Allelic chromatin structure primes imprinted expression of Kcnk9 during neurogenesis

Differences in chromatin state inherited from parental gametes can influence the regulation of maternal and paternal alleles in offspring. This phenomenon, known as genomic imprinting, results in genes preferentially transcribed from one parental allele. While some epigenetic marks that lead to these allelic differences have been identified, like DNA methylation, questions remain about how these epigenetic marks promote allelic differences over broad stretches of chromatin. Here we characterize the mechanisms underlying brain-specific imprinted expression of the Peg13-Kcnk9 locus, an imprinted gene cluster associated with intellectual disability. We performed region capture Hi-C during in vitro neuron differentiation and found that allelic differences in DNA methylation cause allelic binding of the chromatin organizing factor CTCF, leading to differences in large-scale chromatin folding patterns between the two parental alleles. On the maternal allele, an enhancer-promoter contact formed early in development primes the potassium leak channel Kcnk9 for maternal expression upon neurogenesis. In contrast, this enhancer-promoter contact is blocked by CTCF on the paternal allele, preventing paternal Kcnk9 activation. Therefore, pre-existing differences in the chromatin contacts between the two parental alleles drive neuronal Kcnk9 imprinted expression. This work provides a high-resolution map of imprinted chromatin structure and demonstrates that chromatin state established in early development can promote proper gene expression patterns upon differentiation.