Nucleosomes and gene expression in plants
We have an ongoing collaboration with Dr. Shinhan Shiu (Dept. of Plant Biology) and Dr. Gregg Howe (Dept. of Biochem. and Mol. Bio.) to study nucleosome binding in plants. In a recent study we investigated nucleosome positioning in Arabidopsis thaliana and showed that, in contrast to yeast and mammals, nucleosome depleted regions tend to be GC-rich in this organism (Liu et al., 2015). In particular, we found that nucleosome depleted 6-mers that presumably correspond to TF-binding sites have a higher G/C-content than nucleosome depleted regions in yeast.
Nucleosome positioning and occupancy in embryonic stem cells
We are collaborating with Dr. Jason Knott (Dept. of Animal Science) and Dr. Amy Ralston (Dept. of Biochem. and Mol. Bio.) to investigate nucleosome positioning and occupancy in mouse embryonic stem cells.