Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types

Autor: Yip, Chi Wai, Hon, Chung-Chau, Yasuzawa, Kayoko, Sivaraman, Divya M., Ramilowski, Jordan A., Shibayama, Youtaro, Agrawal, Saumya, Prabhu, Anika V., Parr, Callum, Severin, Jessica, Lan, Yan Jun, Dostie, Josée, Petri, Andreas, Nishiyori-Sueki, Hiromi, Tagami, Michihira, Itoh, Masayoshi, López-Redondo, Fernando, Kouno, Tsukasa, Chang, Jen-Chien, Luginbühl, Joachim, Kato, Masaki, Murata, Mitsuyoshi, Yip, Wing Hin, Shu, Xufeng, Abugessaisa, Imad, Hasegawa, Akira, Suzuki, Harukazu, Kauppinen, Sakari, Yagi, Ken, Okazaki, Yasushi, Kasukawa, Takeya, de Hoon, Michiel, Carninci, Piero, Shin, Jay W.

Publikováno v: In Cell Reports 27 December 2022 41(13)

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Functional annotation of human long noncoding RNAs via molecular phenotyping

Autor: Ramilowski, Jordan A., Yip, Chi Wai, Agrawal, Saumya, Chang, Jen-Chien, Ciani, Yari, Kulakovskiy, Ivan V., Mendez, Mickaël, Ooi, Jasmine Li Ching, Ouyang, John F., Parkinson, Nicholas J., Petri, Andreas, Roos, Leonie, Severin, Jessica, Yasuzawa, Kayoko, Abugessaisa, Imad, Akalin, Altuna, Antonov, Ivan V., Arner, Erik, Bonetti, Alessandro, Bono, Hidemasa, Borsari, Beatrice, Brombacher, Frank, Cameron, Christopher J.F., Cannistraci, Carlo V., Cardenas, Ryan, Cardon, Melissa, Chang, Howard, Dostie, Josée, Ducoli, Luca, Favorov, Alexander V., Fort, Alexandre, Garrido, Diego, Gil, Noa, Gimenez, Juliette, Guler, Reto, Handoko, Lusy, Harshbarger, Jayson, Hasegawa, Akira, Hasegawa, Yuki, Hashimoto, Kosuke, Hayatsu, Norihito, Heutink, Peter, Hirose, Tetsuro, Imada, Eddie L., Itoh, Masayoshi, Kaczkowski, Bogumil, Kanhere, Aditi S., Kawabata, Emily, Kawaji, Hideya, Kawashima, Tsugumi, Kelly, S. Thomas, Kojima, Miki, Kondo, Naoto, Koseki, Haruhiko, Kouno, Tsukasa, Kratz, Anton, Kurowska-Stolarska, Mariola S., Kwon, Andrew Tae Jun, Leek, Jeffrey T., Lennartsson, Andreas, Lizio, Marina, López-Redondo, Fernando, Luginbühl, Joachim, Maeda, Shiori, Makeev, Vsevolod, Marchionni, Luigi, Medvedeva, Yulia A., Minoda, Aki, Müller, Ferenc, Muñoz-Aguirre, Manuel, Murata, Mitsuyoshi, Nishiyori, Hiromi, Nitta, Kazuhiro R., Noguchi, Shuhei, Noro, Yukihiko, Nurtdinov, Ramil N., Okazaki, Yasushi, Orlando, Valerio, Paquette, Denis, Parr, Callum J.C., Rackham, Owen J.L., Rizzu, Patrizia, Sánchez Martinez, Diego Fernando, Sandelin, Albin, Sanjana, Pillay, Semple, Colin A.M., Shibayama, Youtaro, Sivaraman, Divya M., Szumowski, Suzannah C., Tagami, Michihira, Taylor, Martin S., Terao, Chikashi, Thodberg, Malte, Thongjuea, Supat, Tripathi, Vidisha, Ulitsky, Igor, Verardo, Roberto, Vorontsov, Ilya E., Yamamoto, Chinatsu, Baillie, J. Kenneth, Forrest, Alistair R.R., Guigó, Roderic, Hoffman, Michael, Hon, Chungchau, Kasukawa, Takeya, Kauppinen, Sakari, Kere, Jura, Lenhard, Boris, Schneider, Claudio, Suzuki, Harukazu, Yagi, Ken, de Hoon, Michiel J.L., Shin, Jay W., Carninci, Piero

