Small Cajal body-associated RNA 2 (scaRNA2) regulates DNA repair pathway choice by inhibiting DNA-PK

Sofie Bergstrand,Sandro Schmidli,Chiara Pederiva,Julienne J O’Rourke,Eleanor M O’Brien,Soniya Dhanjal,Marianne Farnebo,Lee Siggens,Oliver Mortusewicz,Dominika Hrossova,Dimitra Peirasmaki,Christos Coucoravas

doi:10.1038/s41467-022-28646-5

Sofie Bergstrand, Sandro Schmidli + Show 10 more

Open Access

https://doi.org/10.1038/s41467-022-28646-5

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Journal: Nature Communications	Publication Date: Feb 23, 2022
Citations: 15	License type: open-access

Affiliation: Karolinska Institutet

Abstract

Evidence that long non-coding RNAs (lncRNAs) participate in DNA repair is accumulating, however, whether they can control DNA repair pathway choice is unknown. Here we show that the small Cajal body-specific RNA 2 (scaRNA2) can promote HR by inhibiting DNA-dependent protein kinase (DNA-PK) and, thereby, NHEJ. By binding to the catalytic subunit of DNA-PK (DNA-PKcs), scaRNA2 weakens its interaction with the Ku70/80 subunits, as well as with the LINP1 lncRNA, thereby preventing catalytic activation of the enzyme. Inhibition of DNA-PK by scaRNA2 stimulates DNA end resection by the MRN/CtIP complex, activation of ATM at DNA lesions and subsequent repair by HR. ScaRNA2 is regulated in turn by WRAP53β, which binds this RNA, sequestering it away from DNA-PKcs and allowing NHEJ to proceed. These findings reveal that RNA-dependent control of DNA-PK catalytic activity is involved in regulating whether the cell utilizes NHEJ or HR.

Highlights

Evidence that long non-coding RNAs participate in DNA repair is accumulating, whether they can control DNA repair pathway choice is unknown
We reasoned that greater insight into the organization of small Cajal body-associated RNAs (scaRNAs) genes in humans might reveal novel functions of these molecules, similar to the manner in which small nucleolar RNAs (snoRNAs) were found to be involved in ribosome biogenesis[41–43]
To explore their potential involvement in DNA repair, we chose to focus on scaRNA2, since it associates extensively with WRAP53β23,26,27,30, shows altered processing following DNA damage[44] and its overexpression has been connected with cancer progression and chemoresistance[45]

Summary

Introduction

Evidence that long non-coding RNAs (lncRNAs) participate in DNA repair is accumulating, whether they can control DNA repair pathway choice is unknown. Inhibition of DNA-PK by scaRNA2 stimulates DNA end resection by the MRN/CtIP complex, activation of ATM at DNA lesions and subsequent repair by HR. ScaRNA2 is regulated in turn by WRAP53β, which binds this RNA, sequestering it away from DNA-PKcs and allowing NHEJ to proceed These findings reveal that RNA-dependent control of DNA-PK catalytic activity is involved in regulating whether the cell utilizes NHEJ or HR. It appears likely that RNA regulates DNA repair in other ways as well In this context, it is noteworthy that small nucleolar RNAs (snoRNAs) assembled in the nucleolus where they regulate ribosomal RNAs can stimulate the activities of the repair enzymes DNA-PK and PARP1 in the absence of DNA damage[17,18]. In contrast to snoRNAs, which usually contain only one of these boxes, scaRNAs often contain two C/D or H/ACA domains or one of each (and are referred to as mixed-domain scaRNAs)[19,22]

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