Functional annotation of human long noncoding RNAs via molecular phenotyping.
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Genome Res.-2020-Ramilowski-1060-72.pdf
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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
KAUST Department
Biological and Environmental Sciences and Engineering (BESE) DivisionBioscience Program
Date
2020-07-27Online Publication Date
2020-07-27Print Publication Date
2020-07Submitted Date
2019-07-12Permanent link to this record
http://hdl.handle.net/10754/664570
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Show full item recordAbstract
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.Citation
Ramilowski, J. A., Yip, C. W., Agrawal, S., Chang, J.-C., Ciani, Y., Kulakovskiy, I. V., … Parkinson, N. (2020). Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Research. doi:10.1101/gr.254219.119Sponsors
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.Publisher
Cold Spring Harbor LaboratoryJournal
Genome researchPubMed ID
32718982Additional Links
http://genome.cshlp.org/lookup/doi/10.1101/gr.254219.119ae974a485f413a2113503eed53cd6c53
10.1101/gr.254219.119
Scopus Count
Except where otherwise noted, this item's license is described as This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International).
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