Three classes of epigenomic regulators converge to hyperactivate the essential maternal gene deadhead within a heterochromatin mini-domain

Abstract

ABSTRACTThe formation of a diploid zygote is a highly complex cellular process that is entirely controlled by maternal gene products stored in the egg cytoplasm. This highly specialized transcriptional program is tightly controlled at the chromatin level in the female germline. As an extreme case in point, the massive and specific ovarian expression of the essential thioredoxin Deadhead (DHD) is critically regulated in Drosophila by the histone demethylase Lid and its partner, the histone deacetylase complex scaffold Sin3A, via yet unknown mechanisms. Here, we identified the Brahma chromatin remodeler sub-unit Snr1 and the insulator component Mod(mdg4) as essential for dhd expression and investigated how these epigenomic effectors act with Lid and Sin3A to hyperactivate dhd. Using Cut&Run chromatin profiling with a dedicated data analysis procedure, we found that dhd is intriguingly embedded in an H3K27me3/H3K9me3-enriched mini-domain flanked by DNA regulatory elements, including a dhd promoter-proximal element essential for its expression. Surprisingly, Lid, Sin3A, Snr1 and Mod(mdg4) impact H3K27me3 and this regulatory element in distinct manners. However, we show that these effectors activate dhd independently of H3K27me3/H3K9me3, and that these marks are not required to repress dhd. Together, our study demonstrates an atypical and critical role for chromatin regulators Lid, Sin3A, Snr1 and Mod(mdg4) to trigger tissue-specific hyperactivation within a unique heterochromatin mini-domain.AUTHOR SUMMARYGene expression is tightly regulated by conserved protein complexes that act at the chromatin level to allow or restrict transcription. Such epigenetic control of gene activity defines the identity of different cell types during development, as well as their response to environmental cues. Yet, how multiple chromatin factors converge to achieve precise gene regulation remains difficult to address, partly due to the lack of biological situations where these intricate relationships can be studied. In this paper, we have addressed this issue by dissecting the regulation of deadhead, an essential gene specifically and massively expressed in the Drosophila germline. Unexpectedly, we found that its hyperactivation occurs despite deadhead being embedded in an apparently unfavorable chromatin mini-domain, notably featuring repressive histone modifications. We further demonstrate that four chromatin effectors, Lid, Sin3A, Snr1 and Mod(mdg4), have distinct, atypical and essential roles to ensure deadhead expression within this chromatin environment. Together, our findings put into perspective our understanding on these regulatory factors by illustrating how they can exert a biologically essential function via non-canonical mechanisms.