Short tandem repeats susceptible to pathogenic instability linked to chromatin domain disruption

More than 25 inherited human disorders are caused by the unstable expansion of repetitive DNA sequences termed short tandem repeats (STRs). A fundamental unresolved question is why some STRs are susceptible to pathologic expansion, whereas thousands of repeat tracts across the human genome are relatively stable. Here, we discover that nearly all disease-associated STRs (daSTRs) are located at boundaries demarcating 3D chromatin domains. We identify a subset of boundaries with markedly higher CpG island density compared to the rest of the genome. daSTRs specifically localize to ultra-high-density CpG island boundaries, suggesting they might be hotspots for epigenetic misregulation or topological disruption upon STR expansion. Fragile X Syndrome (FXS) patients exhibit severe boundary disruption in a manner that correlates with local loss of CTCF occupancy and the degree of FMR1 silencing. Our data uncover higher-order chromatin architecture as a new dimension in understanding repeat expansion disorders. Overall design: Chromosome-Conformation-Capture-Carbon-Copy (5C) was used to interrogate the three-dimensional structure of the genome at the FMR1 locus in 2 normal and 3 FXS B-lymphocyte samples, 1 normal and 1 FXS fibroblast samples, and 2 normal and 2 FXS postmortem cerebellum tissue samples. CTCF ChIP-seq was used to map the binding profile of CTCF genome-wide in 1 normal and 2 FXS B-lymphocyte samples. Two biological replicates of each sample are included.