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Functional annotation of human long non-coding RNAs via molecular phenotyping

Item Type:Preprint
Title:Functional annotation of human long non-coding RNAs via molecular phenotyping
Creators Name:Ramilowski, J. and Yip, C.W. and Agrawal, S. and Chang, J.C. and Ciani, Y. and Kulakovskiy, I.V. and Mendez, M. and Ooi, J.L.C. and Ouyang, J.F. and Parkinson, N. and Petri, A. and Roos, L. and Severin, J. and Yasuzawa, K. and Abugessaisa, I. and Akalin, A. and Antonov, I. and Arner, E. and Bonetti, A. and Bono, H. and Borsari, B. and Brombacher, F. and Cannistraci, C.V. and Cameron, C.J.F. and Cardenas, R. and Cardon, M. and Chang, H. and Dostie, J. and Ducoli, L. and Favorov, A. and Fort, A. and Garrido, D. and Gil, N. and Gimenez, J. and Guler, R. and Handoko, L. and Harshbarger, J. and Hasegawa, A. and Hasegawa, Y. and Hashimoto, K. and Hayatsu, N. and Heutink, P. and Hirose, T. and Imada, E.L. and Itoh, M. and Kaczkowski, B. and Kanhere, A. and Kawabata, E. and Kawaji, H. and Kawashima, T. and Kelly, T. and Kojima, M. and Kondo, N. and Koseki, H. and Kouno, T. and Kratz, A. and Kurowska-Stolarska, M. and Kwon, A.T.J. and Leek, J. and Lennartsson, A. and Lizio, M. and Lopez, F. and Luginbühl, J. and Maeda, S. and Makeev, V. and Marchionni, L. and Medvedeva, Y.A. and Minoda, A. and Müller, F. and Aguirre, M.M. and Murata, M. and Nishiyori, H. and Nitta, K. and Noguchi, S. and Noro, Y. and Nurtdinov, R. and Okazaki, Y. and Orlando, V. and Paquette, D. and Parr, C. and Rackham, O.J.L. and Rizzu, P. and Sanchez, D.F. and Sandelin, A. and Sanjana, P. and Semple, C.A.M. and Sharma, H. and Shibayama, Y. and Sivaraman, D. and Suzuki, T. and Szumowski, S. and Tagami, M. and Taylor, M.S. and Terao, C. and Thodberg, M. and Thongjuea, S. and Tripathi, V. and Ulitsky, I. and Verardo, R. and Vorontsov, I. and Yamamoto, C. and Young, R.S. and Baillie, J.K. and Forrest, A.R.R. and Guigó, R. and Hoffman, M.M. and Hon, C.C. and Kasukawa, T. and Kauppinen, S. and Kere, J. and Lenhard, B. and Schneider, C. and Suzuki, H. and Yagi, K. and de Hoon, M. and Shin, J.W. and Carninci, P.
Abstract:Long non-coding RNAs (lncRNAs) constitute the majority of transcripts in mammalian genomes and yet, their functions remain largely unknown. We systematically suppressed 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). The resulting transcriptomic profiles recapitulated the observed cellular phenotypes, yielding specific roles for over 40% of analyzed lncRNAs in regulating distinct biological pathways, transcriptional machinery, alternative promoter activity and architecture usage. Overall, combining cellular and molecular profiling provided a powerful approach to unravel the distinct functions of lncRNAs, which we highlight with specific functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
Publisher:Cold Spring Harbor Laboratory Press
Article Number:700864
Date:18 July 2019
Official Publication:https://doi.org/10.1101/700864

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