Whole-genome DNA methylation patterns and complex associations with gene structure and expression during flower development in Arabidopsis
Whole-genome DNA methylation patterns and complex associations with gene structure and expression during flower development in Arabidopsis
复制标题
拟南芥花发育过程中全基因组 DNA 甲基化模式和转录调控的复杂功能
DOI：
10.1111/tpj.12726
复制
发表时间：
2015-01-01
期刊：
影响因子：
7.2
通讯作者：
Ma, Hong
中科院分区：
文献类型：
--
作者：
Yang, Hongxing;Chang, Fang;Ma, Hong
花的发育是一个复杂的过程，需要许多基因在适当的时空表达。越来越多的证据表明，表观遗传机制，包括DNA甲基化，在调节基因表达中发挥重要作用。然而，很少有研究在基因组尺度上研究DNA甲基化与花基因表达之间的关系。在这里，我们在单碱基分辨率下详细分析了拟南芥三个花期的DNA甲基组：分生组织、早期花和晚期花。我们检测到150万个甲基胞嘧啶，并估计了24035个基因的甲基化水平。我们发现，从分生组织到花前期，许多胞嘧啶位点被甲基化，从花前期到花后期，许多位点被去甲基化。比较相同三个时期的转录组数据发现，甲基化和去甲基化过程与>3000基因的表达变化相关，其中许多基因对正常的花发育很重要。我们还发现三个序列上下文((m)CG, （m)CHG和(CHH)-C-m）和不同基因区域的甲基化模式不同，可能在基因表达中起不同的作用。本研究鉴定了花发育不同时期DNA甲基化与基因表达的高分辨率全基因组动态模式，并分析了花发育过程中DNA甲基化与基因表达的复杂关系。全基因组DNA甲基化和基因表达数据及其相互作用的假设为未来的功能研究提供了重要的基础。
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 24035 genes. We found that many cytosine sites were methylated denovo 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 (CHH)-C-m) 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.