Abstract
The maize endosperm consists of three major compartmentalized cell types: the starchy endosperm (SE), the basal endosperm transfer cell layer (BETL), and the aleurone cell layer (AL). Differential genetic programs are activated in each cell type to construct functionally and structurally distinct cells. To compare gene expression patterns involved in maize endosperm cell differentiation, we isolated transcripts from cryo-dissected endosperm specimens enriched with BETL, AL, or SE at 8, 12, and 16 days after pollination (DAP). We performed transcriptome profiling of coding and long noncoding transcripts in the three cell types during differentiation and identified clusters of the transcripts exhibiting spatio-temporal specificities. Our analysis uncovered that the BETL at 12 DAP undergoes the most dynamic transcriptional regulation for both coding and long noncoding transcripts. In addition, our transcriptome analysis revealed spatio-temporal regulatory networks of transcription factors, imprinted genes, and loci marked with histone H3 trimethylated at lysine 27. Our study suggests that various regulatory mechanisms contribute to the genetic networks specific to the functions and structures of the cell types of the endosperm.
Highlights
Maize (Zea mays L.) is a major source of carbohydrate, protein, fat, and other nutrients for humans and livestock through its grain and biomass[1,2,3,4]
Previous transcriptome analyses of the maize endosperm were performed on transcripts obtained from dissected endosperm tissues at a certain developmental stage[10, 16, 18, 19, 22, 23, 25, 26] or from whole endosperms from different developmental stages[17, 20, 21, 24]
Our analysis revealed 7,054 spatio-temporally regulated protein-coding transcripts, indicating that massive transcriptional regulations are involved in maize endosperm development
Summary
Maize (Zea mays L.) is a major source of carbohydrate, protein, fat, and other nutrients for humans and livestock through its grain and biomass[1,2,3,4]. Distinct functions of the three cell types in the endosperm make it an excellent model for study of cell differentiation and gene regulation mechanisms. Given that BETL, AL, and SE are derived from a single cell type but that they express distinct sets of genes, studying chromatin modifications involved in their specialization could reveal molecular mechanisms of epigenetic regulation controlling cell differentiation in eukaryotes. We identified transcripts that are differentially regulated during the endosperm development by carrying out a spatio-temporal analysis of coding and noncoding transcripts in the three endosperm cell types at three stages of their development. Correlative changes in histone modifications and expression of lncRNAs in the vicinity of genes exhibiting spatio-temporal patterns suggest that gene regulatory programs involving chromatin modification operate in cell-type-specific manners in the maize endosperm during its development
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