Henikoff, SteveAnderson, James2023-09-272023-09-272023-09-272023Anderson_washington_0250E_26162.pdfhttp://hdl.handle.net/1773/50880Thesis (Ph.D.)--University of Washington, 2023The male germline of Drosophila melanogaster is a powerful system for investigating chromatin regulation in a differentiating tissue. Testis-specific genes utilize a distinct system of gene activation, involving tissue-specific rather than general transcription factors, and a unique promoter architecture. Furthermore, the sex chromosomes are regulated quite distinctly in the pre-meiotic male germline, with diminishing transcription of X-linked genes and hyperactivation of the spermatogenesis genes on the heterochromatic Y chromosome. It has been unclear which chromatin components are associated with the unique chromosome-specific trends of expression in the male germline. This dissertation advances our understanding of how chromatin relates to gene expression in the differentiating male germline, particularly regarding: unique patterns of histone 3 lysine 4 dimethylation (H3K4me2) and elongating RNA Polymerase II (RNA PolII ser2phos) at promoters and gene bodies of active spermatogenesis genes; loss of dosage compensation from the X chromosome; the apparent lack of silencing of the X chromosome; and the broad enrichment of ubiquitylated histone H2A (uH2A) across the hyperactivated Y chromosome in spermatocytes. These findings resolve long-open questions about the X chromosome in the male germline, by concluding that the X is neither dosage compensated nor silenced. Intriguingly, the finding of a uH2A body on the Y chromosome in spermatocytes provides new evidence that uH2A plays more versatile roles in chromatin regulation aside from just Polycomb repression. More broadly, this dissertation contributes—from the perspective of chromatin—to recent efforts such as the Fly Cell Atlas to understand what drives gene expression and cell type differences across differentiation and cell types of the fly.application/pdfen-USnonechromatinDrosophilamale germlinenucleosomesGeneticsBiologyDevelopmental biologyMolecular and cellular biologyThesis