First, we are interested elucidating the mechanisms by which the core histone tail domains define the structural and functional state of nucleosomes and the chromatin fiber. To this end we prepare well-defined model chromatin complexes and chemically and spectroscopically probe structure and interactions in solution. Our goal is to understand the complex set of interactions of the core histone tail domains in single nucleosomes and ultimately in oligonucleosomal complexes and how critical posttranslational modifications of the tails alter these interactions.

Second, in a collaboration with Dr. Robert Bambara's laboratory at the UR we are investigating how chromatin structure affects the activity of DNA-modifying enzymes involved in DNA replication and base-excision repair (BER). Specifically, we have found that two enzymes involved in these processes, human DNA ligase I and FEN1, are able to operate surprisingly efficiently on nucleosome substrates. We are currently investigating the mechanism of these enzymes and other components of the BER pathways.

Third, we have developed an in vivo approach using the slime mold Physarum polycephalum as a model organism that allows investigation of histone structure/function relationships within a living cell. This approach exploits the natural cell cycle synchrony and ability of this organism to internalize exogenous proteins, without disruption of structure. We have used this system to analyze the subtype-specific effects of linker histones and to show that the H2A/H2B tail domains are required for replication-dependent chromatin assembly in vivo. Currently, we are investigating the role of the tails in replication-coupled and independent chromatin assembly and elucidating specific amino acids or posttranslational modifications that may be critical in this process.

Last, We have been investigating the mechanisms by which chromatin remodeling complexes use the energy of ATP hydrolysis to alter structure and accessibility in nucleosomes. A collaboration with Bob Kingston's group has allowed us to investigate several aspects of the hSWI/SNF complex and recently we have begun a collaboration with Paul Wade's group at Emory University to carry out similar studies on the Xenopus Mi2 complex.