Theabilitytoexpressdifferentgenesindifferentcelltypesiscrucialtodevelopmentofa multicellular organism. This cell-type specific gene expression relies on memory of activation and repression of genes through successive rounds of cell division as the organismdevelopsfromanembryotoanadult.Animportantcomponentofthememory ofcellularidentityisthecell?schromatinstate.Tomaintainatranscriptionalprogram,the cell has to maintain accessibility at active promoters and enhancers and occlusion at repressed promoters and enhancers. However, the passage of replication forks during everycellcycleobliteratescell-typespecificchromatinlandscapes.Ouroverarchinggoal istodeterminehowchromatinlandscapesaresustainedinspiteofnucleosomedynamics throughout the cell cycle, thus maintaining cellular memory. Here, we will use genomic methods we develop(ed) to identify cellular mechanisms that maintain chromatin landscapes despite the erasing effects of replication. We will pursue two lines of investigations:First,wewillidentifyhowtranscriptionfactorsfindtheirbindingsitesafter being stripped from the DNA during process of replication. We have shown that transcription factors are replaced by nucleosomes genome-wide post-replication. By tracking transcription factor binding to DNA and DNA accessibility as a function of time post-replication, we will uncover the determinants of transcription factor site selectivity. We will also study the effect of chromatin remodeler function in creating transcription factor binding sitespost-replication. Second,we will elucidate cellular mechanisms that maintain repressed chromatin landscapes through replication at epigenetically silenced domainsthatarecharacterizedbytrimethylatedhistoneH3(H3K27me3),whichwecall ?Polycomb domains?. Polycomb group proteins maintain repressed states at these domains. Mechanisms that carry memory of repression through replication have to act within a single cell cycle, every cell cycle. We will combine tracking chromatin states genome-wide post-replication with carefully chosen perturbations of Polycomb group proteins to uncover mechanisms that maintain this repressed state through replication. Takentogether,thesestudieswillnotonlyresolvelong-standingquestionsintranscription factor-site selectivity and Polycomb repression, but will also serve as a framework to understand how chromatin dynamics can shape genome function in many biological contexts.
A cell?s identity is tied to how its genome is packaged. This cell type specific genome packagingisessentialfornormaldevelopmentoftheorganismandisfrequentlydisrupted indisease.Thisproposalwillidentifyhowacellremembersthespecificpackagingofits genome every time it replicates its genome so as to maintain its identity during normal growthandhowperturbationofthismemorycanleadtoaberrantcellstates.
