The Mest DMR regulates Klf14 imprinting via allele-specific sub-TAD structures

The maternally-expressed gene Klf14 is located ~200 kb downstream of Mest. Although its promoter CGI is kept unmethylated in most tissues, maternally-inherited DNAme is paradoxically required for Klf14 expression.

Here, we show that Mest and Klf14 reside within the same topologically associating domain (TAD) in mouse embryonic stem cells (ESCs), defined by sites of biallelic CTCF binding at the boundaries. Using allele-specific 4C-seq in F1 hybrid ESCs, we show that CTCF binding to the unmethylated Mest gDMR generates a paternal allele-specific sub-TAD required for Klf14 silencing. These observations, supported by analysis of CRISPR-mediated deletions of the Mest gDMR, define a new role for maternally methylated gDMRs, which are all associated with promoter-proximal functions: our results show they can also exert long-range effects via allele-specific modulation of TAD structures.