Institute of Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris Sud, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France.
Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, F-75205, France.
Microbiol Spectr. 2014 Dec;2(6). doi: 10.1128/microbiolspec.MDNA3-0035-2014.
Programmed genome rearrangements in the ciliate Paramecium provide a nice illustration of the impact of transposons on genome evolution and plasticity. During the sexual cycle, development of the somatic macronucleus involves elimination of ∼30% of the germline genome, including repeated DNA (e.g., transposons) and ∼45,000 single-copy internal eliminated sequences (IES). IES excision is a precise cut-and-close process, in which double-stranded DNA cleavage at IES ends depends on PiggyMac, a domesticated piggyBac transposase. Genome-wide analysis has revealed that at least a fraction of IESs originate from Tc/mariner transposons unrelated to piggyBac. Moreover, genomic sequences with no transposon origin, such as gene promoters, can be excised reproducibly as IESs, indicating that genome rearrangements contribute to the control of gene expression. How the system has evolved to allow elimination of DNA sequences with no recognizable conserved motif has been the subject of extensive research during the past two decades. Increasing evidence has accumulated for the participation of noncoding RNAs in epigenetic control of elimination for a subset of IESs, and in trans-generational inheritance of alternative rearrangement patterns. This chapter summarizes our current knowledge of the structure of the germline and somatic genomes for the model species Paramecium tetraurelia, and describes the DNA cleavage and repair factors that constitute the IES excision machinery. We present an overview of the role of specialized RNA interference machineries and their associated noncoding RNAs in the control of DNA elimination. Finally, we discuss how RNA-dependent modification and/or remodeling of chromatin may guide PiggyMac to its cognate cleavage sites.
草履虫中的程序性基因组重排为转座子对基因组进化和可塑性的影响提供了很好的例证。在有性周期中，体细胞大核的发育涉及到约 30%的生殖系基因组的消除，包括重复 DNA（例如转座子）和约 45000 个单拷贝内部缺失序列（IES）。IES 的切除是一个精确的切割和封闭过程，其中 IES 末端的双链 DNA 切割依赖于 PiggyMac，一种驯化的 piggyBac 转座酶。全基因组分析表明，至少一部分 IES 起源于与 piggyBac 无关的 Tc/mariner 转座子。此外，没有转座子起源的基因组序列，如基因启动子，可以作为 IES 被重复切除，这表明基因组重排有助于基因表达的控制。这个系统是如何进化到允许消除没有可识别的保守基序的 DNA 序列的，这是过去二十年广泛研究的主题。越来越多的证据表明，非编码 RNA 参与了一部分 IES 的消除的表观遗传调控，以及替代重排模式的跨代遗传。本章总结了我们目前对模式生物四膜虫的生殖系和体细胞基因组结构的认识，并描述了构成 IES 切除机制的 DNA 切割和修复因子。我们概述了专门的 RNA 干扰机制及其相关非编码 RNA 在 DNA 消除控制中的作用。最后，我们讨论了 RNA 依赖性修饰和/或重塑染色质如何引导 PiggyMac 到其同源切割位点。
