大豆与拟南芥种子甲基化组之间的相似性和非CG甲基化的缺失不影响种子发育

2017年11月7日，PNAS 文章：Similarity between soybean and Arabidopsis seedmethylomes and loss of non-CG methylation does not affect seed development

意义：

我们描述了大豆和拟南芥种子甲基化组在发育过程中的时空分布。 CHH甲基化在所有的从受精到休眠种子的部分，普遍增加；发芽后减少，并且主要以转座子为靶标。相比之下，CG-和CHG-的甲基化在整个种子发育过程中保持不变。缺失非CG甲基化的突变种子正常发育，但具有一组上调的转座子RNAs，表明CHH甲基化增加可能是加强转座子沉默的失败保护机制。种子基因的主要类别具有类似的甲基化模式，而无论它们是否有活性。我们的研究结果表明，大豆和拟南芥种子甲基化组是相似的，而且DNA甲基化在调控种子发育重要基因方面，没有重要的作用。

Significance：

We describe the spatial and temporal profiles of soybean and Arabidopsis seed methylomes during development. CHH

methylation increases globally from fertilization through dormancy

in all seed parts, decreases following germination, and

targets primarily transposons. By contrast, CG- and CHGcontext

methylation remains constant throughout seed development.

Mutant seeds lacking non-CG methylation develop

normally, but have a set of up-regulated transposon RNAs

suggesting that the CHH methylation increase may be a failsafe

mechanism to reinforce transposon silencing. Major classes of

seed genes have similar methylation profiles, whether they are

active or not. Our results suggest that soybean and Arabidopsis

seed methylomes are similar, and that DNA methylation does

not play a significant role in regulating many genes important

for seed development.

摘要：

我们分析了大豆和拟南芥从球形胚阶段，经过休眠到萌发的甲基化组模式，以此来了解甲基化在种子形成中的作用。 CHH甲基化在整个种子发育过程中显著增加，主要靶向转座子（TEs），在内部复制过程中保持不变，并在发芽幼苗中急剧下降。相反，在同一个发育阶段，CG和CHG的甲基化没有发生显著的变化。缺乏CHH和CHG甲基化的拟南芥ddcc突变体不影响种子发育，萌发或基因表达的主要模式，这意味着CHH和CHG甲基化在种子发育或调节种子基因活性中不起重要作用。相反，超过100个TEs在ddcc种子转录水平被激活，表明CHH-甲基化的增加可能是加强转座子沉默的失败保护机制。编码种子蛋白质的重要种类的许多基因，例如贮藏蛋白质，油类生物合成酶和转录因子，存在于种子发育的任何阶段缺乏甲基化的基因组区域中。这些类别中的许多其他基因具有相似的甲基化模式，无论基因是活跃还是抑制。我们的研究结果表明甲基化在调节大豆和拟南芥菜种子发育的重要基因调控中不起重要作用。我们得出结论，了解控制种子发育的机制将需要确定顺式调控元件及其同源转录因子是如何在遗传调控网络中进行组织的。

Abstract

We profiled soybean and Arabidopsis methylomes from the globular

stage through dormancy and germination to understand the

role of methylation in seed formation. CHH methylation increases

significantly during development throughout the entire seed, targets

primarily transposable elements (TEs), is maintained during

endoreduplication, and drops precipitously within the germinating

seedling. By contrast, no significant global changes in CG- and CHGcontext

methylation occur during the same developmental period.

An Arabidopsis ddcc mutant lacking CHH and CHG methylation

does not affect seed development, germination, or major patterns

of gene expression, implying that CHH and CHG methylation does

not play a significant role in seed development or in regulating

seed gene activity. By contrast, over 100 TEs are transcriptionally

de-repressed in ddcc seeds, suggesting that the increase in CHHcontext

methylation may be a failsafe mechanism to reinforce

transposon silencing. Many genes encoding important classes of

seed proteins, such as storage proteins, oil biosynthesis enzymes,

and transcription factors, reside in genomic regions devoid of

methylation at any stage of seed development. Many other genes

in these classes have similar methylation patterns, whether the

genes are active or repressed. Our results suggest that methylation

does not play a significant role in regulating large numbers

of genes important for programming seed development in both

soybean and Arabidopsis. We conclude that understanding the

mechanisms controlling seed development will require determining

how cis-regulatory elements and their cognate transcription

factors are organized in genetic regulatory networks.

Fig. 9. TE transcriptional activity in Arabidopsis wild-type and ddcc pmg seeds.