biostudies-literatureMalachowski TNSFNew York Stem Cell FoundationNICHD NIH HHSNIDA NIH HHSNIMH NIH HHSBlavatnik Family FoundationNational Institutes of HealthChan Zuckerberg InitiativeNIMHNIDDK NIH HHSNINDS NIH HHSNIDANIDDKNIGMS NIH HHS5840-5858.e36https://www.ebi.ac.uk/biostudies/studies/S-EPMC10794044biostudies-literatureUnknown186(26)Short tandem repeat (STR) instability causes transcriptional silencing in several repeat expansion disorders. In fragile X syndrome (FXS), mutation-length expansion of a CGG STR represses FMR1 via local DNA methylation. Here, we find megabase-scale H3K9me3 domains on autosomes and encompassing FMR1 on the X chromosome in FXS patient-derived iPSCs, iPSC-derived neural progenitors, EBV-transformed lymphoblasts, and brain tissue with mutation-length CGG expansion. H3K9me3 domains connect via inter-chromosomal interactions and demarcate severe misfolding of TADs and loops. They harbor long synaptic genes replicating at the end of S phase, replication-stress-induced double-strand breaks, and STRs prone to stepwise somatic instability. CRISPR engineering of the mutation-length CGG to premutationCellSpatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome.PMC10794044R37 MH120269F300HD098015DP1 MH129957U01 DK127405R35 GM128903F30 HD098015F31NS129317R01 MH120269F31 NS129317U01 DA052715Ge CZhou LSu CNguyen SCTitus KRChandradoss KRPham KPhillips-Cremins JEMalachowski TWallace OJoyce EFGong WWu HHaws SARyu HSBoya RRojas LAKim JHCook ALLuppino JMfalseSpatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome.Short tandem repeat (STR) instability causes transcriptional silencing in several repeat expansion disorders. In fragile X syndrome (FXS), mutation-length expansion of a CGG STR represses FMR1 via local DNA methylation. Here, we find megabase-scale H3K9me3 domains on autosomes and encompassing FMR1 on the X chromosome in FXS patient-derived iPSCs, iPSC-derived neural progenitors, EBV-transformed lymphoblasts, and brain tissue with mutation-length CGG expansion. H3K9me3 domains connect via inter-chromosomal interactions and demarcate severe misfolding of TADs and loops. They harbor long synaptic genes replicating at the end of S phase, replication-stress-induced double-strand breaks, and STRs prone to stepwise somatic instability. CRISPR engineering of the mutation-length CGG to premutation2023-01-01T00:00:00Z2023 Dec2026-05-20T03:12:40.466Z2025-04-06T22:14:27.286ZS-EPMC107940443813487610.1016/j.cell.2023.11.019