Systematic identification of mouse asynchronous replicating regions reveals differential chromatin accessibility and chromosomal coordination

DNA replication takes place in an ordered manner, with each genomic region undergoing synthesis at a specific time in S phase. Although this generally occurs in a synchronous bi-allelic manner, a number of individual regions have been shown to replicate asynchronously (AS), with one allele being copied earlier than the other.
We have developed a whole-genome approach to map all of these differential replication-timing loci by taking advantage of clonal pre-B cell populations derived from C57BL6/Castaneous hybrid mice to identify each allele separately.

These novel regions (~400) are characterized by differential chromatin accessibility, accompanied by mono-allelic expression, in which the early allele is the more accessible and expressed allele. Our comprehensive list of AS replicating regions includes new gene families involved in specifying cell identity. Interestingly, while the mono-allelic expression and probably also the differential chromatin accessibility exist only in certain tissues, we found that the AS replication exists in all examined tissues, suggesting it
was set at early developmental stages prior to tissue differentiation.

Similarly, while any given AS site replicates early on the paternal allele in some cells and on the maternal in others, each individual chromosome is characterized by a fixed pattern of parallel and anti-parallel loci that is identical in all cell types. This finding suggests a coordination of the AS replication pattern between multiple loci that is set up in early embryonic stages.

Taken together, our results suggest that AS replication timing is a highly regulated epigenetic mark set up during early embryogenesis for facilitating the programming of mono-allelic choice throughout development.