CBX1 variants cause a neurodevelopmental syndrome due to facultative heterochromatin dysfunction

Abstract

AbstractThe heterochromatin protein 1 (HP1) family of proteins represents an essential structural component of heterochromatin formation and organization. Although HP1β, which is encoded by the CBX1 gene, is essential for brain development in mouse, no human disorders involving HP1 proteins have ever been reported. Through exome sequencing, we identified two heterozygous de novo CBX1 variants in two unrelated individuals with developmental delay, hypotonia and autistic features. Identified variants are in the known functional domain of HP1β, chromodomain, which mediates interaction with chromatin. We examined the effects of the variants using protein structural prediction models and molecular assays. Initial in silico analyses of these missense variants predict that they are highly pathogenic and disrupt protein structure for chromatin binding. Subsequent molecular assays confirmed that the identified variants abolished HP1β-chromatin interactions. Transcriptome and epigenome analyses of human patient-derived lymphoblastoid cell lines with RNA-seq and ATAC-seq, respectively, detected global transcriptional and chromatin organizational alterations, particularly in the context of facultative heterochromatin (i.e. reversibly repressed genomic regions), while chromatin organization was unchanged in constitutional heterochromatin. Overall, the genes harboring H3K27me3 were upregulated, while genes harboring H3K9me3 did not reveal transcriptional alterations. Chromatin was globally more open in the CBX1 mutant sample detected by ATAC-seq. These chromodomain HP1β variants highlight the importance of HP1β chromatin binding particularly in the functional regulation of facultative heterochromatin during neurocognitive development, and confirm the role of CBX1 in intellectual disability and autism spectrum disorder.