by David M. Gilbert, Laboratory of Chromosome Replication and Epigenome Regulation, San Diego Biomedical Research Institute, CA, USA
The mammalian genome is replicated in a defined temporal sequence during S phase of each cell cycle known as the replication timing program. Since chromatin is assembled at the replication fork, and different types of chromatin are assembled at different times, replication timing is positioned to be central to maintenance or alteration of chromatin states. We have found that replication timing is a highly stable cell-type specific epigenetic property that also exhibits stable disease-specific alterations. However, when mouse or human embryonic stem cells are stimulated to differentiate into different tissue types, widespread developmental changes in replication timing take place in discrete units of ~0.5 Mb that we call replication domains. These changes are accompanied by changes in 3D organization, chromatin composition and transcription that are confined to the affected chromosome domains. Recently, we demonstrated the existence of discrete cis-acting elements (Early Replication Control Elements; ERCEs) that regulate early replication timing, transcription and 3D organization of their domains. Further dissection of ERCEs suggests that they are genetic, developmentally regulated enhancers of replication. We have also identified the first trans-acting factor whose depletion causes a nearly complete elimination of the replication timing program, allowing us to finally ask questions about the function of replication timing. Cells with disrupted replication timing exhibit widespread re-distribution of histone post-translational modifications and alterations in genome architecture that require replication, demonstrating that replication timing is necessary for the maintenance of chromatin (epigenetic) states. Current work is aimed at uncoupling control of replication timing, transcription, chromatin modifications and 3D chromosome architecture to understand mechanisms behind the longstanding correlations between these structural and functional characteristics of chromosomes and their relationship to human disease.