DNA Replication Timing
Each dividing cell must undergo precise DNA replication to ensure faithful transmission of its DNA to its daughter cells. In eukaryotic cells, replication occurs according to a tightly regulated temporal program with some regions being replicated earlier and others later. This timing program significantly correlates with many genomic features such as mutation rates and is thus an important mechanism for understanding changes occurring to the DNA both in inheritance and in disease such as cancer. We have established novel statistical and computational methods to analyze replication timing profiles of different cells to better understand how replication timing works and how the changes in this program affect the genome in both healthy and disease states.
The following image shows an example of replication timing plots of different MEF samples.
Though usually both alleles of a genes replicate at the same time, occasionally the same gene will replicate each allele at different times resulting in asynchronous replication. Asynchronous replication is assumed to be an important regulatory feature to allow the cell to express only one copy of the allele. This occurs by imprinted genes as well as by other mono-allelically expressed genes. Despite the importance of this mechanism, to date, no comprehensive studies have determined the genome wide map of asynchronous replication of a clonal cell line. Using F1 mice, from Castaneous and C57BL/6 mouse offspring and separating alleles according to specie-specific SNPs, we have created a genome wide map of asynchronous replication and are characterizing asynchronous regions in order to further understand the mechanisms and regulation of asynchronicity as well as its role in disease.
Cancer replication timing
Deregulated replication timing has been discovered in a number of cancers and influences the pattern of genomic instability. To better understand the function and importance of these changes, we are studying replication timing alterations occurring during the development of Ras induced cancer. We have created inducible cancerous cell systems in which we are measuring the replication timing along cancer progression in order to elucidate the connection between the replication timing program and cancer. With these results, we hope to shed light on important mechanisms which lead to the accumulation of mutations in cancer.
Tissue Specific Structural Variations
Structural variations of cellular DNA are known to distinguish between different species or cell types. We are currently investigating the possibility that unique chromosomal variations also exist between different tissue types. By analyzing existing WGS data of different healthy tissues, we are studying the frequency of different structural variations in a tissue specific manner.