Functional annotation of human long noncoding RNAs via molecular phenotyping

Ramilowski, Jordan A.; Borsari, Beatrice, 1992-; Garrido Martín, Diego, 1992-; Muñoz-Aguirre, Manuel; Nurtdinov, Ramil; Guigó Serra, Roderic; Carninci, Piero

doi:http://dx.doi.org/10.1101/gr.254219.119

Functional annotation of human long noncoding RNAs via molecular phenotyping

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Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV et al. Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Res. 2020; 30(7):1060-72. DOI: 10.1101/gr.254219.119

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.