Abstract
| Original language | English (US) |
|---|---|
| Journal | Genome research |
| DOIs | |
| State | Published - Jul 29 2020 |
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Functional annotation of human long noncoding RNAs via molecular phenotyping. / 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, Nick; 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, Chris J F; Cannistraci, Carlo Vittorio; Cardenas, Ryan; Cardon, Melissa; Chang, Howard; Dostie, Josée; Ducoli, Luca; Favorov, Alexander; 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; Kawabata, Emily; Kawaji, Hideya; Kawashima, Tsugumi; Kelly, S Thomas; Kojima, Miki; Kondo, Naoto; Koseki, Haruhiko; Kouno, Tsukasa; Kratz, Anton; Kurowska-Stolarska, Mariola; Kwon, Andrew Tae Jun; Leek, Jeffrey; Lennartsson, Andreas; Lizio, Marina; López-Redondo, Fernando; Luginbühl, Joachim; Maeda, Shiori; Makeev, Vsevolod J; 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; 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; Suzuki, Takahiro; 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; Young, Robert S; Baillie, J Kenneth; Forrest, Alistair R R; Guigó, Roderic; Hoffman, Michael M; Hon, Chung Chau; Kasukawa, Takeya; Kauppinen, Sakari; Kere, Juha; Lenhard, Boris; Schneider, Claudio; Suzuki, Harukazu; Yagi, Ken; de Hoon, Michiel J L; Shin, Jay W; Carninci, Piero.
In: Genome research, 29.07.2020.Research output: Contribution to journal › Article › peer-review
TY - JOUR
T1 - Functional annotation of human long noncoding RNAs via molecular phenotyping.
AU - Ramilowski, Jordan A
AU - Yip, Chi Wai
AU - Agrawal, Saumya
AU - Chang, Jen-Chien
AU - Ciani, Yari
AU - Kulakovskiy, Ivan V
AU - Mendez, Mickaël
AU - Ooi, Jasmine Li Ching
AU - Ouyang, John F
AU - Parkinson, Nick
AU - Petri, Andreas
AU - Roos, Leonie
AU - Severin, Jessica
AU - Yasuzawa, Kayoko
AU - Abugessaisa, Imad
AU - Akalin, Altuna
AU - Antonov, Ivan V
AU - Arner, Erik
AU - Bonetti, Alessandro
AU - Bono, Hidemasa
AU - Borsari, Beatrice
AU - Brombacher, Frank
AU - Cameron, Chris J F
AU - Cannistraci, Carlo Vittorio
AU - Cardenas, Ryan
AU - Cardon, Melissa
AU - Chang, Howard
AU - Dostie, Josée
AU - Ducoli, Luca
AU - Favorov, Alexander
AU - Fort, Alexandre
AU - Garrido, Diego
AU - Gil, Noa
AU - Gimenez, Juliette
AU - Guler, Reto
AU - Handoko, Lusy
AU - Harshbarger, Jayson
AU - Hasegawa, Akira
AU - Hasegawa, Yuki
AU - Hashimoto, Kosuke
AU - Hayatsu, Norihito
AU - Heutink, Peter
AU - Hirose, Tetsuro
AU - Imada, Eddie L
AU - Itoh, Masayoshi
AU - Kaczkowski, Bogumil
AU - Kanhere, Aditi
AU - Kawabata, Emily
AU - Kawaji, Hideya
AU - Kawashima, Tsugumi
AU - Kelly, S Thomas
AU - Kojima, Miki
AU - Kondo, Naoto
AU - Koseki, Haruhiko
AU - Kouno, Tsukasa
AU - Kratz, Anton
AU - Kurowska-Stolarska, Mariola
AU - Kwon, Andrew Tae Jun
AU - Leek, Jeffrey
AU - Lennartsson, Andreas
AU - Lizio, Marina
AU - López-Redondo, Fernando
AU - Luginbühl, Joachim
AU - Maeda, Shiori
AU - Makeev, Vsevolod J
AU - Marchionni, Luigi
AU - Medvedeva, Yulia A
AU - Minoda, Aki
AU - Müller, Ferenc
AU - Muñoz-Aguirre, Manuel
AU - Murata, Mitsuyoshi
AU - Nishiyori, Hiromi
AU - Nitta, Kazuhiro R
AU - Noguchi, Shuhei
AU - Noro, Yukihiko
AU - Nurtdinov, Ramil
AU - Okazaki, Yasushi
AU - Orlando, Valerio
AU - Paquette, Denis
AU - Parr, Callum J C
AU - Rackham, Owen J L
AU - Rizzu, Patrizia
AU - Sánchez Martinez, Diego Fernando
AU - Sandelin, Albin
AU - Sanjana, Pillay
AU - Semple, Colin A M
AU - Shibayama, Youtaro
AU - Sivaraman, Divya M
AU - Suzuki, Takahiro
