Selective chr21 homolog silencing reveals polymorphisms influence the epigenetic silencing and functional dosage of...

Polymorphisms that affect chromosome 21 (chr21) gene expression have significance for both variable severity in Down syndrome and common multifactorial conditions. Here, results demonstrate that "selective homolog silencing" in cells from one individual can provide a valuable complement to population-level studies. In trisomic induced pluripotent stem cell (iPSC) subclones that silence different chr21 homologs (via XIST-based silencing), we discovered unusually large, homolog-specific differences in RWDD2B expression in iPSCs, cortical organoids, and endothelial cells. RNA fluorescence in situ hybridization (FISH) showed that RWDD2B transcription arose almost entirely from a particular homolog (H1) correlated with CpG promoter methylation differences. Polymorphisms differing on H1, versus H2/H3, had stronger GTEx expression quantitative trait loci (eQTLs), especially in brain. Collective results indicate that RWDD2B functional dosage is more frequently disconnected from copy number, even compared to neighboring genes. Although RWDD2B function is unknown, methyl-eQTLs link it to osteoarthritis, and we suggest possible roles in immunity or inflammation. This study has significance for RWDD2B regulation and demonstrates a cell-based methodology to study polymorphisms.