Genomic characterization of variable surface antigens reveals a telomere position effect as a prerequisite for RNA interference-mediated silencing in Paramecium tetraurelia.
Genomic characterization of variable surface antigens reveals a telomere position effect as a prerequisite for RNA interference-mediated silencing in Paramecium tetraurelia.
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DOI：
10.1128/mbio.01328-14
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发表时间：
2014-11-11
期刊：
影响因子：
6.4
通讯作者：
Simon M
中科院分区：
文献类型：
--
作者：
Baranasic D;Oppermann T;Cheaib M;Cullum J;Schmidt H;Simon M
抗原性或表型变异是真核微生物上表达可变表面蛋白外壳的一种普遍现象。为了阐明互斥基因表达背后的机制，我们研究了纤毛虫草履虫表面抗原多基因家族的遗传特性以及控制表达和沉默的表观遗传因素。基因组分析表明，多基因家族由染色体内和亚端粒基因组成；这两类基因明显起源于不同的基因复制事件：全基因组复制和染色体内复制。表达分析提供了端粒位置效应的证据，因为只有亚端粒基因遵循相互排斥的转录。微阵列分析缺乏Rdr3的培养物，与血清型纯野生型培养物相比，Rdr3是一种依赖RNA的RNA聚合酶，显示出部分亚端粒基因的共转录，表明端粒位置效应是由于Rdr3介导的沉默在亚端粒区域选择性地发生。我们提出了一个通过染色体内基因复制来维持结构相关区域的阳性选择的表面抗原进化模型。对染色体异质性的进一步分析表明，交替的端粒加入区明显影响密切相关基因的转录。因此，染色体片段化对于表面抗原的表达和进化至关重要。我们的数据表明，RNAi通过反式作用的RNAs介导的对这个遗传网络的控制，允许通过表型变异和抗原基因达尔文进化的长期遗传适应相结合的快速表观遗传适应。几乎所有真核微生物的表面蛋白结构都有变化，并描述了多种功能，如毒力因子、黏附分子和分子伪装。因此，控制可变表面蛋白的基因表达的机制是病原微生物和自由生活的真核微生物中快速表型变异的有力工具。然而，控制单个基因同步表达和沉默的表观遗传机制几乎不清楚。利用纤毛虫草履虫作为表观遗传模型，我们发现亚端粒的基因位置效应与RNAi介导的沉默表面蛋白基因的选择性发生有关，这表明小干扰RNA(SiRNA)介导的沉默和活性表面抗原基因之间的表观遗传交互作用。我们的基因组和分子相结合的方法揭示了基因位置效应和siRNA介导的反式沉默之间的相关性，从而为相互排斥的基因表达的调控和变异基因家族的基因组组织提供了两个新的参数。
Antigenic or phenotypic variation is a widespread phenomenon of expression of variable surface protein coats on eukaryotic microbes. To clarify the mechanism behind mutually exclusive gene expression, we characterized the genetic properties of the surface antigen multigene family in the ciliate Paramecium tetraurelia and the epigenetic factors controlling expression and silencing. Genome analysis indicated that the multigene family consists of intrachromosomal and subtelomeric genes; both classes apparently derive from different gene duplication events: whole-genome and intrachromosomal duplication. Expression analysis provides evidence for telomere position effects, because only subtelomeric genes follow mutually exclusive transcription. Microarray analysis of cultures deficient in Rdr3, an RNA-dependent RNA polymerase, in comparison to serotype-pure wild-type cultures, shows cotranscription of a subset of subtelomeric genes, indicating that the telomere position effect is due to a selective occurrence of Rdr3-mediated silencing in subtelomeric regions. We present a model of surface antigen evolution by intrachromosomal gene duplication involving the maintenance of positive selection of structurally relevant regions. Further analysis of chromosome heterogeneity shows that alternative telomere addition regions clearly affect transcription of closely related genes. Consequently, chromosome fragmentation appears to be of crucial importance for surface antigen expression and evolution. Our data suggest that RNAi-mediated control of this genetic network by trans-acting RNAs allows rapid epigenetic adaptation by phenotypic variation in combination with long-term genetic adaptation by Darwinian evolution of antigen genes. Alternating surface protein structures have been described for almost all eukaryotic microbes, and a broad variety of functions have been described, such as virulence factors, adhesion molecules, and molecular camouflage. Mechanisms controlling gene expression of variable surface proteins therefore represent a powerful tool for rapid phenotypic variation across kingdoms in pathogenic as well as free-living eukaryotic microbes. However, the epigenetic mechanisms controlling synchronous expression and silencing of individual genes are hardly understood. Using the ciliate Paramecium tetraurelia as a (epi)genetic model, we showed that a subtelomeric gene position effect is associated with the selective occurrence of RNAi-mediated silencing of silent surface protein genes, suggesting small interfering RNA (siRNA)-mediated epigenetic cross talks between silent and active surface antigen genes. Our integrated genomic and molecular approach discloses the correlation between gene position effects and siRNA-mediated trans-silencing, thus providing two new parameters for regulation of mutually exclusive gene expression and the genomic organization of variant gene families.