Functional annotation of human long noncoding RNAs via molecular phenotyping

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 V. Antonov, Erik Arner, Alessandro Bonetti, Hidemasa BonoBeatrice Borsari, Frank Brombacher, Chris J.F. Cameron, Carlo Vittorio Cannistraci, Ryan Cardenas, Melissa Cardon, Howard Chang, Josée Dostie, Luca Ducoli, Alexander Favorov, Alexandre Fort, Diego Garrido, 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, Bogumil Kaczkowski, Aditi Kanhere, Emily Kawabata, Hideya Kawaji, Tsugumi Kawashima, S. Thomas Kelly, Miki Kojima, Naoto Kondo, Haruhiko Koseki, Tsukasa Kouno, Anton Kratz, Mariola Kurowska-Stolarska, Andrew Tae Jun Kwon, Jeffrey Leek, Andreas Lennartsson, Marina Lizio, Fernando López-Redondo, 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 J.C. Parr, Owen J.L. Rackham, Patrizia Rizzu, Diego Fernando Sánchez Martinez, Albin Sandelin, Pillay Sanjana, Colin A.M. 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 J.L. De Hoon, Jay W. Shin, Piero Carninci

Research output: Contribution to journalArticlepeer-review

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-todate 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.

Original languageEnglish (US)
Pages (from-to)1060-1072
Number of pages13
JournalGenome research
Volume30
Issue number7
DOIs
StatePublished - Jul 2020

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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