Monitoring the interplay between transposable element families and DNA methylation in maize
Monitoring the interplay between transposable element families and DNA methylation in maize
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DOI：
10.1371/journal.pgen.1008291
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发表时间：
2019-09-01
期刊：
影响因子：
4.5
通讯作者：
Springer, Nathan M.
中科院分区：
文献类型：
--
作者：
Noshay, Jaclyn M.;Anderson, Sarah N.;Springer, Nathan M.
DNA甲基化和表观遗传沉默在许多真核生物基因组中对转座因子的调控起着重要作用。玉米基因组的大部分来源于TE，TE可以分别基于其转座机制和序列相似性被分类为不同的目和科。TE本身是高度甲基化的，因此很容易将它们视为一个单一的统一组。然而，侧翼区DNA甲基化谱的分析为不同TE家族的不同染色质性质组提供了证据。TE家族间的这些差异在不同组织和不同自交系中是可重复的。在侧翼区域具有不同水平的DNA甲基化的TE家族也显示出TE内的染色质可及性和修饰的不同模式。TE家族侧翼DNA甲基化模式的差异来自TE家族的非随机插入偏好、TE插入引发的DNA甲基化变化和随后的选择压力的组合。使用四个组装的玉米基因组中的一组近70，000个TE多态性来监测具有和不具有TE插入的单倍型的DNA甲基化水平。在许多情况下，在侧翼序列中具有高水平DNA甲基化的TE家族富含插入高度甲基化区域。> 2，500个TE插入未甲基化区域中的大多数导致具有TE的单倍型中DNA甲基化的变化，表明TE插入调节基因组保守区域中改变的甲基化的广泛潜力。这项研究突出了TEs和主要作物物种的甲基化组之间的相互作用。作者总结玉米和许多其他作物一样，具有复杂的基因组，主要由转座因子（TEs）组成。这些TE在形成表观基因组中起着重要作用，并有可能影响基因或调控区域。尽管许多研究评估了所有TE的染色质平均模式，但有证据表明不同TE家族之间存在显著差异。我们发现TE家族在侧翼区域具有不同的DNA甲基化模式。这些差异可以通过一些家族优先插入甲基化或未甲基化的基因组区域以及一些TE家族触发侧翼区域甲基化的潜力的组合来解释。了解TE家族和染色质的相互作用有助于了解TE影响基因和塑造作物基因组的机制。
DNA methylation and epigenetic silencing play important roles in the regulation of transposable elements (TEs) in many eukaryotic genomes. A majority of the maize genome is derived from TEs that can be classified into different orders and families based on their mechanism of transposition and sequence similarity, respectively. TEs themselves are highly methylated and it can be tempting to view them as a single uniform group. However, the analysis of DNA methylation profiles in flanking regions provides evidence for distinct groups of chromatin properties at different TE families. These differences among TE families are reproducible in different tissues and different inbred lines. TE families with varying levels of DNA methylation in flanking regions also show distinct patterns of chromatin accessibility and modifications within the TEs. The differences in the patterns of DNA methylation flanking TE families arise from a combination of non-random insertion preferences of TE families, changes in DNA methylation triggered by the insertion of the TE and subsequent selection pressure. A set of nearly 70,000 TE polymorphisms among four assembled maize genomes were used to monitor the level of DNA methylation at haplotypes with and without the TE insertions. In many cases, TE families with high levels of DNA methylation in flanking sequence are enriched for insertions into highly methylated regions. The majority of the >2,500 TE insertions into unmethylated regions result in changes in DNA methylation in haplotypes with the TE, suggesting the widespread potential for TE insertions to condition altered methylation in conserved regions of the genome. This study highlights the interplay between TEs and the methylome of a major crop species.Author summary Maize, like many other crops, has a complex genome that is primarily composed of transposable elements (TEs). These TEs play major roles in shaping the epigenome and have the potential to influence genes or regulatory regions. Although many studies assess the average patterns of chromatin at all TEs, there is evidence for significant variation among different TE families. We find that TE families have distinct patterns of DNA methylation in flanking regions. These differences can be explained by a combination of preferential insertion of some families into methylated or unmethylated genomic regions as well as the potential for some TE families to trigger methylation of flanking regions. Understanding the interplay of TE families and chromatin can help understand the mechanisms through which TEs influence genes and shape crop genomes.