Publikováno v: Genome Research, 30 (7)

Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human derm

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1d5a1f97f79581c06928dffa7f9fe536
https://hdl.handle.net/20.500.11850/438210

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

Autor: Hurst, Laurence D., Ghanbarian, Avazeh T., Forrest, Alistair R R, Huminiecki, Lukasz, Rehli, Michael, Kenneth Baillie, J., de Hoon, Michiel J L, Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicolas, Jørgensen, Mette, Dimont, Emmanuel, Arner, Erik, Schmidl, Christian, Schaefer, Ulf, Medvedeva, Yulia A., Plessy, Charles, Vitezic, Morana, Severin, Jessica, Semple, Colin A., Ishizu, Yuri, Young, Robert S., Francescatto, Margherita, Alam, Intikhab, Albanese, Davide, Altschuler, Gabriel M., Arakawa, Takahiro, Archer, John A C, Arner, Peter, Babina, Magda, Baker, Sarah, Balwierz, Piotr J., Beckhouse, Anthony G., Pradhan, Swati Bhatt, Blake, Judith A., Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Maxwell Burroughs, A., Califano, Andrea, Cannistraci, Carlo V., Carbajo, Daniel, Chen, Yun, Chierici, Marco, Ciani, Yari, Clevers, Hans C., Dalla, Emiliano, Davis, Carrie A., Detmar, Michael, Diehl, Alexander D., Dohi, Taeko, Drabløs, Finn, Edge, Albert S B, Edinger, Matthias, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Fagiolini, Michela, Fairbairn, Lynsey, Fang, Hai, Farach-Carson, Mary C., Faulkner, Geoffrey J., Favorov, Alexander V., Fisher, Malcolm E., Frith, Martin C., Fujita, Rie, Fukuda, Shiro, Furlanello, Cesare, Furuno, Masaaki, Furusawa, Jun ichi, Geijtenbeek, Teunis B., Gibson, Andrew, Gingeras, Thomas, Goldowitz, Daniel, Gough, Julian, Guhl, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J., Hamaguchi, Masahide, Hara, Mitsuko, Harbers, Matthias, Harshbarger, Jayson, Hasegawa, Akira, Hasegawa, Yuki, Hashimoto, Takehiro, Herlyn, Meenhard, Hitchens, Kelly J., Ho Sui, Shannan J., Hofmann, Oliver M., Hoof, Ilka, Hori, Fumi, Iida, Kei, Ikawa, Tomokatsu, Jankovic, Boris R., Jia, Hui, Joshi, Anagha, Jurman, Giuseppe, Kaczkowski, Bogumil, Kai, Chieko, Kaida, Kaoru, Kaiho, Ai, Kajiyama, Kazuhiro, Kanamori, Mutsumi Katayama, Kasianov, Artem S., Kasukawa, Takeya, Katayama, Shintaro, Kato, Sachi, Kawaguchi, Shuji, Kawamoto, Hiroshi, Kawamura, Yuki I., Kawashima, Tsugumi, Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon M., Kitamura, Toshio, Peter Klinken, S., Knox, Alan J., Kojima, Miki, Kojima, Soichi, Kondo, Naoto, Koseki, Haruhiko, Koyasu, Shigeo, Krampitz, Sarah, Kubosaki, Atsutaka, Kwon, Andrew T., Laros, Jeroen F J, Lee, Weonju, Lennartsson, Andreas, Li, Kang, Lilje, Berit, Lipovich, Leonard, Mackay, Alan sim, Manabe, Riichiroh, Mar, Jessica C., Marchand, Benoit, Mathelier, Anthony, Mejhert, Niklas, Meynert, Alison, Mizuno, Yosuke, de Lima Morais, David A., Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Motakis, Efthymios, Motohashi, Hozumi, Mummery, Christine L., Murata, Mitsuyoshi, Nagao, Sayaka Sato, Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nakazato, Kenichi, van Nimwegen, Erik, Ninomiya, Noriko, Nishiyori, Hiromi, Noma, Shohei, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohmiya, Hiroko, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada, Mariko Hatakeyama, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A., Pain, Arnab, Passier, Robert, Patrikakis, Margaret, Persson, Helena, Piazza, Silvano, Prendergast, James G D, Rackham, Owen J L, Ramilowski, Jordan A., Rashid, Mamoon, Ravasi, Timothy, Rizzu, Patrizia, Roncador, Marco, Roy, Sugata, Rye, Morten B., Saijyo, Eri, Sajantila, Antti, Saka, Akiko, Sakaguchi, Shimon, Sakai, Mizuho, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schneider, Claudio, Schultes, Erik A., Schulze-Tanzil, Gundula G., Schwegmann, Anita, Sengstag, Thierry, Sheng, Guojun, Shimoji, Hisashi, Shimoni, Yishai, Shin, Jay W., Simon, Christophe, Sugiyama, Daisuke, Sugiyama, Takaaki, Suzuki, Masanori, Suzuki, Naoko, Swoboda, Rolf K., 't Hoen, Peter A C, Tagami, Michihira, Takahashi, Naoko, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tatum, Zuotian, Thompson, Mark, Toyoda, Hiroo, Toyoda, Tetsuro, Valen, Eivind, van de Wetering, Marc, van den Berg, Linda M., Verardo, Roberto, Vijayan, Dipti, Vorontsov, Ilya E., Wasserman, Wyeth W., Watanabe, Shoko, Wells, Christine A., Winteringham, Louise N., Wolvetang, Ernst, Wood, Emily J., Yamaguchi, Yoko, Yamamoto, Masayuki, Yoneda, Misako, Yonekura, Yohei, Yoshida, Shigehiro, Zabierowski, Suzan E., Zhang, Peter G., Zhao, Xiaobei, Zucchelli, Silvia, Summers, Kim M., Suzuki, Harukazu, Daub, Carsten O., Kawai, Jun, Heutink, Peter, Hide, Winston, Freeman, Tom C., Lenhard, Boris, Bajic, Vladimir B., Taylor, Martin S., Makeev, Vsevolod J., Sandelin, Albin Gustav, Hume, David A., Carninci, Piero, Hayashizaki, Yoshihide

