Chromosome Dynamics and Genome Stability

DNA replication and transcription complexes initiate the synthesis of complementary DNA or RNA strands from distinct genomic locations, termed origins and promoters, respectively. Importantly, chromatin presents the natural substrate of these DNA-templated processes. Eukaryotic chromatin is associated, interpreted, and modified by numerous constituents, including DNA and RNA metabolizing machineries, transcription factors, chromatin-modifying proteins, and more. To understand the molecular basis of these DNA transactions, it is critical to define the collective changes of the chromatin structure at the genomic regions where the transcription and replication machineries assemble and drive their biological reactions.

We aim to identify the molecular players and the sequence of events that allow replication and transcription initiation. Our studies will expand our knowledge about how replication timing and gene expression are coordinated in eukaryotic cells and deregulated in a myriad of human disease states.

Once initiated, transcription and replication machineries translocate along the same DNA template, often in opposing directions and at different rates. Mounting evidence suggests that transcription complexes can encounter replication forks on eukaryotic chromosomes. Cells rely on numerous mechanisms to tolerate and resolve such transcription-replication conflicts. The absence of these mechanisms can lead to catastrophic effects on genome stability and cell viability.

We recently established an in vivo system to reconstitute and analyze encounters between the replication fork and a specific type of transcriptional barrier named R-loop in an inducible and localized fashion. Using this system and other cell biological, genetic and proteomic approaches, we aim to elucidate the genetic and epigenetic mechanisms how cells respond, tolerate and resolve different types of transcription-replication conflicts. Our studies will provide insights into how transcription-replication conflicts causes genome instability, often seen during development, in cancer, and many other physiological and disease contexts.

Eukaryotic DNA replication starts at multiple sites throughout the genome and is necessarily coordinated with other chromosomal processes including transcription, chromatin assembly and maturation, recombination and DNA repair. Notably, chromosomes provide the fundamental scaffold for all these dynamic and in part simultaneously occurring processes. Our ultimate goal is to understand the genetic and epigenetic principles of how these fundamental processes are regulated and coordinated to work together on the genome of eukaryotic cells.

We use innovative cell biological, genetic and proteomic approaches in yeast and human cells. We are particularly interested to identify the molecular players and characterize the sequence of events that allow DNA replication and transcription to occur simultaneously on our chromosomes - without major accidents leading to DNA damage and genome instability, a hallmark of cancer and many other human diseases.