DNA methylation and lncRNA control asynchronous DNA replication at specific imprinted gene domains

Besides genome-wide patterns of replication timing (RT), some genes display allelic replication asynchrony in stem cells, brought about by stochastic events and genetic polymorphisms. Whether epigenetic modifications control asynchronous replication remains unclear. Here, we explore domains controlled by genomic imprinting, where parental DNA methylation imprints mediate allele-specific gene expression. Our genome-wide and locus-specific assays in mono-parental and hybrid mouse ESCs reveal pronounced RT asynchrony-which is parent-of-origin dependent and lost upon neural differentiation-at the Dlk1-Dio3 and Snrpn domains, which both comprise lncRNA polycistrons. Generating a range of mutant lines, we find that asynchronous replication at Dlk1-Dio3 is mediated by differential DNA methylation, and that the lncRNA Meg3 controls early replication across parts of the domain on the maternal chromosome. Moreover, we find no evidence that RT and organisation into TADs are linked in this domain. The combined replication timing, DNA methylation, 3D chromatin structure, and gene expression data highlight how parental methylation imprints and lncRNA expression control replication and can override RT domain organisation.