Functional annotation of human long noncoding RNAs via molecular phenotyping.
AuthorsRamilowski, Jordan A
Yip, Chi Wai
Kulakovskiy, Ivan V
Ooi, Jasmine Li Ching
Ouyang, John F
Antonov, Ivan V
Cameron, Chris J F
Cannistraci, Carlo Vittorio
Imada, Eddie L
Kelly, S Thomas
Kwon, Andrew Tae Jun
Makeev, Vsevolod J
Medvedeva, Yulia A
Nitta, Kazuhiro R
Parr, Callum J C
Rackham, Owen J L
Sánchez Martinez, Diego Fernando
Semple, Colin A M
Sivaraman, Divya M
Szumowski, Suzannah C
Taylor, Martin S
Vorontsov, Ilya E
Young, Robert S
Baillie, J Kenneth
Forrest, Alistair R R
Hoffman, Michael M
Hon, Chung Chau
de Hoon, Michiel J L
Shin, Jay W
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Online Publication Date2020-07-27
Print Publication Date2020-07
Permanent link to this recordhttp://hdl.handle.net/10754/664570
MetadataShow full item record
AbstractLong 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.
CitationRamilowski, J. A., Yip, C. W., Agrawal, S., Chang, J.-C., Ciani, Y., Kulakovskiy, I. V., … Parkinson, N. (2020). Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Research. doi:10.1101/gr.254219.119
SponsorsWe thank Linda Kostrencic, Hiroto Atsui, Emi Ito, Nobuyuki Takeda, Tsutomu Saito, Teruaki Kitakura, Yumi Hara, Machiko Kashiwagi, and Masaaki Furuno at RIKEN Yokohama for assistance in arranging collaboration agreements, ethics applications, computational infrastructure, and the FANTOM6 meetings. We also thank RIKEN GeNAS for generation and sequencing of the CAGE libraries and subsequent data processing. FANTOM6 was made possible by a Research Grant for RIKEN Center for Life Science Technology, Division of Genomic Technologies (CLST DGT) and RIKEN Center for Integrative Medical Sciences (IMS) from MEXT, Japan. I.V.K. and I.E.V. were supported by Russian Foundation for Basic Research (RFBR) 18-34-20024, B.B. is supported by the fellowship 2017FI_B00722 from the Secretaria d'Universitats i Recerca del Departament d'Empresa i Coneixement (Generalitat de Catalunya) and the European Social Fund (ESF), A. Favorov was supported by National Institutes of Health (NIH) P30 CA006973 and RFBR 17-00-00208, D.G. is supported by a “la Caixa”-Severo Ochoa pre-doctoral fellowship (LCF/BQ/SO15/52260001), E.L.I. and L.M. were supported by NIH National Cancer Institute Grant R01CA200859 and Department of Defense (DOD) award W81XWH-16-1-0739, M.K.-S. was supported by Versus Arthritis UK 20298, A.L. was supported by the Swedish Cancer Society, The Swedish Research Council, the Swedish Childhood Cancer fund, Radiumhemmets forsknigsfonder; V.J.M. was supported by the Russian Academy of Sciences Project 0112-2019-0001; Y.A.M. was supported by Russian Science Foundation (RSF) grant 18-14-00240, A.S. was supported by Novo Nordisk Foundation, Lundbeck Foundation, Danish Cancer Society, Carlsberg Foundation, Independent Research Fund Denmark, A.R.R.F. is currently supported by an Australian National Health and Medical Research Council Fellowship APP1154524, M.M.H. was supported by Natural Sciences and Engineering Research Council of Canada (RGPIN-2015-3948), C.S. was supported by the Interuniversity Consortium for Biotechnology (CIB) from the Italian Ministry of Education, University and Research (MIUR) grant n.974,CMPT177780. J. Luginbühl was supported by Japan Society for the Promotion of Science (JSPS) Postdoctoral Fellowship for Foreign Researchers. C.J.C.P. was supported by RIKEN Special Post-Doctoral Research (SPDR) fellowship.
PublisherCold Spring Harbor Laboratory
Except where otherwise noted, this item's license is described as This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International).
- Roles of long noncoding RNAs in brain development, functional diversification and neurodegenerative diseases.
- Authors: Wu P, Zuo X, Deng H, Liu X, Liu L, Ji A
- Issue date: 2013 Aug
- Long noncoding RNA CCDC144NL-AS1 knockdown induces naïve-like state conversion of human pluripotent stem cells.
- Authors: Wang Y, Guo B, Xiao Z, Lin H, Zhang X, Song Y, Li Y, Gao X, Yu J, Shao Z, Li X, Luo Y, Li S
- Issue date: 2019 Jul 29
- FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs.
- Authors: Abugessaisa I, Ramilowski JA, Lizio M, Severin J, Hasegawa A, Harshbarger J, Kondo A, Noguchi S, Yip CW, Ooi JLC, Tagami M, Hori F, Agrawal S, Hon CC, Cardon M, Ikeda S, Ono H, Bono H, Kato M, Hashimoto K, Bonetti A, Kato M, Kobayashi N, Shin J, de Hoon M, Hayashizaki Y, Carninci P, Kawaji H, Kasukawa T
- Issue date: 2021 Jan 8
- Knockdown of Long Noncoding RNAs Hepatocyte Nuclear Factor 1<i>α</i> Antisense RNA 1 and Hepatocyte Nuclear Factor 4<i>α</i> Antisense RNA 1 Alters Susceptibility of Acetaminophen-Induced Cytotoxicity in HepaRG Cells.
- Authors: Chen L, Wang P, Manautou JE, Zhong XB
- Issue date: 2020 Apr
- Computational approaches towards understanding human long non-coding RNA biology.
- Authors: Jalali S, Kapoor S, Sivadas A, Bhartiya D, Scaria V
- Issue date: 2015 Jul 15