Histones, small basic proteins that package DNA into nucleosomes and chromatin, strongly repress gene expression. We study the effects of dynamic and site-specific modification of core histones, especially of histones H3 and H4, on chromatin function. Many chromatin functions affect chromatin structure is specific ways, and distinct structural chromatin changes are required for specific functions. We focus primarily on those aspects involved in chromatin transcription: the dynamic modification and regulated stability of nucleosomes, and the assembly of nucleosomes with various functionally distinct core histone variants. A large part of this research is experimental, studying histone acetylation, methylation and protein turnover in a variety of model systems. Past projects have used plants such as alfalfa and Arabidopsis, algae like Chlamydomonas, the yeast Saccharomyces cerevisiae, and Physarum polycephalum. Currently, these studies are being extended to the basidiomycete Ustilago maydis and selected protista using as basic techniques protein purification, in vivo radiotracer labeling, HPLC and gel electrophoresis. This research is predicated on interpreting a broad evolutionary analysis of histone H3 variants with specific replication- and transcription-related functions. It appears that the gene for the central nucleosomal core histone H3 duplicated multiple times independently during early evolution (0.4 – 1.5 billion years). In each case two co-expressed but functionally distinct and highly conserved histone H3 proteins arose: the more ancient Replication-Independent form which is assembled into Replacement nucleosomes across transcribed gene sequences where transcription caused loss of nucleosomes, and into nucleosomes on newly replicated DNA, and a novel, Replication-Coupled form which is assembled into nucleosomes on newly replicated DNA due to an S-phase pattern of expression. Exclusion of RC histone H3 from transcription-associated nucleosome assembly appears variable across the independent duplication events in metazoa, basidiomycota, archaeplastida and alveolata.