Whole-genome DNA methylation patterns and complex associations with gene structure and expression during flower development in Arabidopsis

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Flower development is a complex process requiring proper spatiotemporal expression of numerous genes. Accumulating evidence indicates that epigenetic mechanisms, including DNA methylation, play essential roles in modulating gene expression. However, few studies have examined the relationship between DNA methylation and floral gene expression on a genomic scale. Here we present detailed analyses of DNA methylomes at single-base resolution for three Arabidopsis floral periods: meristems, early flowers and late flowers. We detected 1.5 million methylcytosines, and estimated the methylation levels for 24 035 genes. We found that many cytosine sites were methylatedde novofrom the meristem to the early flower stage, and many sites were demethylated from early to late flowers. A comparison of the transcriptome data of the same three periods revealed that the methylation and demethylation processes were correlated with expression changes of >3000 genes, many of which are important for normal flower development. We also found different methylation patterns for three sequence contexts (mCG, mCHG and mCHH) and in different genic regions, potentially with different roles in gene expression.

Significance Statement

In this study high-resolution genome-wide dynamic patterns of DNA methylation and gene expression of different floral developmental periods have been identified and the complex relationship has been analyzed between DNA methylation and gene expression during flower development. The whole-genome DNA methylation and gene expression data and hypotheses of their interactions provide an important foundation for future functional studies.

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