FMRP bridges R-loops and DHX9 through direct interactions

Fragile X Syndrome (FXS) occurs when mutations in the FMR1 gene cause the absence or dysfunction of FMRP, known mainly as a translation repressor. We recently showed that FXS cells suffer genome-wide DNA double-strand breaks near R-loops under replication stress. The expression of FMRP, and not an FMRP-I304N mutant of the K-homology 2 RNA-binding domain, suppresses the R-loop-induced DNA breakage. These observations led us to hypothesize that FMRP safeguards the genome through promotion of R-loop detection and/or resolution. Here, we demonstrate that FMRP directly binds R-loops through multivalent interactions between the carboxy-terminal intrinsically disordered region and the R-loop sub-structures. We also show that the amino-terminal folded domain of FMRP directly binds DHX9, an R-loop resolvase, in a KH2-dependent manner. The FMRP-DHX9 interaction is recapitulated by co-immunoprecipitation in human cells. Our findings are consistent with a model in which FMRP recruits DHX9 to R-loop forming sites by bridging their interaction through its amino- and carboxy-termini, respectively.