BRCA1 binds TERRA RNA and suppresses R-Loop-based telomeric DNA damage

Abstract

R-loop structures act as modulators of physiological processes such as transcription termination, gene regulation, and DNA repair. However, they can cause transcription-replication conflicts and give rise to genomic instability, particularly at telomeres, which are prone to forming DNA secondary structures. Here, we demonstrate that BRCA1 binds TERRA RNA, directly and physically via its N-terminal nuclear localization sequence, as well as telomere-specific shelterin proteins in an R-loop-, and a cell cycle-dependent manner. R-loop-driven BRCA1 binding to CpG-rich TERRA promoters represses TERRA transcription, prevents TERRA R-loop-associated damage, and promotes its repair, likely in association with SETX and XRN2. BRCA1 depletion upregulates TERRA expression, leading to overly abundant TERRA R-loops, telomeric replication stress, and signs of telomeric aberrancy. Moreover, BRCA1 mutations within the TERRA-binding region lead to an excess of TERRA-associated R-loops and telomeric abnormalities. Thus, normal BRCA1/TERRA binding suppresses telomere-centered genome instability.

Making Connections: Integrative Signaling Mechanisms Coordinate DNA Break Repair in Chromatin

“…Interestingly, this study showed that expression of RNaseH1 in IR-treated cells impaired BRCA1 recruitment to damage sites. An association between TERRA R-loops and BRCA1 was also recently described at telomeres and it was found that BRCA1 can associate directly with TERRA RNA through interactions mediated by the BRCA1 N-terminal NLS region ( Vohhodina et al, 2021 ). Binding of RNA via NLS sequences has been identified in other factors including the ribonuclease Dicer, which can be attributed to the density of positive charged amino acids in these regions that can facilitate binding to the ribonucleotide backbone ( LaCasse and Lefebvre, 1995 ).…”

“…Binding of RNA via NLS sequences has been identified in other factors including the ribonuclease Dicer, which can be attributed to the density of positive charged amino acids in these regions that can facilitate binding to the ribonucleotide backbone ( LaCasse and Lefebvre, 1995 ). The binding of TERRA by BRCA1 results in the suppression of TERRA transcription and promotes the repair or R-loop associated DNA damage at telomeres ( Vohhodina et al, 2021 ). The association of BRCA1 and R-loops at sites of DNA damage may also occur through NLS mediated interactions ( San Martin Alonso and Noordermeer, 2021 ).…”

Telomeric Repeat-Containing RNA (TERRA): A Review of the Literature and First Assessment in Cutaneous T-Cell Lymphomas

“…Moreover, as previously mentioned, telomerase-negative ALT-positive cancer cells present higher levels of R-loops at their telomeres [ 79 ]. It has been recently reported that BRCA1 (Breast cancer gene 1) binds TERRA RNA as well as telomere-specific shelterin proteins in the R-loop, and in a cell cycle-dependent manner, suggesting that normal BRCA1/TERRA binding suppresses telomeric genome instability [ 101 ]. Additionally, BRCA2 deletion was reported to trigger TERRA overexpression and ALT mechanisms in colon cancer cells in the presence of telomerase activity [ 102 ].…”

The makings of TERRA R-loops at chromosome ends

“…Notably, these results are strikingly different from what has been seen for highly transcribed genes, which may retain R-loops from transcription and for which BRCA2 was reported to diminish R-loops through a collaboration with the TREX-2 mRNP biogenesis and export complex [ 35 ]. Interestingly, BRCA1 – which among others also promotes RAD51-mediated homologous recombination for DNA repair – is a second DNA recombination factor that was recently shown to physically interact with TERRA as well as TERRA R-loops [ 36 ]. In contrast to RAD51, however, BRCA1 counteracts telomeric R-loops [ 36 ].…”

“…Interestingly, BRCA1 – which among others also promotes RAD51-mediated homologous recombination for DNA repair – is a second DNA recombination factor that was recently shown to physically interact with TERRA as well as TERRA R-loops [ 36 ]. In contrast to RAD51, however, BRCA1 counteracts telomeric R-loops [ 36 ]. The underlying mechanism remains uncertain, but it was proposed to involve BRCA1 interactions with XRN2, which is the ortholog of yeast Rat1.…”