Systematic loss-of-function screens identify pathway-specific functional circular RNAs

Ling Liu, Matthew Neve, Laura Perlaza-Jimenez, Xinqi Xi, Jacob Purcell, Azelle Hawdon, Simon J. Conn, Jennifer Zenker, Pablo Tamayo, Gregory J. Goodall, Joseph Rosenbluh

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)

Abstract

Circular RNA (circRNA) is covalently closed, single-stranded RNA produced by back-splicing. A few circRNAs have been implicated as functional; however, we lack understanding of pathways that are regulated by circRNAs. Here we generated a pooled short-hairpin-RNA library targeting the back-splice junction of 3,354 human circRNAs that are expressed at different levels (ranging from low to high) in humans. We used this library for loss-of-function proliferation screens in a panel of 18 cancer cell lines from four tissue types harbouring mutations leading to constitutive activity of defined pathways. Both context-specific and non-specific circRNAs were identified. Some circRNAs were found to directly regulate their precursor, whereas some have a function unrelated to their precursor. We validated these observations with a secondary screen and uncovered a role for circRERE(4–10) and circHUWE1(22,23), two cell-essential circRNAs, circSMAD2(2–6), a WNT pathway regulator, and circMTO1(2,RI,3), a regulator of MAPK signalling. Our work sheds light on pathways regulated by circRNAs and provides a catalogue of circRNAs with a measurable function.
Original languageEnglish
Pages (from-to)1359-1372
Number of pages14
JournalNature Cell Biology
Volume26
Issue number8
DOIs
Publication statusPublished - Aug 2024

Keywords

  • Functional genomics
  • Non-coding RNAs

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