TY - UNPB
T1 - Systematic loss of function screens identify pathway specific functional circular RNAs
AU - Liu, Ling
AU - Neve, Matthew
AU - Perlaza-Jimenez, Laura
AU - Hawdon, Azelle
AU - Conn, Simon J
AU - Zenker, Jennifer
AU - Tamayo, Pablo
AU - Goodall, Gregory J.
AU - Rosenbluh, Joseph
PY - 2022/10/22
Y1 - 2022/10/22
N2 - Circular RNAs (circRNAs) are covalently closed single stranded RNAs that are produced by RNA back-splicing. A small number of circRNAs have been implicated as functional, however, we still lack systematic understanding of cellular processes and signalling pathways that are regulated by circRNAs. A major gap, in understanding circRNAs functions is the ability to define pathways that are regulated by circRNAs. Here, we generated a pooled shRNA library targeting the back-splice junction of 3,354 human circRNAs that are expressed at low to high levels in humans. We used this library for loss of function proliferation screens in a panel of 18 cancer cell lines from four tissue types that harbour mutations leading to constitutive activity of defined pathways. Using this dataset, we identify context specific and non-specific circRNAs. We validated these observations with a secondary screen and uncovered a role for circRERE, a cell essential circRNA that regulates ferroptosis. Furthermore, we characterised the functional roles of pathway-specific circRNA, circSMAD2, a novel regulator of the WNT pathway and circMTO1, a regulator of MAPK signalling in a PTEN dependent manner. Our work sheds light on molecular pathways regulated by circRNAs and provides a catalogue of circRNAs with a measurable function in human cells.
AB - Circular RNAs (circRNAs) are covalently closed single stranded RNAs that are produced by RNA back-splicing. A small number of circRNAs have been implicated as functional, however, we still lack systematic understanding of cellular processes and signalling pathways that are regulated by circRNAs. A major gap, in understanding circRNAs functions is the ability to define pathways that are regulated by circRNAs. Here, we generated a pooled shRNA library targeting the back-splice junction of 3,354 human circRNAs that are expressed at low to high levels in humans. We used this library for loss of function proliferation screens in a panel of 18 cancer cell lines from four tissue types that harbour mutations leading to constitutive activity of defined pathways. Using this dataset, we identify context specific and non-specific circRNAs. We validated these observations with a secondary screen and uncovered a role for circRERE, a cell essential circRNA that regulates ferroptosis. Furthermore, we characterised the functional roles of pathway-specific circRNA, circSMAD2, a novel regulator of the WNT pathway and circMTO1, a regulator of MAPK signalling in a PTEN dependent manner. Our work sheds light on molecular pathways regulated by circRNAs and provides a catalogue of circRNAs with a measurable function in human cells.
KW - Systematic Loss
KW - Pathway
KW - Functional Circular RNAs
U2 - 10.1101/2022.10.22.513321
DO - 10.1101/2022.10.22.513321
M3 - Preprint
T3 - bioRxiv
BT - Systematic loss of function screens identify pathway specific functional circular RNAs
PB - bioRxiv, Cold Spring Harbor Laboratory
ER -