Identifying determinants of chromosomal domains as defined by time of replication

Abstract

The genome is organized into functional domains in which gene expression, chromatin modifications, and DNA replication is coordinately regulated. The time at which a genomic locus replicates during S phase appears to be dependent on subnuclear positioning and chromatin conformation. Recently, our lab generated a high resolution replication timing profile for 30 Mb of the human genome (1%) as part of the ENCODE consortium. Using a computational approach, we have identified regions of rapid transition in replication timing that coincide with changes in chromatin modifications. We hypothesize that these regions contain genomic elements, such as nuclear matrix attachment regions and binding sites for insulator proteins, that that are responsible for the organization of chromatin into functional domains. To test this hypothesis, we are mapping matrix attachment sites in HeLa cells and utilizing enhancer‐blocking insulator assays to identify potential boundary elements in these regions. These results will yield a better understanding of how replication domains are organized and insight to the mechanisms that regulate chromatin domain structure. This work is supported by NIH R01 CA089406 to A.D.