Mosaic H3K9me3 at BREACHes predicts synaptic gene expression associated with fragile X syndrome cognitive severity

Diseases vary in clinical presentation across individuals despite the same molecular diagnosis. In fragile X syndrome (FXS), mutation-length expansion of a CGG short tandem repeat (STR) in FMR1 causes reduced gene expression and FMRP loss. Nevertheless, FMR1 and FMRP are limited predictors of adaptive functioning and cognition in FXS patients, suggesting that molecular correlates of clinical measures would add diagnostic value. We recently uncovered Megabase-scale domains of heterochromatin (BREACHes) in FXS patient-derived iPSCs. Here, we identify BREACHes in FXS brain tissue (N=4) and absent from sex/age-matched neurotypical controls (N=4). BREACHes span >250 genes and exhibit patient-specific H3K9me3 variation. Using N=4 FXS iPSC lines and N=7 single-cell isogenic FXS iPSC subclones, we observe a strong correlation between inter-sample H3K9me3 variation and heterogeneous BREACH gene repression. We demonstrate improved prediction of cognitive metrics in FXS patients with an additive model of blood FMRP and mRNA levels of H3K9me3-mosaic, but not H3K9me3-invariant, BREACH genes. Our results highlight the utility of H3K9me3 variation at BREACHes for identifying genes associated with FXS clinical metrics.