Functional annotation of human long noncoding RNAs via molecular phenotyping
Jordan A. Ramilowski(RIKEN Center for Integrative Medical Sciences), Chi Wai Yip(RIKEN Center for Integrative Medical Sciences), Saumya Agrawal(RIKEN Center for Integrative Medical Sciences), Jen-Chien Chang(RIKEN Center for Integrative Medical Sciences), Yari Ciani(Consorzio Interuniversitario per le Biotecnologie), Ivan V. Kulakovskiy(Engelhardt Institute of Molecular Biology), Mickaël Mendez(University of Toronto), Jasmine Li Ching Ooi, John F. Ouyang(National University of Singapore), Nick Parkinson(Roslin Institute), Andreas Petri(Aalborg University), Leonie Roos(NIHR Imperial Biomedical Research Centre), Jessica Severin(RIKEN Center for Integrative Medical Sciences), Kayoko Yasuzawa(RIKEN Center for Integrative Medical Sciences), Imad Abugessaisa(RIKEN Center for Integrative Medical Sciences), Altuna Akalin(Max Delbrück Center), Ivan Antonov(Russian Academy of Sciences), Erik Arner(RIKEN Center for Integrative Medical Sciences), Alessandro Bonetti, Hidemasa Bono(Hiroshima University), Beatrice Borsari(Centre for Genomic Regulation), Frank Brombacher(South African Medical Research Council), Christopher J. F. Cameron(Yale University), Carlo Vittorio Cannistraci(Center for Systems Biology Dresden), Ryan Cardenas(University of Birmingham), Mélissa Cardon(RIKEN Center for Integrative Medical Sciences), Howard Y. Chang(Stanford University), Josée Dostie(McGill University), Luca Ducoli(École Polytechnique Fédérale de Lausanne), Alexander V. Favorov(Johns Hopkins University), Alexandre Fort, Diego Garrido-Martín(Centre for Genomic Regulation), Noa Gil(Weizmann Institute of Science), Juliette Gimenez(Fondazione Santa Lucia), Reto Guler(South African Medical Research Council), Lusy Handoko, Jayson Harshbarger, Akira Hasegawa(RIKEN Center for Integrative Medical Sciences), Yuki Hasegawa, Kosuke Hashimoto(RIKEN Center for Integrative Medical Sciences), Norihito Hayatsu(RIKEN Center for Integrative Medical Sciences), Peter Heutink(German Center for Neurodegenerative Diseases), Tetsuro Hirose(The University of Osaka), Eddie L. Imada(Johns Hopkins University), Masayoshi Itoh(RIKEN), Bogumił Kaczkowski(RIKEN Center for Integrative Medical Sciences), Aditi Kanhere(University of Birmingham), Emily Kawabata, Hideya Kawaji(RIKEN), Tsugumi Kawashima(RIKEN Center for Integrative Medical Sciences), S. Thomas Kelly(RIKEN Center for Integrative Medical Sciences), Miki Kojima(RIKEN Center for Integrative Medical Sciences), Naoto Kondo, Haruhiko Koseki(RIKEN Center for Integrative Medical Sciences), Tsukasa Kouno(RIKEN Center for Integrative Medical Sciences), Anton Kratz, Mariola Kurowska‐Stolarska(Institute of Infection and Immunity), Andrew Tae-Jun Kwon(RIKEN Center for Integrative Medical Sciences), Jeffrey T. Leek(Johns Hopkins University), Andreas Lennartsson(Karolinska Institutet), Marina Lizio(RIKEN Center for Integrative Medical Sciences), Fernando Martínez López(RIKEN Center for Integrative Medical Sciences), Joachim Luginbühl(RIKEN Center for Integrative Medical Sciences), Shiori Maeda(RIKEN Center for Integrative Medical Sciences), Vsevolod J. Makeev(Moscow Institute of Physics and Technology), Luigi Marchionni(Johns Hopkins University), Yulia A. Medvedeva(Russian Academy of Sciences), Aki Minoda(RIKEN Center for Integrative Medical Sciences), Ferenc Müller(University of Birmingham), Manuel Muñoz-Aguirre(Centre for Genomic Regulation), Mitsuyoshi Murata(RIKEN Center for Integrative Medical Sciences), Hiromi Nishiyori(RIKEN Center for Integrative Medical Sciences), Kazuhiro R. Nitta(RIKEN Center for Integrative Medical Sciences), Shuhei Noguchi(RIKEN Center for Integrative Medical Sciences), Yukihiko Noro, Ramil Nurtdinov(Centre for Genomic Regulation), Yasushi Okazaki(RIKEN Center for Integrative Medical Sciences), Valerio Orlando(King Abdullah University of Science and Technology), Denis Paquette(McGill University), Callum Parr(RIKEN Center for Integrative Medical Sciences), Owen J. L. Rackham(National University of Singapore), Patrizia Rizzu(German Center for Neurodegenerative Diseases), Diego F. Sánchez(Johns Hopkins University), Albin Sandelin(University of Copenhagen), Sanjana Pillay(University of Birmingham), Colin A. Semple(Institute of Genetics and Cancer), Youtaro Shibayama(RIKEN Center for Integrative Medical Sciences), Divya M. Sivaraman(RIKEN Center for Integrative Medical Sciences), Takahiro Suzuki(RIKEN Center for Integrative Medical Sciences), Suzannah C. Szumowski, Michihira Tagami(RIKEN Center for Integrative Medical Sciences), Martin S. Taylor(Institute of Genetics and Cancer), Chikashi Terao(RIKEN Center for Integrative Medical Sciences), Malte Thodberg(University of Copenhagen), Supat Thongjuea, Vidisha Tripathi(National Centre for Cell Science), Igor Ulitsky(Weizmann Institute of Science), Roberto Verardo(Consorzio Interuniversitario per le Biotecnologie), Ilya E. Vorontsov(Vavilov Institute of General Genetics), Chinatsu Yamamoto, Robert S. Young(University of Edinburgh), J. Kenneth Baillie(Roslin Institute), Alistair R. R. Forrest(The University of Western Australia), Roderic Guigó(Universitat Pompeu Fabra), Michael M. Hoffman(Princess Margaret Cancer Centre), Chung-Chau Hon(RIKEN Center for Integrative Medical Sciences), Takeya Kasukawa(RIKEN Center for Integrative Medical Sciences), Sakari Kauppinen(Aalborg University), Juha Kere(University of Helsinki), Boris Lenhard(NIHR Imperial Biomedical Research Centre), Claudio Schneider(University of Udine), Harukazu Suzuki(RIKEN Center for Integrative Medical Sciences), Ken Yagi(RIKEN Center for Integrative Medical Sciences), Michiel de Hoon(RIKEN Center for Integrative Medical Sciences), Jay W. Shin(RIKEN Center for Integrative Medical Sciences), Piero Carninci(RIKEN Center for Integrative Medical Sciences)
Cited by 196Open Access
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 .
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