Functional annotation of human long noncoding RNAs via molecular phenotyping
File(s)
Published version
Author(s)
Type
Journal Article
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.
Date Issued
2020-07-01
Date Acceptance
2020-06-24
Citation
Genome Research, 2020, 30 (7), pp.1060-1072
ISSN
1054-9803
Publisher
Cold Spring Harbor Laboratory Press
Start Page
1060
End Page
1072
Journal / Book Title
Genome Research
Volume
30
Issue
7
Copyright Statement
© 2020 Ramilowski et al.; Published by Cold Spring Harbor Laboratory Press
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
License URL
Sponsor
Wellcome Trust
Identifier
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000554900100011&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
Grant Number
106954/Z/15/Z
Subjects
Science & Technology
Life Sciences & Biomedicine
Biochemistry & Molecular Biology
Biotechnology & Applied Microbiology
Genetics & Heredity
ADULT HUMAN FIBROBLASTS
GENE-EXPRESSION
UNIQUE FEATURES
CELLS
TRANSCRIPTION
REVEALS
DIFFERENTIATION
TRANSLATION
PRINCIPLES
REGULATORS
Publication Status
Published
Date Publish Online
2020-07-27