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 language | English |
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Pages (from-to) | 1060-1072 |
Number of pages | 13 |
Journal | Genome Research |
Volume | 30 |
Issue number | 7 |
DOIs | |
Publication status | Published - Jul 2020 |
Bibliographical note
Funding Information:We 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 forsknigs-fonder; 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.
Funding Information:
We 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. Luginb?hl 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.
Publisher Copyright:
© 2020 Ramilowski et al.
ASJC Scopus subject areas
- Genetics
- Genetics(clinical)