Histone H4 lysine16 acetylation instructs chromatin compartment transitions

This thesis examines how regulatory mechanisms with evolutionary links to the Drosophila Male-Specific Lethal (MSL) system have diverged to support genome and transcriptome stability in mammals. Although the canonical MSL complex functions in dosage compensation in flies, its components and orthologues have acquired distinct roles in higher organisms. Two projects investigate this diversification at the levels of chromatin architecture and RNA quality control. The first project focuses on H4K16ac, deposited by the conserved acetyltransferase MOF. Integrative Hi-C, CUT&Tag, and RNA-seq analyses demonstrate that H4K16ac is a strong predictor of A/B compartment identity and contributes to the maintenance of higher-order genome organization. Acute depletion of MOF disrupts the H4K16ac landscape and weakens compartment segregation before major transcriptional changes occur, accompanied by modest H3K9me3 redistribution and activation of compensatory pathways. During meiosis, the natural loss of H4K16ac on the X chromosome coincides with broad H3K9me3 spreading, further supporting its role in stabilizing active chromatin domains. The second project analyzes DHX9, the mammalian orthologue of the MSL helicase MLE, which no longer functions within the MSL complex. The study identifies DHX9 as a marker of a UV-induced, non-canonical stress granule that sequesters RNA-protein crosslinking-damaged intronic transcripts. This compartment reduces the accumulation and transmission of aberrant dsRNA species to daughter cells, thereby preserving transcriptome integrity under genotoxic stress. Together, these studies illustrate how conserved chromatin- and RNA-regulatory modules have diverged to perform specialized functions in mammals. From the stabilization of 3D genome architecture through H4K16ac to the protection of RNA fidelity by DHX9, the work highlights evolutionarily adapted strategies that maintain genomic and transcriptomic stability across cell cycle and developmental transitions