Patrick Lynch

The construction of silent chromatin domains can be divided into two phases: recruitment of the Sir protein complex to a silencer and spreading of the Sir complex across the chromosome. A hallmark of silencing is sequence independence. However, silent chromatin accounts for less than 10% of the S. cerevisiae genome and encroachment of silencing into essential and important genetic loci would be lethal; therefore stopping the spread of the Sir complex is itself an essential process. A model for regulation suggests that a competitive balance exists between active and silent chromatin. According to this model, the active genome is equipped with obstacles to spreading such as acetylated histones and nucleosome gaps. For most silent domains, this competition is manifest in a tapering of silencing proportional to spreading distance.

The focus of my research is to examine the kinetics of Sir complex spreading across chromatin with the objective of clarifying the mechanisms that regulate spreading. Using chromatin immunoprecipitation (ChIP) for Sir2p, the histone deacetylase of the Sir complex, the kinetics of Sir migration across the chromatin landscape can be followed over time during the de novo establishment of silencing. Collecting kinetic data on spreading in vivo enables me to ask questions about the different factors that alter spreading rates and quantify their contributions. Specifically, I’m interested in examining the limitations on spreading that are intrinsic to the Sir proteins themselves. I’m also interesting in assaying the importance of chromosomal context as well as extrinsic chromatin modifying factors on limiting the spread of silent chromatin. Ultimately, by following the dynamics of silent chromatin progression in detail, my project seeks to further examine the phenomena of spreading and its regulation.

Publication

Lynch, P.J., Fraser, B.H., Sevastopoulos, E., Rine, J., and Rusche, L.N. (2005). “Sum1p, the Origin Recognition Complex, and the spreading of a promoter-specific repressor in Saccharomyces cerevisiae.” Mol. Cell. Biol. 25:5920.