Viviana Risca, Ph.D., Rockefeller University
Probing Sub-kilobase Chromatin Fiber Folding and its Regulation
The kilobase-scale architecture of chromatin effectively defines the epigenomic landscape on which DNA-based processes operate. We have been developing tools to probe the local three-dimensional interactions of nucleosomes in order to understand how they are shaped by chromatin architectural factors, such as linker histones, by histone variants, by histone modifications, and by nucleosome positions. These tools include an improved version of RICC-seq, an ionizing radiation-based method for probing DNA-DNA contacts in intact cells, computational tools to interpret DNA-DNA contact data, and a novel Hi-C variant with improved genome-wide performance that allows us to follow nucleosome-scale contact “walks” along chromosomes. We have applied these as well as established methods for chromatin analysis to understand how linker histone contributes to chromatin compaction in situ and how chromatin compaction relates to histone modifications and three-dimensional chromatin architecture. We have also begun to explore chromatin on viral genomes as a model system for the detailed study of the relationship between kilobase-scale chromatin architecture and gene expression. All together, we seek to understand how kilobase-scale chromatin organization and compaction relate to functional properties like the accessibility of DNA binding sites, the ability of nucleosomes to be modified, and the control of looping contacts between regulatory regions on DNA.