Genetic and epigenetic variation in transposable element expression responses to abiotic stress in maize
Genetic and epigenetic variation in transposable element expression responses to abiotic stress in maize
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DOI：
10.1093/plphys/kiab073
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发表时间：
2021-02-16
期刊：
影响因子：
7.4
通讯作者：
Springer, Nathan M.
中科院分区：
文献类型：
--
作者：
Liang, Zhikai;Anderson, Sarah N.;Springer, Nathan M.
转座元件（TE）遍布大多数真核生物基因组。 TE 的重复性质使其表达分析变得复杂。对遭受热或冷胁迫的三种玉米（Zea mays）自交系的叶组织中 TE 家族（使用独特和多重映射读数）和特定元件（使用独特映射读数）的表达进行评估，没有发现 TE 在全基因组范围内激活的证据；然而，一些特定的 TE 家族仅在压力条件下生成转录本。 TE 家族在不同基因型中表现出应激反应性表达存在很大差异。为了了解驱动 TE 表达的因素，我们关注了一个家族子集，在其中我们可以监测单个元素的表达。 TE 家族的应激反应性激活通常可归因于该家族中含有缺乏 DNA 甲基化区域的少数元件。不同基因型中 TE 表达的比较揭示了遗传和表观遗传变异。许多在一种近交系中应激时被激活的特定 TE 在另一种近交系中不存在，这解释了缺乏激活的原因。在两个基因组共有但仅在一种基因型中表达的元件中，我们发现许多元件在DNA甲基化方面表现出差异，使得不表达的基因型完全甲基化。这项研究提供了对正常和应激条件下 TE 表达调节的见解，并强调了家族中元素之间或基因型之间染色质变异对表达变异的影响。许多 TE 的高度重复性使其表达分析变得复杂。尽管大多数 TE 不表达，但有些 TE 在某些组织或条件下表现出表达。我们监测了遭受热或冷胁迫的三种玉米（Zea mays）自交系的叶组织中 TE 家族（使用独特和多重映射读数）和特定元素（使用独特映射读数）的表达。虽然 TE 的全基因组激活并未发生，但一些 TE 家族仅在应激条件下产生转录本，且因基因型而异。为了更好地了解驱动 TE 表达的因素，我们重点研究了一个家族子集，在其中我们可以监测各个元素的表达。在大多数情况下，TE 家族的应激反应性激活归因于该家族中的少数元素。含有缺乏 DNA 甲基化区域的小区域的元件表现出丰富的表达，而完全甲基化的元件在对照或胁迫条件下很少表达。不同基因型中表达差异的原因是遗传和表观遗传变异。一种近交系中由应激激活的许多特定 TE 在另一种近交系中并不存在。在两个基因组共有的元件中，完全甲基化抑制了其中一种基因型的表达。这项研究提供了对正常和应激条件下 TE 表达调节的见解，并强调了家族中元素之间或基因型之间染色质变异对表达的作用。
Transposable elements (TEs) pervade most eukaryotic genomes. The repetitive nature of TEs complicates the analysis of their expression. Evaluation of the expression of both TE families (using unique and multi-mapping reads) and specific elements (using uniquely mapping reads) in leaf tissue of three maize (Zea mays) inbred lines subjected to heat or cold stress reveals no evidence for genome-wide activation of TEs; however, some specific TE families generate transcripts only in stress conditions. There is substantial variation for which TE families exhibit stress-responsive expression in the different genotypes. In order to understand the factors that drive expression of TEs, we focused on a subset of families in which we could monitor expression of individual elements. The stress-responsive activation of a TE family can often be attributed to a small number of elements in the family that contains regions lacking DNA methylation. Comparisons of the expression of TEs in different genotypes revealed both genetic and epigenetic variation. Many of the specific TEs that are activated in stress in one inbred are not present in the other inbred, explaining the lack of activation. Among the elements that are shared in both genomes but only expressed in one genotype, we found that many exhibit differences in DNA methylation such that the genotype without expression is fully methylated. This study provides insights into the regulation of expression of TEs in normal and stress conditions and highlights the role of chromatin variation between elements in a family or between genotypes for contributing to expression variation. The highly repetitive nature of many TEs complicates the analysis of their expression. Although most TEs are not expressed, some exhibits expression in certain tissues or conditions. We monitored the expression of both TE families (using unique and multi-mapping reads) and specific elements (using uniquely mapping reads) in leaf tissue of three maize (Zea mays) inbred lines subjected to heat or cold stress. While genome-wide activation of TEs did not occur, some TE families generated transcripts only in stress conditions with variation by genotype. To better understand the factors that drive expression of TEs, we focused on a subset of families in which we could monitor expression of individual elements. In most cases, stress-responsive activation of a TE family was attributed to a small number of elements in the family. The elements that contained small regions lacking DNA methylation regions showed enriched expression while fully methylated elements were rarely expressed in control or stress conditions. The cause of varied expression in the different genotypes was due to both genetic and epigenetic variation. Many specific TEs activated by stress in one inbred were not present in the other inbred. Among the elements shared in both genomes, full methylation inhibited expression in one of the genotypes. This study provides insights into the regulation of TE expression in normal and stress conditions and highlights the role of chromatin variation between elements in a family or between genotypes for contributing to expression.