The prevalence, evolution and chromatin signatures of plant regulatory elements
Ontology highlight
ABSTRACT:
ORGANISM(S): Brachypodium distachyon Hordeum vulgare Phaseolus vulgaris Populus trichocarpa Oryza sativa Eutrema salsugineum Zea mays Arabidopsis thaliana Setaria viridis Glycine max Asparagus officinalis Spirodela polyrhiza Sorghum bicolor
PROVIDER: GSE128434 | GEO | 2019/09/19
REPOSITORIES: GEO
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Project description:Differential gene transcription enables development and homeostasis in all animals and is regulated by two major classes of distal cis-regulatory DNA elements (CREs), enhancers and silencers. While enhancers have been thoroughly characterized, the properties and mechansisms of silencers remain largely unknown. By an unbiased genome-wide functional screen in Drosophila melanogaster S2 cells, we discover a class of silencers that bind one of three transcription factors (TFs) and are generally not included in chromatin-defined CRE catalogs, as they mostly lack detectable DNA accessibility. The silencer-binding TF CG11247, which we term Saft, safeguards cell fate decisions in vivo and functions via a highly-conserved domain we term ZAC and the corepressor G9a, independently of G9a’s H3K9-methyltransferase activity. Overall, our identification of silencers with unexpected properties and mechanisms has important implications for the understanding and future study of repressive CREs, as well as the functional annotation of animal genomes.
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Project description:Cis-regulatory elements (CREs) are essential in precisely regulating gene expression, contributing significantly to the evolution of species. Identifying cell-type-specific CREs is essential for understanding plant evolution, domestication, and improving crops through genome editing. Here, we built a cis-regulatory atlas in Oryza sativa, encompassing 106,143 nuclei representing 138 discrete cell states from nine distinct organs. Within syntenic regions shared with four other grass species (Zea mays, Sorghum bicolor, Panicum miliaceum, and Urochloa fusca), we identified 10,219 cell-type-specific accessible chromatin regions (ACRs), serving as sources for investigating divergence of these species. To elucidate the roles of cell-type-specific ACRs in species divergence, we focused on leaf cells in O. sativa and the aforementioned grass species. We observed species-specific candidate CREs (cCREs) potentially associated with cell differentiation, especially in epidermal cells across species. These data also revealed presence of H3K27me3-associated ACRs in the majority of cell types across different organs and species, potentially harboring silencer cCREs. Together, this study significantly advances our understanding of the role of cCREs during cell differentiation, shedding light on their contribution to species divergence in plants
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