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On the Role of Transposable Elements in the Regulation of Gene Expression and Subgenomic Interactions in Crop Genomes
Critical Reviews in Plant Sciences ( IF 6.9 ) Pub Date : 2021-05-24 , DOI: 10.1080/07352689.2021.1920731
Rafaqat A. Gill 1 , Federico Scossa 2, 3 , Graham J. King 4 , Agnieszka A. Golicz 5 , Chaobo Tong 1 , Rod J. Snowdon 5 , Alisdair R. Fernie 2 , Shengyi Liu 1
Affiliation  

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.



中文翻译:

转座因子在作物基因组中基因表达和亚基因组相互作用的调控中的作用

摘要

转座因子(TEs)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显了不同TE物种作为作物育种中有用的遗传工具的重要性。TEs可以引起基因表达模式的改变,并通过多种方式调节基因功能,例如通过在启动子,内含子,外显子和下游区域的插入以及反式插入,顺式或上下调节附近的基因。通过两个RNA定向DNA甲基化(RdDM)途径产生短干扰RNA(siRNA)。通过不同的RdDM途径生成的siRNA长度不同,并且对TE的影响不同。例如,由RNA聚合酶IV产生的非编码siRNA 20–60 nt(不依赖于分子)和由Pol II产生的21/22 nt(不依赖于基因)与TE IV相比,对TE的影响较小,而由Pol IV产生的非编码siRNA则为24(nt / dic)。依赖性途径)。在异源多倍体中多倍体化之后的全基因组复制(WGD)事件之后,来自任一亲本的TE都能够诱导siRNA来调节复杂的多倍体基因组。那些被指定为“控制者”的人通常居住在显性父母中,并影响隐性父母的TE。因此,亚基因组串扰似乎有助于表观遗传调控以及亚基因组的改组或重组以及基因表达新模式的创建/局部或全局拷贝数的变化。在这篇综述中,我们关注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TEs在基因表达调控中的作用的最新进展,并探讨古代WGD和最近的多倍体如何影响TE诱导的进化。表观遗传机制。

更新日期:2021-05-24
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