Chromatin Conformation Capture Reveals Disrupted Genome Folding in Down Syndrome
DOI:
https://doi.org/10.5281/zenodo.22761157Keywords:
Down syndrome, trisomy 21, Hi-C, chromosome territory, TAD boundary, iPSC-derived neurons, genome folding, allele-specific expressionAbstract
Trisomy 21 causes Down syndrome through a poorly understood combination of direct gene dosage effects from
the triplicated chromosome and secondary, genome-wide transcriptional dysregulation, and whether this
genome-wide dysregulation involves altered three-dimensional genome folding beyond the triplicated chromosome
itself has not been directly tested at high resolution. We generated isogenic trisomy 21 and euploid induced
pluripotent stem cell (iPSC) lines from the same Down syndrome donor by spontaneous chromosome loss,
differentiated both into cortical excitatory neurons, and performed in situ Hi-C, RNA-sequencing and ATAC-seq at
three differentiation time points to map genome folding changes associated with trisomy 21. Chromosome 21 itself
showed altered inter-chromosomal contact frequency with multiple other chromosomes in trisomy 21 neurons, most
prominently increased contact with chromosome 11, but topologically associating domain (TAD) boundaries and
intra-chromosomal contact structure on chromosome 21 were largely preserved between genotypes. In contrast, we
identified 312 TAD boundaries genome-wide, distributed across every other chromosome, that were significantly
weakened or lost specifically in trisomy 21 neurons, significantly enriched near the 743 genes showing the largest
trisomy-associated expression changes outside chromosome 21 itself. Allele-specific analysis at heterozygous
variants distinguishing the two chromosome 21 homologs showed no consistent asymmetry in contact behavior,
indicating that all three copies participate comparably in the altered contacts observed. CRISPR-mediated
restoration of a representative weakened TAD boundary near the disomic gene RUNX1 partially normalized RUNX1
expression toward the euploid level, supporting a causal contribution of boundary weakening to expression
dysregulation. These results indicate that trisomy 21 disrupts genome folding well beyond the triplicated
chromosome itself, implicating three-dimensional chromatin architecture as a contributor to Down
syndrome-associated gene dysregulation.
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