Abstract
The genome is reprogrammed during development to produce diverse cell types, largely through altered expression and activity of key transcription factors. The accessibility and critical functions of epidermal cells have made them a model for connecting transcriptional events to development in a range of model systems. In Arabidopsis thaliana and many other plants, fertilization triggers differentiation of specialized epidermal seed coat cells that have a unique morphology caused by large extracellular deposits of polysaccharides. Here, we used DNase I-seq to generate regulatory landscapes of A. thaliana seeds at two critical time points in seed coat maturation (4 and 7 DPA), enriching for seed coat cells with the INTACT method. We found over 3,000 developmentally dynamic regulatory DNA elements and explored their relationship with nearby gene expression. The dynamic regulatory elements were enriched for motifs for several transcription factors families; most notably the TCP family at the earlier time point and the MYB family at the later one. To assess the extent to which the observed regulatory sites in seeds added to previously known regulatory sites in A. thaliana, we compared our data to 11 other data sets generated with 7-day-old seedlings for diverse tissues and conditions. Surprisingly, over a quarter of the regulatory, i.e. accessible, bases observed in seeds were novel. Notably, plant regulatory landscapes from different tissues, cell types, or developmental stages were more dynamic than those generated from bulk tissue in response to environmental perturbations, highlighting the importance of extending studies of regulatory DNA to single tissues and cell types during development.
Highlights
Spatial and temporal regulation of gene expression is critical for development and specialization of tissues and cell types. cis-Regulatory DNA elements, and the trans-acting factors that bind them, are a primary mechanism for regulating gene expression
We sampled whole siliques, which encase 40 to 60 seeds, at 4 and 7 days postanthesis (DPA), to capture the regulatory landscape before and after mucilage production begins in the seed coat
DNase I-hypersensitive sites (DHSs) are a hallmark of regulatory DNA and dynamic DHSs often reside in close proximity to genes with changing expression
Summary
Spatial and temporal regulation of gene expression is critical for development and specialization of tissues and cell types. cis-Regulatory DNA elements, and the trans-acting factors that bind them, are a primary mechanism for regulating gene expression. Spatial and temporal regulation of gene expression is critical for development and specialization of tissues and cell types. Cis-Regulatory DNA elements, and the trans-acting factors that bind them, are a primary mechanism for regulating gene expression. Active cis-regulatory elements such as promoters, enhancers, insulators, silencers, and locus control regions can be identified by their characteristic hypersensitivity to cleavage by DNase I Cell-type–enriched, and ideally cell-type– specific, approaches to gene regulation and expression are fundamental for understanding development. We use DNase I-seq to examine the regulatory landscape of seeds at two critical developmental time points, 4 and 7 days postanthesis, enriching for seed coat cells as they transition from the non-mucous-secreting state to the mucous-secreting state
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