Eight principal chromatin states functionally segregate the fly genome into developmental and housekeeping roles

Different chromatin forms, or states, represent a fundamental means of controlling gene regulation. Chromatin states have been studied through either the distribution of histone modifications (e.g. 1–5 ) or more rarely via the occupancy of chromatin proteins 6–8 . However, these two approaches disagree on the nature and composition of active chromatin states 2,9 and modelling chromatin via both histone marks and chromatin proteins has been lacking. Here, combining protein and histone mark profiles, we show that chromatin in Drosophila melanogaster is organised into eight principle chromatin states that have consistent forms and constituents across cell types. These states form through the association of the Swi/Snf chromatin remodelling complex, Polycomb Group (PcG)/H3K27me3, HP1a/H3K9me3 or H3K36me3 complexes with either active complexes (RNA Pol/COM-PASS/H3K4me3/NuRF) or repressive marks (histone H1 and nuclear lamin occupancy). Enhancers, core promoters, transcription factor motifs, and gene bodies show distinct chromatin state preferences that separate by developmental and housekeeping/metabolic gene ontology. Within the 3D genome, chromatin states add an additional level of compartmentalisation through self-association of topologically associated domains (TADs) of the same state. Our results suggest that the epigenetic landscape is organised by the binding of chromatin remodellers and repressive complexes, and that through chromatin states the genome is fundamentally segregated into developmental and housekeeping/metabolic roles.