Exploring The Structure And Function Of Large Multi-Protein Mammalian Class I Histone Deacetylase Complexes Via An Electron Microscopy Approach

Histone deacetylases (HDACs) are enzymes that catalyse the removal of acetyl groups from lysine residue side chains and target a vast range of proteins, including histones. class I HDACs (1, 2 and 3) are core protein subunits of large multi-protein transcriptional repression complexes which regulate local chromatin structure by recruiting HDAC activity to specific gene loci/promoters. These complexes have essential functions in development and determining cell lineage and an alteration to their activity has been strongly linked to various diseases including cancer. Despite major progress into understanding the function, composition and structure of these complexes, for most complexes the architecture and detailed molecular mechanism of function remains poorly understood. Insight into the architectures of HDAC containing complexes would be vital for the design of therapeutics, particularly those aimed at disrupting complex formation, for oncological treatment. This thesis focuses on the structure determination and functional analysis of three transcriptional repression complexes: the nucleosome remodelling and deacetylase (NuRD) complex, the mitotic deacetylase (MiDAC) complex and the CoREST complex. Using single particle electron microscopy reconstruction, it was possible to obtain a negative stain-EM density map of the NuRD and CoREST complex and a cryo-EM density map of the MiDAC complex. The newly generated EM density maps were used to generate structural models based on fitting of currently available solution NMR and X-ray crystallography structures. Using the electrophoretic mobility shift assay (EMSA) technique, the ability of the complexes mentioned above to bind DNA of varying sequence and length and to bind oligo-nucleosomes was assessed. Intriguingly, the assays indicate that only the MiDAC complex can form a stable complex with oligonucleosomes.