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Whole-genome-scale identification of novel non-protein-coding RNAs controlling cell proliferation and survival through a functional forward genetics strategy

Darling, D; Farzaneh, F; Williams, GT; Tonge, DP

Whole-genome-scale identification of novel non-protein-coding RNAs controlling cell proliferation and survival through a functional forward genetics strategy Thumbnail


Authors

D Darling

F Farzaneh

GT Williams



Abstract

<jats:title>Abstract</jats:title><jats:p>Identification of cell fate-controlling lncRNAs is essential to our understanding of molecular cell biology. Here we present a human genome-scale forward-genetics approach for the identification of lncRNAs based on gene function. This approach can identify genes that play a causal role, and immediately distinguish them from those that are differentially expressed but do not affect cell function. Our genome-scale library plus next-generation-sequencing and bioinformatic approach, radically upscales the breadth and rate of functional ncRNA discovery. Human gDNA was digested to produce a lentiviral expression library containing inserts in both sense and anti-sense orientation. The library was used to transduce human Jurkat T-leukaemic cells. Cell populations were selected using continuous culture?±?anti-FAS IgM, and sequencing used to identify sequences controlling cell proliferation. This strategy resulted in the identification of thousands of new sequences based solely on their function including many ncRNAs previously identified as being able to modulate cell survival or to act as key cancer regulators such as <jats:italic>AC084816.1</jats:italic>*, <jats:italic>AC097103.2</jats:italic>, <jats:italic>AC087473.1</jats:italic>, <jats:italic>CASC15*</jats:italic>, <jats:italic>DLEU1</jats:italic>*, <jats:italic>ENTPD1-AS1</jats:italic>*, <jats:italic>HULC</jats:italic>*, <jats:italic>MIRLET7BHG</jats:italic>*, <jats:italic>PCAT-1</jats:italic>, <jats:italic>SChLAP1</jats:italic>, and <jats:italic>TP53TG1</jats:italic>. Independent validation confirmed 4 out of 5 sequences that were identified by this strategy, conferred a striking resistance to anti-FAS IgM-induced apoptosis.</jats:p>

Citation

Darling, D., Farzaneh, F., Williams, G., & Tonge, D. (2022). Whole-genome-scale identification of novel non-protein-coding RNAs controlling cell proliferation and survival through a functional forward genetics strategy. Scientific reports, 12, Article 182. https://doi.org/10.1038/s41598-021-03983-5

Journal Article Type Article
Acceptance Date Dec 13, 2021
Online Publication Date Jan 7, 2022
Publication Date Dec 1, 2022
Publicly Available Date May 30, 2023
Journal Scientific Reports
Print ISSN 2045-2322
Electronic ISSN 2045-2322
Publisher Nature Publishing Group
Peer Reviewed Peer Reviewed
Volume 12
Article Number 182
DOI https://doi.org/10.1038/s41598-021-03983-5
Publisher URL https://www.nature.com/articles/s41598-021-03983-5