Functional annotation of human long noncoding RNAs via molecular phenotyping
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Published:2020-07
Issue:7
Volume:30
Page:1060-1072
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ISSN:1088-9051
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Container-title:Genome Research
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language:en
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Short-container-title:Genome Res.
Author:
Ramilowski Jordan A.ORCID, 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 HidemasaORCID, Borsari Beatrice, Brombacher Frank, Cameron Christopher J.F., Cannistraci Carlo VittorioORCID, 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. ThomasORCID, 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 ManuelORCID, 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.ORCID, Terao Chikashi, Thodberg Malte, Thongjuea Supat, Tripathi Vidisha, Ulitsky Igor, Verardo Roberto, Vorontsov Ilya E., Yamamoto Chinatsu, Young Robert S., Baillie J. KennethORCID, Forrest Alistair R.R., Guigó Roderic, Hoffman Michael M.ORCID, Hon Chung Chau, Kasukawa Takeya, Kauppinen Sakari, Kere Juha, Lenhard Boris, Schneider Claudio, Suzuki Harukazu, Yagi Ken, de Hoon Michiel J.L.ORCID, Shin Jay W.ORCID, Carninci PieroORCID
Abstract
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.
Funder
RIKEN Center for Life Science Technology, Division of Genomic Technologies RIKEN Center for Integrative Medical Sciences Russian Foundation for Basic Research Secretaria d'Universitats i Recerca del Departament d'Empresa i Coneixement European Social Fund National Institutes of Health RFBR NIH National Cancer Institute Versus Arthritis UK Swedish Cancer Society Swedish Research Council, the Swedish Childhood Cancer fund Russian Academy of Sciences Russian Science Foundation Novo Nordisk Foundation, Lundbeck Foundation, Danish Cancer Society, Carlsberg Foundation, Independent Research Fund Denmark Australian National Health and Medical Research Council Fellowship Natural Sciences and Engineering Research Council of Canada Japan Society for the Promotion of Science RIKEN Special Post-Doctoral Research
Publisher
Cold Spring Harbor Laboratory
Subject
Genetics(clinical),Genetics
Cited by
114 articles.
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