Functional annotation of human long noncoding RNAs via molecular phenotyping

by Ramilowski JA, Yip CW, Agrawal S,, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC,, Ouyang JF, Parkinson N, Petri A, Roos L,, Severin J, Yasuzawa K, Abugessaisa I,, Akalin A, Antonov IV, Arner E,, Bonetti A, Bono H, Borsari B, Brombacher F,, Cameron CJ, Cannistraci CV, Cardenas R, Cardon M,, Chang H, Dostie J, Ducoli L, Favorov A, Fort A,, Garrido D, Gil N, Gimenez J,, Guler R, Handoko L, Harshbarger J,, Hasegawa A, Hasegawa Y, Hashimoto K,, Hayatsu N, Heutink P, Hirose T,, Imada EL, Itoh M, Kaczkowski B, Kanhere A,, Kawabata E, Kawaji H, Kawashima T,, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T,, Kratz A, Kurowska-Stolarska M, Kwon ATJ,, Leek J, Lennartsson A, Lizio M, López-Redondo F,, Luginbühl J, Maeda S, Makeev VJ, Marchionni L,, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M,, Murata M, Nishiyori H, Nitta KR,, Noguchi S, Noro Y, Nurtdinov R,, Okazaki Y, Orlando V,, Please refer to the link to find the other authors

Year: 2020 DOI: 10.1101/gr.254219.119

Extra Information

Genome Res. 2020 Jul;30(7):1060-1072. doi: 10.1101/gr.254219.119. Epub 2020 Jul 27.PMID: 32718982

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-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.