On transposon silencing and DNA methylation

LU Yaping; ZHOU Mingbing

doi:10.11833/j.issn.2095-0756.20200338

Volume 38 Issue 3

Jun. 2021

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LU Yaping, ZHOU Mingbing. On transposon silencing and DNA methylation[J]. Journal of Zhejiang A&F University, 2021, 38(3): 634-643. doi: 10.11833/j.issn.2095-0756.20200338

Citation:

LU Yaping, ZHOU Mingbing. On transposon silencing and DNA methylation[J]. Journal of Zhejiang A&F University, 2021, 38(3): 634-643. doi: 10.11833/j.issn.2095-0756.20200338

On transposon silencing and DNA methylation

doi: 10.11833/j.issn.2095-0756.20200338

LU Yaping,
ZHOU Mingbing^,

State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China

Received Date: 2020-05-22
Rev Recd Date: 2021-01-11

Available Online: 2021-06-09

Publish Date: 2021-06-09

Abstract

Transposable elements (TEs) can be moved by means of transposition or reverse transposition in the genome of an organism, whose copy number in large numbers is an important factor for genome instability. Therefore, it is the direction of host evolution to maintain TEs silence. DNA methylation, generally considered to be a heritable epigenetic modification method for silencing TEs, plays a role in the maintainance of genome stability, genetic imprinting and the regulation of gene expression. This study is aimed at an overview of the impact of TEs on the evolution of biological genome and gene expression, a summary of the latest research progress of transposon silencing mechanism dominated by DNA methylation, and an investigation of the mechanism of environmental factors that regulate transposon jumping via DNA demethylation. [Ch, 4 fig. 82 ref.]
- botany,
- transposon,
- transposon silence,
- DNA methylation,
- stress

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转座子(transposable elements，TEs)被定义为能够在生物体基因组中移动的DNA序列，能在同一染色体的不同位点或者不同染色体之间转移^[1]。由于起源和进化路径的差异，TEs包含不同的家族。FINNEGAN^[2]首次根据TEs的转座中间体和转座机制将转座子分为Ⅰ类RNA转座子(retrotransposons)和Ⅱ类DNA转座子(DNA transposons)。Ⅰ类通过RNA介导的复制-粘贴过程迅速增殖，RNA转座子进一步分为：长末端重复序列反转录转座子(long terminal repeat，LTR，也称为内源性逆转录病毒)、非LTR反转录转座子(non-LTR)、PLEs(penelope-like elements)、DIRS(dictyostelium intermediate repeat sequence)^[3]。Ⅱ类使用剪切-粘贴机制增加拷贝数^[4-5]，包括末端反向重复序列(terminal inverted repeat，TIR)、微型反向重复序列转座子(miniature inverted repeat transposable elements，MITEs)和Helitrons^[2]。自然选择和遗传漂变导致TEs在不同物种中类别的比例和含量都不相同，在同一物种的个体之间也存在差异^[6]。研究表明：人类基因组大约一半为TEs^[7]，其中RNA反转座子约42%^[8]，LTR反转座子约8%^[9]；在小鼠Mus musculus和人类的基因组中，长散在核元件(long interspersed nuclear elements-1，LINE-1)大约20%^[10]；小麦Triticum aestivum和小麦白粉病真菌Blumeria graminis基因组中，90%的序列是TEs^[11]；水稻Oryza sativa转座子的20%~40%中，Ⅱ类DNA转座子含量甚至高于Ⅰ类RNA转座子4倍以上^[12]，其中LTR约14%，而non-LTR反转座子却只有1%^[13]。在玉米Zea mays基因组中，TEs含量高达85%，其中LTR反转座子和其他TEs家族含量分别为70%和15%^[14-15]。通常，TEs对宿主有很多积极的影响。例如，TEs的插入控制着包括牵牛花Ipomoea purpurea在内的所有花色变化^[16]，贡献了可供选择的性状。反转录转座子的正常转座不仅可以产生果肉呈红色的血橙Citrus sinensis^[17]，还控制着葡萄Vitis vinifera^[18]和番茄Solanum lycopersicum^[19]等果实的颜色和形状，也参与着番茄茎尖分生组织的形成^[20]，还影响着哺乳动物骨骼的发育^[21]。并且，可以利用TEs的激活诱导疾病的发生，从而明确疾病的机理，寻找出治疗的药物与方法。然而，由于TEs的负面影响而被称为“垃圾DNA”。例如，LINE-1是人类基因组中唯一的自主转座元件，它的表达成为许多恶性肿瘤的标志^[22]，并且导致包括精神分裂症在内的众多精神疾病^[23]，人类的120多种遗传疾病都是由于LINE-1的插入而引起的^[24]，其拷贝数的增加会导致腺瘤性息肉病基因(APC)肿瘤抑制基因突变从而引发人类直肠癌(colorectal cancer，CRC)^[25]。ZmNAC111基因是维持玉米幼苗耐旱性的关键基因，MITE转座子的插入会下调ZmNAC111的表达，从而引起玉米幼苗的干旱敏感性增强^[26]。在小鼠生殖系中，TEs增加拷贝数会导致其不育^[27]，并有调控具有双向命运细胞的潜能^[28]。TEs插入基因组中不仅破坏基因的功能，而且对邻近基因的表达有极性影响^[29]，对着丝粒稳定性同样具有重要的作用。由此可见，TEs转座破坏了宿主基因组的稳定，也搅动了宿主的基因表达调控网络，因此，TEs活性通常受到宿主多种表观遗传修饰机制的调控，例如，DNA甲基化、抑制性组蛋白修饰、小RNA途径和染色质途径。DNA甲基化是高等真核生物中广泛存在的保持TEs沉默的表观遗传修饰方式，包括从头甲基化、维持甲基化和脱甲基3个水平^[30]。哺乳动物基因组中主要为CG二核苷酸序列环境的胞嘧啶甲基化，由DNA甲基转移酶1(DNA methyltransferase 1，DNMT1)和DNA甲基转移酶3(DNA methyltransferase 3，DNMT3)维持，植物中还具有CHG和CHH(H表示A、T或C)胞嘧啶环境的甲基化^[31]，则是由与DNMT3相似的域重排甲基转移酶1(domains rearranged methyltransferase 1，DRM1)和域重排甲基转移酶2(domains rearranged methyltransferase 2，DRM2)催化^[32]。本研究论述了TEs沉默与DNA甲基化的关系，重点总结了以DNA甲基化为主的转座子沉默机制最新研究进展，归纳了环境因素通过DNA去甲基化调控转座子跳跃的机理。

