Allelic chromatin structure is a pervasive feature of imprinted domains and functions cooperatively with cis-acting long non-coding RNAs

Genomic imprinting is an epigenetic phenomenon in which genes exhibit restricted or biased expression from one allele according to parental origin. Imprinted gene expression plays crucial roles in embryonic growth and brain development. Higher-order chromatin structure has long been associated with gene regulation, particularly in the context of spatial enhancer-promoter interactions. Because imprinted genes exhibit allele-biased expression, it is compelling to ask whether differences in the three-dimensional organization of maternal and paternal genomes underlie this regulation. Using a capture Hi-C approach, we identified parental allele-specific higher-order chromatin structures across multiple imprinted domains in the mouse brain. These allele-specific structural features largely stem from annotated imprinting control regions (ICRs), concomitant with allele-specific binding of CTCF. The transcription start sites of active and inactive alleles of imprinted genes engage in distinct distal chromatin interactions that differ in number and in the epigenetic states of their contact regions. CRISPR interference (CRISPRi) screening identified a distal cis-regulatory element that modulates imprinted expression at the Mest-Copg2 locus in neurons, with its regulatory activity closely linked to allele-specific chromatin interactions. Further investigation revealed that both a cis-acting long non-coding RNA and allele-specific enhancer-promoter architecture modulates Mest-Copg2 imprinted expression in neurons. Together, this study highlights the interplay between chromatin structure and regulatory landscapes that modulate allele-specific expression of imprinted genes.