Functional annotation of human long noncoding RNAs via molecular phenotyping.


Ramilowski, Jordan A ORCID: 0000-0002-3156-6416, Yip, Chi Wai, Agrawal, Saumya ORCID: 0000-0002-5524-6206, Chang, Jen-Chien, Ciani, Yari ORCID: 0000-0002-9635-2830, Kulakovskiy, Ivan V, Mendez, Mickaël, Ooi, Jasmine Li Ching, Ouyang, John F, Parkinson, Nick ORCID: 0000-0001-6336-5654 et al (show 106 more authors) (2020) Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome research, 30 (7). pp. 1060-1072.

Access the full-text of this item by clicking on the Open Access link.

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 <i>ZNF213-AS1</i> and <i>lnc-KHDC3L-2</i>.

Item Type: Article
Uncontrolled Keywords: Fibroblasts, Humans, Oligonucleotides, Antisense, RNA, Small Interfering, Cell Growth Processes, Cell Movement, KCNQ Potassium Channels, Molecular Sequence Annotation, RNA, Long Noncoding
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: 18 Mar 2024 01:16
DOI: 10.1101/gr.254219.119
Open Access URL: http://doi.org/10.1101/gr.254219.119
Related URLs:
URI: https://livrepository.liverpool.ac.uk/id/eprint/3129861
Dimensions
Altmetric
CORE (COnnecting REpositories)