Publikováno v: PLoS Biology, Vol 13, Iss 12, p e1002315 (2015)
PLoS Biol, 13(12). Public Library of Science
PLoS Biology
PLoS Biology, 13(12). Public Library of Science
Hurst, L D, Ghanbarian, A T, Forrest, A R R, Huminiecki, L, Rehli, M, Kenneth Baillie, J, de Hoon, M J L, Haberle, V, Lassmann, T, Kulakovskiy, I V, Lizio, M, Itoh, M, Andersson, R, Mungall, C J, Meehan, T F, Schmeier, S, Bertin, N, Jørgensen, M, Dimont, E, Arner, E, Schmidl, C, Schaefer, U, Medvedeva, Y A, Plessy, C, Vitezic, M, Severin, J, Semple, C A, Ishizu, Y, Young, R S, Francescatto, M, Alam, I, Albanese, D, Altschuler, G M, Arakawa, T, Archer, J A C, Arner, P, Babina, M, Baker, S, Balwierz, P J, Beckhouse, A G, Pradhan, S B, Blake, J A, Blumenthal, A, Bodega, B, Bonetti, A, Briggs, J, Brombacher, F, Maxwell Burroughs, A, Califano, A, Cannistraci, C V, Carbajo, D, Chen, Y, Chierici, M, Ciani, Y, Clevers, H C, Dalla, E, Davis, C A, Detmar, M, Diehl, A D, Dohi, T, Drabløs, F, Edge, A S B, Edinger, M, Ekwall, K, Endoh, M, Enomoto, H, Fagiolini, M, Fairbairn, L, Fang, H, Farach-Carson, M C, Faulkner, G J, Favorov, A V, Fisher, M E, Frith, M C, Fujita, R, Fukuda, S, Furlanello, C, Furuno, M, Furusawa, J I, Geijtenbeek, T B, Gibson, A, Gingeras, T, Goldowitz, D, Gough, J, Guhl, S, Guler, R, Gustincich, S, Ha, T J, Hamaguchi, M, Hara, M, Harbers, M, Harshbarger, J, Hasegawa, A, Hasegawa, Y, Hashimoto, T, Herlyn, M, Hitchens, K J, Ho Sui, S J, Hofmann, O M, Hoof, I, Hori, F, Huminiecki, L, Iida, K, Ikawa, T, Jankovic, B R, Jia, H, Joshi, A, Jurman, G, Kaczkowski, B, Kai, C, Kaida, K, Kaiho, A, Kajiyama, K, Kanamori, M K, Kasianov, A S, Kasukawa, T, Katayama, S, Kato, S, Kawaguchi, S, Kawamoto, H, Kawamura, Y I, Kawashima, T, Kempfle, J S, Kenna, T J, Kere, J, Khachigian, L M, Kitamura, T, Peter Klinken, S, Knox, A J, Kojima, M, Kojima, S, Kondo, N, Koseki, H, Koyasu, S, Krampitz, S, Kubosaki, A, Kwon, A T, Laros, J F J, Lee, W, Lennartsson, A, Li, K, Lilje, B, Lipovich, L, Mackay, A S, Manabe, R, Mar, J C, Marchand, B, Mathelier, A, Mejhert, N, Meynert, A, Mizuno, Y, de Lima Morais, D A, Morikawa, H, Morimoto, M, Moro, K, Motakis, E, Motohashi, H, Mummery, C L, Murata, M, Nagao, S