TY - JOUR
T1 - Systematic loss-of-function screens identify pathway-specific functional circular RNAs
AU - Liu, Ling
AU - Neve, Matthew
AU - Perlaza-Jimenez, Laura
AU - Xi, Xinqi
AU - Purcell, Jacob
AU - Hawdon, Azelle
AU - Conn, Simon J.
AU - Zenker, Jennifer
AU - Tamayo, Pablo
AU - Goodall, Gregory J.
AU - Rosenbluh, Joseph
PY - 2024/8
Y1 - 2024/8
N2 - 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.
AB - 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.
KW - Functional genomics
KW - Non-coding RNAs
UR - http://www.scopus.com/inward/record.url?scp=85200404512&partnerID=8YFLogxK
UR - http://purl.org/au-research/grants/NHMRC/GNT1198014
U2 - 10.1038/s41556-024-01467-y
DO - 10.1038/s41556-024-01467-y
M3 - Article
AN - SCOPUS:85200404512
SN - 1465-7392
VL - 26
SP - 1359
EP - 1372
JO - Nature Cell Biology
JF - Nature Cell Biology
IS - 8
ER -