On the Role of Transposable Elements in the Regulation of Gene Expression and Subgenomic Interactions in Crop Genomes

IF 6 2区生物学 Q1 PLANT SCIENCES

Critical Reviews in Plant Sciences Pub Date : 2021-03-04 DOI:10.1080/07352689.2021.1920731

R. Gill, F. Scossa, G. King, Agnieszka A. Golicz, Chaobo Tong, R. Snowdon, A. Fernie, Shengyi Liu

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引用次数: 20

Abstract

Abstract Transposable elements (TEs) represent a major and variable portion of plant genomes, and recent progress in genetics and genomics has highlighted the importance of different TE species as a useful genetic tool in crop breeding. TEs can cause changes in the pattern of gene expression, and regulate gene function by various means such as cis- up- or down-regulation of nearby genes through insertion at promoter, intron, exon and down-stream regions, and trans-production of short interfering RNAs (siRNAs) via two RNA-directed DNA methylation (RdDM) pathways. siRNAs generated through different RdDM pathways differ in length and have variable effects on TEs. For instance, noncoding siRNAs of 20–60 nt produced by RNA polymerase IV (dicer-independent) and 21/22 nt by Pol II (dicer-dependent) have only minor effects on TEs compared with 24 nt siRNAs produced by Pol IV (dicer-dependent pathways). Following whole-genome duplication (WGD) events after polyploidization in allopolyploids, TEs from either parent are able to induce siRNAs to regulate the complex polyploid genome. Those designated as ‘controllers’ usually reside in the dominant parent and affect the TEs of the recessive parent. Subgenome cross-talk thus appears to contribute to epigenetic regulation as well as reshuffling or restructuring of subgenomes and creation of novel patterns of genes expression/and variation in local or global copy number. In this review, we focus on recent progress in unraveling the role of TEs in gene expression regulation via TE-derived siRNAs in the context of polyploid plant evolution and environmental stress, and explore how ancient WGD and recent polyploidy affected the evolution of TE-induced epigenetic mechanisms.

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转座子在作物基因组基因表达和亚基因组相互作用调控中的作用

摘要可转座元件（TE）代表了植物基因组的主要和可变部分，遗传学和基因组学的最新进展突出了不同TE物种作为作物育种中有用的遗传工具的重要性。TE可以引起基因表达模式的变化，并通过各种方式调节基因功能，如通过插入启动子、内含子、外显子和下游区域顺式上调或下调附近基因，以及通过两种RNA导向的DNA甲基化（RdDM）途径反式产生短干扰RNA（siRNA）。通过不同的RdDM途径产生的siRNA在长度上不同，并且对TE具有不同的影响。例如，20-60的非编码siRNA RNA聚合酶IV产生的nt（不依赖于dicer）和21/22 与24相比，Pol II的nt（取决于骰子）对TE的影响很小由Pol IV产生的nt siRNA（dicer依赖性途径）。在异倍体中多倍体化后发生全基因组复制（WGD）事件后，来自任一亲本的TE能够诱导siRNA来调节复杂的多倍体基因组。那些被指定为“控制者”的通常存在于显性亲本中，并影响隐性亲本的TE。因此，亚基因组串扰似乎有助于表观遗传学调控、亚基因组的重组或重组以及基因表达/和局部或全局拷贝数变化的新模式的产生。在这篇综述中，我们重点介绍了在多倍体植物进化和环境胁迫的背景下，通过TE衍生的siRNA揭示TE在基因表达调控中的作用的最新进展，并探讨了古老的WGD和最近的多倍体如何影响TE诱导的表观遗传学机制的进化。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Critical Reviews in Plant Sciences 生物-植物科学

CiteScore

12.90

自引率

1.40%

发文量

审稿时长

>12 weeks

期刊介绍： Critical Reviews in Plant Sciences focuses on presenting in-depth and up-to-date reviews of timely and/or cutting-edge subjects in the broad discipline of plant science, ranging from molecular biology/biochemistry through the areas of cell biology, plant pathology and physiology, genetics, classical botany, and ecology, to practical agricultural applications. Articles in the journal provide an up-to-date literature base for researchers and students, pointing the way towards future research needs. The journal is also a significant source of credible, objective information to aid decision makers at all levels.

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