S, Nakachi, Y, Nakahara, F, Nakamura, T, Nakamura, Y, Nakazato, K, van Nimwegen, E, Ninomiya, N, Nishiyori, H, Noma, S, Nozaki, T, Ogishima, S, Ohkura, N, Ohmiya, H, Ohno, H, Ohshima, M, Okada, M H, Okazaki, Y, Orlando, V, Ovchinnikov, D A, Pain, A, Passier, R, Patrikakis, M, Persson, H, Piazza, S, Prendergast, J G D, Rackham, O J L, Ramilowski, J A, Rashid, M, Ravasi, T, Rizzu, P, Roncador, M, Roy, S, Rye, M B, Saijyo, E, Sajantila, A, Saka, A, Sakaguchi, S, Sakai, M, Sato, H, Satoh, H, Savvi, S, Saxena, A, Schneider, C, Schultes, E A, Schulze-Tanzil, G G, Schwegmann, A, Sengstag, T, Sheng, G, Shimoji, H, Shimoni, Y, Shin, J W, Simon, C, Sugiyama, D, Sugiyama, T, Suzuki, M, Suzuki, N, Swoboda, R K, 't Hoen, P A C, Tagami, M, Takahashi, N, Takai, J, Tanaka, H, Tatsukawa, H, Tatum, Z, Thompson, M, Toyoda, H, Toyoda, T, Valen, E, van de Wetering, M, van den Berg, L M, Verardo, R, Vijayan, D, Vorontsov, I E, Wasserman, W W, Watanabe, S, Wells, C A, Winteringham, L N, Wolvetang, E, Wood, E J, Yamaguchi, Y, Yamamoto, M, Yoneda, M, Yonekura, Y, Yoshida, S, Zabierowski, S E, Zhang, P G, Zhao, X, Zucchelli, S, Summers, K M, Suzuki, H, Daub, C O, Kawai, J, Heutink, P, Hide, W, Freeman, T C, Lenhard, B, Bajic, V B, Taylor, M S, Makeev, V J, Sandelin, A G, Hume, D A, Carninci, P & Hayashizaki, Y 2015, ' The constrained maximal expression level owing to haploidy shapes gene content on the mammalian X chromosome ', PLoS Biology, vol. 13, no. 12, e1002315 . https://doi.org/10.1371/journal.pbio.1002315
PLoS biology, vol 13, iss 12
PLoS biology, 13(12). Public Library of Science
PLOS Biology
Huminiecki, L 2015, ' The constrained maximal expression level owing to haploidy shapes gene content on the mammalian X chromosome ', PLoS Biology, vol. 13, no. 12, e1002315 . https://doi.org/10.1371/journal.pbio.1002315
Hurst, L D, Ghanbarian, A T, Forrest, A R R & Huminiecki, L 2015, ' The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome ', PLoS Biology, vol. 13, no. 12, e1002315 . https://doi.org/10.1371/journal.pbio.1002315

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f0d97964e110e6dd328c8b584f2af1a6
https://doaj.org/article/8d6344bf6fbc4759a3a76e15d573f39a