Recruitment of H3.3 histone chaperon activity to R-loops by the Splicing-Factor Proline and Arginine Rich (SFPQ) stabilizes repetitive elements in cancer cells

R-loops are triple-stranded nucleic acid structures containing an RNA moiety paired with its antisense DNA template strand and the loop of the displaced, single-stranded DNA (ssDNA). RNA:DNA hybrids form under normal physiological conditions and exert multiple biological functions. However, persistent R-loops have been shown to mediate replication stress, DNA damage and drive genomic instability, with a particular relevance at vertebrate telomeres. We recently found that the RNA-binding protein SFPQ has a critical role in limiting R-loops formation at telomeres of human cancer cell. In line with this, loss-of-function SFPQ cells show increased levels of RNA:DNA hybrids, replication stress and DNA damage markers and subsequent genomic instability at telomeres level. Here we show that SFPQ function is not limited to telomeres, but expands to other non-coding repeat regions in the human genome, as depicted by ChIP-seq analysis, paralleled by increased R-loop levels and genomic instability. Moreover, SFPQ action is mediated by the its novel interactor DAXX, that allows R-loop suppression by inserting H3.3 histone variant. Finally, RNA-seq analysis pointed out a SFPQ - R-loop dependent signature of innate immune response activation, unveiling a novel connection between non coding genome regulation and immune response, suggesting SFPQ as putative target for sarcoma treatment.

R-loops are triple-stranded nucleic acid structures containing an RNA moiety paired with its antisense DNA template strand and the loop of the displaced, single-stranded DNA (ssDNA). RNA:DNA hybrids form under normal physiological conditions and exert multiple biological functions. However, persistent R-loops have been shown to mediate replication stress, DNA damage and drive genomic instability, with a particular relevance at vertebrate telomeres. We recently found that the RNA-binding protein SFPQ has a critical role in limiting R-loops formation at telomeres of human cancer cell. In line with this, loss-of-function SFPQ cells show increased levels of RNA:DNA hybrids, replication stress and DNA damage markers and subsequent genomic instability at telomeres level. Here we show that SFPQ function is not limited to telomeres, but expands to other non-coding repeat regions in the human genome, as depicted by ChIP-seq analysis, paralleled by increased R-loop levels and genomic instability. Moreover, SFPQ action is mediated by the its novel interactor DAXX, that allows R-loop suppression by inserting H3.3 histone variant. Finally, RNA-seq analysis pointed out a SFPQ - R-loop dependent signature of innate immune response activation, unveiling a novel connection between non coding genome regulation and immune response, suggesting SFPQ as putative target for sarcoma treatment.