CTCF binding controls imprinted gene expression at the Dlk1-Dio3 and Igf2-H19 domains by structuring allele-specific sub-TAD organisation

Mammalian genomic imprinting provides a unique paradigm to explore intra-cellular differences in chromatin structuration. At several imprinted chromosomal domains, germline acquired DNA methylation marks confer parental allele-specific recruitment of CTCF, a protein enriched at the borders of TADs ('Topologically Associating Domains'). Here, we explored the two conserved paternally-imprinted domains in mammals—the Igf2-H19 and Dlk1-Dio3 domains—within the context of TAD organisation. Both domains are located within TADs that show similar borders on the parental chromosomes. However, their sub-TAD organisation is pronouncedly different between the parental chromosomes, both in embryonic stem cells and differentiated cells. Sub-TADs on the paternal chromosomes are structured by bi-allelic CTCF, with additional allele-specific CTCF binding on the maternal chromosome adding a further layer of sub-TAD organization, the latter being essential to maintain the paternally expressed genes in an inactive state.