4. 生物或非生物胁迫通过调控DNA甲基化激活TEs

生物或非生物胁迫会导致DNA甲基化发生改变，例如，强烈的锌缺乏会导致拟南芥全基因组的DNA甲基化水平发生变化^[71]。在CG对称环境中，缺磷对甲基化水平影响较小，但缺氮会导致玉米根甲基化水平降低^[72]。水稻在遭受盐胁迫时，盐敏感的IR29缺乏改变DNA甲基化水平的能力，而耐盐水稻能降低甲基化水平^[73]。双生病毒干扰植物DNA甲基转移酶MET1和CMT3，导致DNA去甲基化^[74]。连作胁迫导致大豆Glycine max基因组DNA去甲基化酶ROS1和DML增加表达，从而降低基因组DNA甲基化水平^[75]。

环境胁迫会降低DNA甲基化水平，可能诱导TEs激活。用鞭毛蛋白衍生肽flg22(flagellin peptide 22)处理拟南芥叶片，会触发DNA去甲基化，导致某些TEs转录增加^[76]。在棉花Gossypium hirsutum基因组中，高温胁迫导致DNA甲基化水平降低，甲基化程度较高的TEs被激活增加拷贝数^[77]。在拟南芥的精子伴细胞(vegetative cell，VC)中，H1组蛋白缺失会使转录起始位点发生去甲基化，从而激活TEs^[78]。用去甲基化剂5-azaC处理水稻种子后，激活Dart1-24 DNA转座子，同时验证了转座子拷贝数增加是5′区域的核苷酸去甲基化导致的^[79]。在磷酸盐缺乏的环境中，水稻基因组DNA甲基化水平优先在TEs中瞬时变化，在抑制TEs方面发挥潜在的作用。磷酸盐不足的压力环境诱导高甲基化，从而沉默TEs^[80]。

5. 结语

通常，TEs对宿主不利影响是由于TEs的插入破坏启动子区域或基因区域，导致基因组重排，以及引起的缺失、重复、倒位等基因组结构变异^[81-82]。调控TEs表达对维持基因组稳定性具有重要意义，DNA修饰是物种进化过程中普遍采用的调控TEs表达的方式。现阶段，基因组学和表观基因组学的快速发展推动了DNA修饰的研究，其中，DNA甲基化是最主要的调控机制之一。然而，DNA修饰的这种作用具有不稳定性，包括在亲缘关系很近的物种中也存在变异^[31]。并且，DNA甲基化水平变化涉及特定酶的参与，影响甲基化酶发挥作用的因素也在间接影响TEs表达。因此，与DNA甲基化相关的酶和基因的作用被进一步发现，可以明确DNA甲基化调控TEs表达的机制。生物或非生物胁迫导致的甲基化水平降低以及主动去甲基化上调TEs，TEs抵抗由DNA甲基化介导的沉默，编码了例如VANC、TnpA等抗沉默蛋白，促进DNA脱甲基从而增加TEs拷贝数^[67-68]。宿主在遗传进化过程中更好适应环境的前提就是基因组的稳定，TEs的表达则是破坏基因组稳定的重要因素，环境因子诱导DNA甲基化水平发生变化，进一步影响TEs的表达。DNA甲基化和TEs响应环境因子的互作机制，以及最终调控宿主基因表达的机制是未来研究的方向。

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On transposon silencing and DNA methylation

doi: 10.11833/j.issn.2095-0756.20200338

Abstract

References

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通讯作者: 陈斌, bchen63@163.com

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