Functional annotation of human long non-coding RNAs via molecular phenotyping
Functional annotation of human long non-coding RNAs via molecular phenotyping
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.
1060-1072
Ramilowski, Jordan A.
7e4df470-69ab-4f1f-862a-b195d3f75330
Yip, Chi-wai
5194232c-c085-466d-8d7d-096ea2c5b8b9
Agrawal, Saumya
3f26e14f-3560-4c4d-a346-8df43ee82a5b
Rackham, Owen J.L.
8122eb1f-6e9f-4da5-90e1-ce108ccbbcbf
27 July 2020
Ramilowski, Jordan A.
7e4df470-69ab-4f1f-862a-b195d3f75330
Yip, Chi-wai
5194232c-c085-466d-8d7d-096ea2c5b8b9
Agrawal, Saumya
3f26e14f-3560-4c4d-a346-8df43ee82a5b
Rackham, Owen J.L.
8122eb1f-6e9f-4da5-90e1-ce108ccbbcbf
Ramilowski, Jordan A., Yip, Chi-wai and Agrawal, Saumya
,
et al.
(2020)
Functional annotation of human long non-coding RNAs via molecular phenotyping.
Genome Research, 30, .
(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.
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700864v3.full
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Genome Res.-2020-Ramilowski-1060-72
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Accepted/In Press date: 24 June 2020
Published date: 27 July 2020
Additional Information:
Corrigendum at: https://genome.cshlp.org/content/30/9/1377-1.short
Identifiers
Local EPrints ID: 502430
URI: http://eprints.soton.ac.uk/id/eprint/502430
ISSN: 1088-9051
PURE UUID: 36ab3de0-4e90-4d64-8f40-b205b2f22ec3
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Date deposited: 26 Jun 2025 16:32
Last modified: 22 Aug 2025 02:30
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Author:
Jordan A. Ramilowski
Author:
Chi-wai Yip
Author:
Saumya Agrawal
Corporate Author: et al.
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