Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome

• Published in: Cell 2023-12, Vol.186 (26), p.5840-5858.e36
• Main Authors: Malachowski, Thomas, Chandradoss, Keerthivasan Raanin, Boya, Ravi, Zhou, Linda, Cook, Ashley L, Su, Chuanbin, Pham, Kenneth, Haws, Spencer A, Kim, Ji Hun, Ryu, Han-Seul, Ge, Chunmin, Luppino, Jennifer M, Nguyen, Son C, Titus, Katelyn R, Gong, Wanfeng, Wallace, Owen, Joyce, Eric F, Wu, Hao, Rojas, Luis Alejandro, Phillips-Cremins, Jennifer E
• Format: Article
• Language: English
• Subjects: DNA Methylation; Fragile X Mental Retardation Protein - genetics; Fragile X Mental Retardation Protein - metabolism; Fragile X Syndrome - genetics; Fragile X Syndrome - metabolism; Humans; Mutation; Trinucleotide Repeat Expansion
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2023.11.019

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 premutation length reverses H3K9me3 on the X chromosome and multiple autosomes, refolds TADs, and restores gene expression. H3K9me3 domains can also arise in normal-length iPSCs created with perturbations linked to genome instability, suggesting their relevance beyond FXS. Our results reveal Mb-scale heterochromatinization and trans interactions among loci susceptible to instability.