There has been extraordinary progress in molecular biology during the 50-year span that began with the discovery of the DNA double helix and culminated with the nearly complete specification of our genetic inheritance. In contrast, the inheritance of differences in gene expression between cells and tissues is poorly understood. To better understand inheritance that does not depend on DNA sequence, we apply genomic tools to the study of epigenetic markers.
The bulk of the eukaryotic genome is packaged into nucleosome particles, each of which comprises an octamer with two copies of each of four core histones--H2A, H2B, H3, and H4--which wrap nearly two turns of DNA. Nucleosomes can be differentiated both by numerous post-translational histone modifications and by incorporation of histone variants.
Recent studies in our lab have focused on understanding the nucleosome dynamics of chromatin, and its relationship to gene expression and epigenetic inheritance. We have developed powerful genome-wide strategies for measuring nucleosome dynamics and mapping epigenomic features of native chromatin at single base-pair resolution, using such tools as salt fractionation to extract classically ‘active’ chromatin; CATCH-IT, a novel metabolic labeling strategy to directly measure nucleosome turnover; and INTACT, a cell-type specific nuclear purification method to determine chromatin differences between tissues. Using these tools we attempt to understand how RNA polymerase II (Pol II), nucleosome remodelers, transcription factors, and histone variants all affect and are affected by dynamic chromatin structure.
We have also long been interested in the special roles and properties of histone variants, such as the class of centromere-specific histone H3 variants, collectively called cenH3 (also known as CENP-A in vertebrates or Cse4 in fungi), the location of which determines the location of the kinetochore that attaches to microtubules to segregate chromosomes in mitosis and meiosis. CenH3-containing nucleosomes have a unique structure and wrap DNA to form positive supercoils, in contrast to conventional nucleosomes that form negative supercoils. We are interested in how the special properties of cenH3 nucleosomes allow the centromere to be stably epigenetically inherited and yet evolve into centromeres as diverse as the point centromeres of budding yeast with a single cenH3 nucleosome, to the holocentric centromeres of the nematode worm Caenorhabditis, in which the entire chromosome appears to act as a centromere.