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Steven Henikoff is interested in inherited differences in gene expression between cells and tissues and how that differential expression is mediated by specialized proteins. To better understand such inheritance that does not rely on DNA sequence, Henikoff and his team develop and apply genomic tools to the study of proteins of the epigenome: histones, transcription factors, nucleosome remodelers, and RNA polymerase II. Application of these tools has elucidated the relationship between transcription, torsion, and nucleosome turnover, and determined the molecular organization of centromeric nucleosomes, among other discoveries.