Open AccessFunctional annotation of human long noncoding RNAs via molecular phenotyping
Author(s) -
Jordan A. Ramilowski,
Chi Wai Yip,
Saumya Agrawal,
Jen-Chien Chang,
Yari Ciani,
Ivan V. Kulakovskiy,
Mickaël Mendez,
Jasmine Li Ching Ooi,
John F. Ouyang,
Nick Parkinson,
Andreas Petri,
Leonie Roos,
Jessica Severin,
Kayoko Yasuzawa,
Imad Abugessaisa,
Altuna Akalin,
Ivan Antonov,
Peter Arner,
Alessandro Bonetti,
Hidemasa Bono,
Beatrice Borsari,
Frank Brombacher,
Christopher JF Cameron,
Carlo Vittorio Cannistraci,
Ryan Cardenas,
Mélissa Cardon,
Howard Y. Chang,
Josée Dostie,
Luca Ducoli,
Alexander V. Favorov,
Alexandre Fort,
Diego Garrido-Martín,
Noa Gil,
Juliette Gimenez,
Reto Guler,
Lusy Handoko,
Jayson Harshbarger,
Akira Hasegawa,
Yuki Hasegawa,
Kosuke Hashimoto,
Norihito Hayatsu,
Peter Heutink,
Tetsuro Hirose,
Eddie L. Imada,
Masayoshi Itoh,
Bogumił Kaczkowski,
Aditi Kanhere,
Emily Kawabata,
Hideya Kawaji,
Tsugumi Kawashima,
S. Thomas Kelly,
Miki Kojima,
Naoto Kondo,
Haruhiko Koseki,
Tsukasa Kouno,
Anton Kratz,
Mariola KurowskaStolarska,
Andrew T. Kwon,
Jeffrey T. Leek,
Andreas Lennartsson,
Marina Lizio,
Fernando Martínez López,
Joachim Luginbühl,
Shiori Maeda,
Vsevolod J. Makeev,
Luigi Marchionni,
Yulia A. Medvedeva,
Aki Minoda,
Ferenc Müller,
Manuel Muñoz-Aguirre,
Mitsuyoshi Murata,
Hiromi Nishiyori,
Kazuhiro R. Nitta,
Shuhei Noguchi,
Yukihiko Noro,
Ramil Nurtdinov,
Yasushi Okazaki,
Valerio Orlando,
Denis Paquette,
Callum Parr,
Owen J. L. Rackham,
Patrizia Rizzu,
Diego F. Sánchez,
Albin Sandelin,
Sanjana Pillay,
Colin A. Semple,
Youtaro Shibayama,
Divya M. Sivaraman,
Takahiro Suzuki,
Suzannah C. Szumowski,
Michihira Tagami,
Martin S. Taylor,
Chikashi Terao,
Malte Thodberg,
Supat Thongjuea,
Vidisha Tripathi,
Igor Ulitsky,
Roberto Verardo,
Ilya E. Vorontsov,
Chinatsu Yamamoto,
Robert S. Young,
J. Kenneth Baillie,
Alistair R. R. Forrest,
Roderic Guigó,
Michael M. Hoffman,
Chung-Chau Hon,
Takeya Kasukawa,
Sakari Kauppinen,
Juha Kere,
Boris Lenhard,
Claudio Schneider,
Harukazu Suzuki,
Ken Yagi,
Michiel de Hoon,
Jay W. Shin,
Piero Carninci
Publication year - 2020
Publication title -
genome research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.556
H-Index - 297
eISSN - 1549-5469
pISSN - 1088-9051
DOI - 10.1101/gr.254219.119
Subject(s) - biology , gene knockdown , transcriptome , phenotype , gene , computational biology , genetics , long non coding rna , genome , gene expression , deep sequencing , regulation of gene expression , gene expression profiling , rna
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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