Biochemical understanding of the control of gene expression, interactions between proteins and DNA that are involved in transcriptional control, chromatin structure and function.
Transcription in eukaryotes is regulated by a host of positive and negative transacting factors. We are focusing on two proteins that are components of yeast chromatin. The first is an abundant protein called SIN1p which binds DNA and regulates the transcription of a specific family of genes. These same genes are activated by a chromatin remodeling complex called SWI/SNF. Using molecular biology techniques, we are trying to understand how the SIN1p molecule modulates the expression of these and other genes. In the course of this research, we have identified a number of proteins with which SIN1p interacts. We are currently trying to understand how these proteins function in conjunction with SIN1p. In addition, we have determined that several domains of SIN1p are able to bind cruciform DNA in a structure-specific way. These data implicate SIN1p as being involved in creating local modifications in DNA structure. Most recently, we have discovered that SIN1p often binds DNA, 3' to the open reading frame, and that it interacts with part of the mRNA polyadenylation complex. These studies indicate that SIN1p is required for efficient recruitment of the polyadenylation complex to the nascent RNA.
The second chromatin protein that we are studying is yeast linker histone H1. We have determined that it is not ubiquitous throughout the chromatin, but rather is found specifically in specific regions of the genome, in particular in the rDNA repeat that encodes ribosomal RNA. Most recently, we have produced a series of mutant strains of yeast that contain different deletions in the gene encoding this histone, and have assayed the transcription of the rDNA and of a foreign gene that has been inserted into the rDNA. We find that different mutants in the linker histone affect the transcription of the foreign gene in a dramatic way. We are using this information to functionally map the linker histone. We have also shown that this yeast linker histone is required for RNA polymerase I to transcribe the rDNA with normal processivity. We are currently working to understand the molecular basis for these observations.