Functional annotation of human long noncoding RNAs via molecular phenotyping



Ramilowski, Jordan A ORCID: 0000-0002-3156-6416, Yip, Chi Wai, Agrawal, Saumya, Chang, Jen-Chien, Ciani, Yari, Kulakovskiy, Ivan V, Mendez, Mickaël, Ooi, Jasmine Li Ching, Ouyang, John F, Parkinson, Nick
et al (show 106 more authors) (2020) Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Research, 30 (7). 1060 - 1072.

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Abstract

<jats:p>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 <jats:italic>ZNF213-AS1</jats:italic> and <jats:italic>lnc-KHDC3L-2</jats:italic>.</jats:p>

Item Type: Article
Divisions: Faculty of Health and Life Sciences
Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology
Depositing User: Symplectic Admin
Date Deposited: 13 Jul 2021 08:26
Last Modified: 05 Oct 2022 20:45
DOI: 10.1101/gr.254219.119
Open Access URL: http://doi.org/10.1101/gr.254219.119
URI: https://livrepository.liverpool.ac.uk/id/eprint/3129861