Characterization of Post-Translational Modifications on Histone H4 and the Histone Chaperone N1 Using Mass Spectrometry

A large amount of genetic information is stored in every cell of our body. The mechanism by which this information is compacted to fit into the small space of the nucleus involves the interaction of DNA and proteins. How this genetic information is stored also has implications for the accessibility of certain regions of the genome. Chromatin is the name given to this protein-DNA complex and is composed of repeating units called nucleosomes. A single nucleosome contains eight proteins (two copies of four different histone proteins) and approximately 146 base pairs of DNA. The repetition of this structure and incorporation of scaffolding proteins results in a compaction of approximately 10,000 fold. Post-translational modifications (PTMs) to the histone core can have a drastic effect on accessibility to the genome by changing the protein-DNA interaction within the nucleosome. Understanding PTMs on histone proteins as well as the proteins involved in the assembly and maintenance of this structure is important in better understanding the factors which can affect gene expression in a variety of biological contexts.
In this dissertation, we utilize high resolution mass spectrometry (MS) and MS appropriate sample preparation techniques including sample derivatization and targeted analysis to study low level modifications on the histone protein H4. We apply similar methods to the study of a histone chaperone protein, N1 and explore methods necessary for the detection of the highly acidic, active region of N1, a feature common to histone chaperone proteins.