AU - Szumowski, Suzannah C
AU - Tagami, Michihira
AU - Taylor, Martin S
AU - Terao, Chikashi
AU - Thodberg, Malte
AU - Thongjuea, Supat
AU - Tripathi, Vidisha
AU - Ulitsky, Igor
AU - Verardo, Roberto
AU - Vorontsov, Ilya E
AU - Yamamoto, Chinatsu
AU - Young, Robert S
AU - Baillie, J Kenneth
AU - Forrest, Alistair R R
AU - Guigó, Roderic
AU - Hoffman, Michael M
AU - Hon, Chung Chau
AU - Kasukawa, Takeya
AU - Kauppinen, Sakari
AU - Kere, Juha
AU - Lenhard, Boris
AU - Schneider, Claudio
AU - Suzuki, Harukazu
AU - Yagi, Ken
AU - de Hoon, Michiel J L
AU - Shin, Jay W
AU - Carninci, Piero
N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: We thank Linda Kostrencic, Hiroto Atsui, Emi Ito, Nobuyuki Takeda, Tsutomu Saito, Teruaki Kitakura, Yumi Hara, Machiko Kashiwagi, and Masaaki Furuno at RIKEN Yokohama for assistance in arranging collaboration agreements, ethics applications, computational infrastructure, and the FANTOM6 meetings. We also thank RIKEN GeNAS for generation and sequencing of the CAGE libraries and subsequent data processing. FANTOM6 was made possible by a Research Grant for RIKEN Center for Life Science Technology, Division of Genomic Technologies (CLST DGT) and RIKEN Center for Integrative Medical Sciences (IMS) from MEXT, Japan. I.V.K. and I.E.V. were supported by Russian Foundation for Basic Research (RFBR) 18-34-20024, B.B. is supported by the fellowship 2017FI_B00722 from the Secretaria d'Universitats i Recerca del Departament d'Empresa i Coneixement (Generalitat de Catalunya) and the European Social Fund (ESF), A. Favorov was supported by National Institutes of Health (NIH) P30 CA006973 and RFBR 17-00-00208, D.G. is supported by a “la Caixa”-Severo Ochoa pre-doctoral fellowship (LCF/BQ/SO15/52260001), E.L.I. and L.M. were supported by NIH National Cancer Institute Grant R01CA200859 and Department of Defense (DOD) award W81XWH-16-1-0739, M.K.-S. was supported by Versus Arthritis UK 20298, A.L. was supported by the Swedish Cancer Society, The Swedish Research Council, the Swedish Childhood Cancer fund, Radiumhemmets forsknigsfonder; V.J.M. was supported by the Russian Academy of Sciences Project 0112-2019-0001; Y.A.M. was supported by Russian Science Foundation (RSF) grant 18-14-00240, A.S. was supported by Novo Nordisk Foundation, Lundbeck Foundation, Danish Cancer Society, Carlsberg Foundation, Independent Research Fund Denmark, A.R.R.F. is currently supported by an Australian National Health and Medical Research Council Fellowship APP1154524, M.M.H. was supported by Natural Sciences and Engineering Research Council of Canada (RGPIN-2015-3948), C.S. was supported by the Interuniversity Consortium for Biotechnology (CIB) from the Italian Ministry of Education, University and Research (MIUR) grant n.974,CMPT177780. J. Luginbühl was supported by Japan Society for the Promotion of Science (JSPS) Postdoctoral Fellowship for Foreign Researchers. C.J.C.P. was supported by RIKEN Special Post-Doctoral Research (SPDR) fellowship.
PY - 2020/7/29
Y1 - 2020/7/29
N2 - 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 dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
AB - 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 dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
UR - http://hdl.handle.net/10754/664570
UR - http://genome.cshlp.org/lookup/doi/10.1101/gr.254219.119
U2 - 10.1101/gr.254219.119
DO - 10.1101/gr.254219.119
M3 - Article
C2 - 32718982
JO - Genome research
JF - Genome research
SN - 1088-9051
ER -