Fragile X Mental Retardation Protein regulates R-loop formation and prevents global chromosome fragility

Fragile X syndrome (FXS) is the most prevalent inherited intellectual disability caused by mutations in the Fragile X Mental Retardation gene (FMR1) and deficiency of its product, FMRP. FMRP is a predominantly cytoplasmic protein thought to bind specific mRNA targets and regulate protein translation. Its potential role in the nucleus is not well understood. We are interested in the global impact on chromosome stability due to FMRP loss. Here we report that compared to an FMRP-proficient normal cell line, cells derived from FXS patients exhibit increased chromosome breaks upon DNA replication stress induced by a DNA polymerase inhibitor, aphidicolin. Moreover, cells from FXS individuals fail to protect genomic regions containing R-loops (co-transcriptional DNA:RNA hybrids) from aphidicolin-induced chromosome breaks. We demonstrate that FMRP is important for abating R-loop accumulation during transcription, particularly in the context of head-on collision with a replication fork, and thereby preventing chromosome breakage. By identifying those FMRP-bound chromosomal loci with overlapping R-loops and fragile sites, we report a list of novel FMRP target loci, many of which have been implicated in neurological disorders. We show that cells from FXS patients have reduced expression of xenobiotics metabolic enzymes, suggesting defective xenobiotics metabolism/excretion might contribute to disease development. Our study provides new insights into the etiological basis of, and enables the discovery of new therapeutic targets for, the FXS.