rizzu, Patrizia and Robert, Christelle and Roos, Marco and Rost, Burkhard and Roudnicky, Filip and Roy, Riti and Rye, Morten B. and Sachenkova, Oxana and Saetrom, Pal and Sai, Hyonmi and Saiki, Shinji and Saito, Mitsue and Saito, Akira and Sakaguchi, Shimon and Sakai, Mizuho and Sakaue, Saori and Sakaue-Sawano, Asako and Sandelin, Albin and Sano, Hiromi and Sasamoto, Yuzuru and Sato, Hiroki and Saxena, Alka and Saya, Hideyuki and Schafferhans, Andrea and Schmeier, Sebastian and Schmidl, Christian and Schmocker, Daniel and Schneider, Claudio and Schueler, Marcus and Schultes, Erik A. and Schulze-Tanzil, Gundula and Semple, Colin A. and Seno, Shigeto and Seo, Wooseok and Sese, Jun and Severin, Jessica and Sheng, Guojun and Shi, Jiantao and Shimoni, Yishai and Shin, Jay W. and SimonSanchez, Javier and Sivertsson, Asa and Sjostedt, Evelina and Soderhall, Cilla and Laurent, Georges St and Stoiber, Marcus H. and Sugiyama, Daisuke and Summers, Kim M. and Suzuki, Ana Maria and Suzuki, Harukazu and Suzuki, Kenji and Suzuki, Mikiko and Suzuki, Naoko and Suzuki, Takahiro and Swanson, Douglas J. and Swoboda, Rolf K. and Tagami, Michihira and Taguchi, Ayumi and Takahashi, Hazuki and Takahashi, Masayo and Takamochi, Kazuya and Takeda, Satoru and Takenaka, Yoichi and Tam, Kin Tung and Tanaka, Hiroshi and Tanaka, Rica and Tanaka, Yuji and Tang, Dave and Taniuchi, Ichiro and Tanzer, Andrea and Tarui, Hiroshi and Taylor, Martin S. and Terada, Aika and Terao, Yasuhisa and Testa, Alison C. and Thomas, Mark and Thongjuea, Supat and Tomii, Kentaro and Triglia, Elena Torlai and Toyoda, Hiroo and Tsang, H. Gwen and Tsujikawa, Motokazu and Uhlén, Mathias and Valen, Eivind and van de Wetering, Marc and van Nimwegen, Erik and Velmeshev, Dmitry and Verardo, Roberto and Vitezic, Morana and Vitting-Seerup, Kristoffer and von Feilitzen, Kalle and Voolstra, Christian R. and Vorontsov, Ilya E. and Wahlestedt, Claes and Wasserman, Wyeth W. and Watanabe, Kazuhide and Watanabe, Shoko and Wells, Christine A. and Winteringham, Louise N. and Wolvetang, Ernst and Yabukami, Haruka and Yagi, Ken and Yamada, Takuji and Yamaguchi, Yoko and Yamamoto, Masayuki and Yamamoto, Yasutomo and Yamamoto, Yumiko and Yamanaka, Yasunari and Yano, Kojiro and Yasuzawa, Kayoko and Yatsuka, Yukiko and Yo, Masahiro and Yokokura, Shunji and Yoneda, Misako and Yoshida, Emiko and Yoshida, Yuki and Yoshihara, Masahito and Young, Rachel and Young, Robert S. and Yu, Nancy Y. and Yumoto, Noriko and Zabierowski, Susan E. and Zhang, Peter G. and Zucchelli, Silvia and Zwahlen, Martin and Chatelain, Clément and Carninci, Piero and de Hoon, Michiel L. and Wasserman, Wyeth W. and Bréhélin, Laurent and Lecellier, Charles-Henri},
abstractNote = {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.},
doi = {10.1038/s41467-021-23143-7},
journal = {Nature Communications},
number = 1,
volume = 12,
place = {United States},
year = {Wed Jun 02 00:00:00 EDT 2021},
month = {Wed Jun 02 00:00:00 EDT 2021}
}
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Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
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