title: Whole-genome DNA methylation patterns and complex associations with gene structure and expression during flower development in Arabidopsis.
abstract: 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 methylated de novo from 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 ((m) CG, (m) CHG and (m) CHH) and in different genic regions, potentially with different roles in gene expression.
authors.affiliation: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China; Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Shanghai Chenshan Botanical Garden, Chinese Academy of Sciences, Shanghai, 201602, China.
authors.forename: Hongxing
authors.initials: H
authors.lastname: Yang
authors.forename: Fang
authors.initials: F
authors.lastname: Chang
authors.forename: Chenjiang
authors.initials: C
authors.lastname: You
authors.forename: Jie
authors.initials: J
authors.lastname: Cui
authors.forename: Genfeng
authors.initials: G
authors.lastname: Zhu
authors.forename: Lei
authors.initials: L
authors.lastname: Wang
authors.forename: Yu
authors.initials: Y
authors.lastname: Zheng
authors.forename: Ji
authors.initials: J
authors.lastname: Qi
authors.forename: Hong
authors.initials: H
authors.lastname: Ma
mesh_terms: D017360:Arabidopsis / Q000378:metabolism* / Q000502:physiology; D003596:Cytosine / Q000378:metabolism; D019175:DNA Methylation / Q000235:genetics / Q000502:physiology; D035264:Flowers / Q000378:metabolism* / Q000502:physiology; D018506:Gene Expression Regulation, Plant; D059467:Transcriptome / Q000235:genetics
chemical_list: D003596:Cytosine
keywords: Arabidopsis DNA methylome; MspJI; RNA-seq; cytosine methylation; flower development; gene expression