1. Three classes of epigenomic regulators converge to hyperactivate the essential maternal gene deadhead within a heterochromatin mini-domain
- Author
-
Béatrice Horard, Daniela Torres-Campana, Benjamin Loppin, Guillermo A. Orsi, Sandrine Denaud, Gérard Benoit, Laboratoire de biologie et modélisation de la cellule (LBMC UMR 5239), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Dynamique du noyau [Institut Curie], Institut Curie [Paris]-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de génétique humaine (IGH), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Loppin, Benjamin, and École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL)
- Subjects
Epigenomics ,Male ,Cancer Research ,Gene Expression ,QH426-470 ,Biochemistry ,Histones ,Thioredoxins ,Heterochromatin ,Invertebrate Genomics ,Medicine and Health Sciences ,Drosophila Proteins ,Regulatory Elements, Transcriptional ,Promoter Regions, Genetic ,Genetics (clinical) ,Histone Demethylases ,Regulation of gene expression ,biology ,Chromosome Biology ,Drosophila Melanogaster ,RNA-Binding Proteins ,Eukaryota ,Animal Models ,Genomics ,Chromatin ,Cell biology ,DNA-Binding Proteins ,Ovaries ,Insects ,Sin3 Histone Deacetylase and Corepressor Complex ,Histone ,Experimental Organism Systems ,Organ Specificity ,[SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,Female ,Epigenetics ,Drosophila ,Maternal Inheritance ,Anatomy ,Research Article ,Arthropoda ,Research and Analysis Methods ,Model Organisms ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,Genetics ,Animals ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Ovary ,Reproductive System ,Organisms ,Membrane Proteins ,Biology and Life Sciences ,Computational Biology ,Proteins ,Cell Biology ,Invertebrates ,Gene Expression Regulation ,Animal Genomics ,Animal Studies ,Histone deacetylase complex ,biology.protein ,Demethylase ,Zoology ,Entomology ,Transcription Factors - Abstract
The 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 Sin3A/Rpd3, via yet unknown mechanisms. Here, we identified Snr1 and 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 dhd remains silent in the absence of these marks. 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 summary Multicellular development depends on a tight control of gene expression in each cell type. This relies on the coordinated activities of nuclear proteins that interact with DNA or its histone scaffold to promote or restrict gene transcription. For example, we previously showed that the histone modifying enzymes Lid and Sin3A/Rpd3 are required in Drosophila ovaries for the massive expression of deadhead (dhd), a gene encoding for a thioredoxin that is essential for fertility. In this paper, we have further identified two additional dhd regulators, Snr1 and Mod(mdg4) and dissected the mechanism behind hyperactivation of this gene. Using the epigenomic profiling method Cut&Run with a dedicated data analysis approach, we unexpectedly found that dhd is embedded in an unusual chromatin mini-domain featuring repressive histone modifications H3K27me3 and H3K9me3 and flanked by two regulatory elements. However, we further showed that Lid, Sin3A, Snr1 and Mod(mdg4) behave like obligatory activators of dhd independently of this mini-domain. Our study unveils how multiple broad-acting epigenomic effectors operate in non-canonical manners to ensure a critical and specialized gene activation event. These findings challenge our knowledge on these regulatory mechanisms and their roles in development and pathology.
- Published
- 2022