Howard Cedar, M.D. - Investigator Profile
Mammalian organisms utilize DNA methylation at cytosine residues as an epigenetic mechanism for bringing about the global repression of non active genes in the genome. Early in development the gamete methylation pattern is erased and a new somatic pattern is established at the time of implantation by de novo methylation of all sequences except CpG islands which are mainly found at the 5' end of housekeeping genes.
Although this process is stage specific, the resulting pattern is genocopied during development by a maintenance methylase (see figure). Tissue specific genes undergo demethylation as part of cell type differentiation, and as a result, the active genes in each cell are unmodified while the rest of the genome is mostly methylated. It is this pattern which ensures that non appropriate gene expression is repressed, and this is probably accomplished through the effect of methylation on chromatin structure.
Projects in the lab are aimed at further elaborating this process. We are using transgenic mice to determine the mechanism by which DNA methylation alters nucleosome and chromatin structure. Studies in tissue culture and in mice are being used to map the cis acting elements which mediate stage or tissue specific demethylation events, and we have also begun to isolate trans acting factors involved in the process. In a separate project the laboratory is attempting to purify demethylation enzymes both to determine their biochemical mode of action and to clone their respective genes. Finally, we are also using a mouse system to decipher the role of DNA methylation in imprinting.
DNA replication timing
The entire genome is replicated in a programmed manner during S-phase with some gene regions undergoing DNA synthesis early in S-phase and others replicating late. This is a developmentally regulated process whereby housekeeping genes are early replicating in all cells, while many tissue specific genes replicate late in most cell types and become early in the tissue of expression.
Evidence indicates that replication origins are used in a fixed manner, but their activation is controlled by cis acting elements which determine when in S-phase the nearby origins fire. Studies in our lab are aimed at identifying these genetic elements and deciphering how they work.
Using a new experimental system whereby DNA is injected in nuclei of cells growing in culture we have shown that transcription complexes on a variety of genes are formed more efficiently when introduced in early S-phase, and this might serve as a basis for understanding how replication timing influences gene expression. Imprinted genes are associated with asynchronous replication where one allele undergoes DNA synthesis prior to the other, and our laboratory is investigating whether this may represent a fundamental property of imprinting which is derived from the gametes and maintained following cell division.
DNA methylation, DNA replication, epigenetics, genome, transgenic mouse models, chromatin structure, gene expression