Mapping and dynamics of regulatory DNA during seed development
bioRxiv(2019)
摘要
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 function of epidermal cells have made them a model for connecting transcriptional events to development in a range of model systems. In Arabidopsis and many other plants, fertilization triggers differentiation of specialized epidermal cells called the seed coat that have a unique morphology caused by large extracellular deposits of pectin. Here, we used DNase I-seq to generate regulatory landscapes of Arabidopsis thaliana seeds at two points in development. To enrich for seed coat signals, we used the INTACT method for capturing nuclei from GL2-expressing cells from whole siliques. Over half of the regulatory (i.e., accessible) bases identified in seeds at these two developmental time points had not been previously identified in seven-day-old seedling. We identified over 3000 regions that were developmentally dynamic (i.e., differentially accessible) at the two timepoints and found that genes neighboring these regions were enriched for gene ontology terms such as development, regulation and pigment. Genes neighboring differentially accessible regions were also significantly more likely to have differing expression at these two timepoints. The differentially accessible regions themselves were enriched for motifs belonging to transcription factors involved in development and environmental response, notably the TCP and MYB families at the earlier and later time points, respectively. These findings are consistent with previous studies, highlighting the dramatic changes that take place in the chromatin landscape during development, and indicating the importance of extending the approach described here to other cell types and developmental processes.
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关键词
regulatory DNA,<italic>Arabidopsis thaliana</italic>,seed development,seed coat maturation,open chromatin
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