Departamento de Microbiologia, Imunologia e Parasitologia Escola Paulista de Medicina, UNIFESP, São Paulo, SP, Brazil.
BMC Genomics. 2012 Jun 8;13:229. doi: 10.1186/1471-2164-13-229.
The subtelomeres of many protozoa are highly enriched in genes with roles in niche adaptation. T. cruzi trypomastigotes express surface proteins from Trans-Sialidase (TS) and Dispersed Gene Family-1 (DGF-1) superfamilies which are implicated in host cell invasion. Single populations of T. cruzi may express different antigenic forms of TSs. Analysis of TS genes located at the telomeres suggests that chromosome ends could have been the sites where new TS variants were generated. The aim of this study is to characterize telomeric and subtelomeric regions of T. cruzi available in TriTrypDB and connect the sequences of telomeres to T. cruzi working draft sequence.
We first identified contigs carrying the telomeric repeat (TTAGGG). Of 49 contigs identified, 45 have telomeric repeats at one end, whereas in four contigs the repeats are located internally. All contigs display a conserved telomeric junction sequence adjacent to the hexamer repeats which represents a signature of T. cruzi chromosome ends. We found that 40 telomeric contigs are located on T. cruzi chromosome-sized scaffolds. In addition, we were able to map several telomeric ends to the chromosomal bands separated by pulsed-field gel electrophoresis.The subtelomeric sequence structure varies widely, mainly as a result of large differences in the relative abundance and organization of genes encoding surface proteins (TS and DGF-1), retrotransposon hot spot genes (RHS), retrotransposon elements, RNA-helicase and N-acetyltransferase genes. While the subtelomeric regions are enriched in pseudogenes, they also contain complete gene sequences matching both known and unknown expressed genes, indicating that these regions do not consist of nonfunctional DNA but are instead functional parts of the expressed genome. The size of the subtelomeric regions varies from 5 to 182 kb; the smaller of these regions could have been generated by a recent chromosome breakage and telomere healing event.
The lack of synteny in the subtelomeric regions suggests that genes located in these regions are subject to recombination, which increases their variability, even among homologous chromosomes. The presence of typical subtelomeric genes can increase the chance of homologous recombination mechanisms or microhomology-mediated end joining, which may use these regions for the pairing and recombination of free ends.
许多原生动物的亚端粒富含在生态位适应中起作用的基因。克氏锥虫的鞭毛体表达表面蛋白来自转涎酶（TS）和分散基因家族-1（DGF-1）超家族，这些蛋白参与宿主细胞的入侵。克氏锥虫的单一群体可能表达不同的 TS 抗原形式。位于端粒的 TS 基因分析表明，染色体末端可能是新的 TS 变体产生的部位。本研究的目的是表征 TriTrypDB 中可获得的克氏锥虫的端粒和亚端粒区，并将端粒序列与克氏锥虫工作草稿序列连接起来。
我们首先鉴定了携带端粒重复序列（TTAGGG）的 contigs。在鉴定的 49 个 contigs 中，有 45 个在一端带有端粒重复序列，而在四个 contigs 中，重复序列位于内部。所有 contigs 都显示出与六聚体重复相邻的保守端粒连接序列，这代表了克氏锥虫染色体末端的特征。我们发现 40 个端粒 contigs 位于克氏锥虫染色体大小的支架上。此外，我们还能够将几个端粒末端映射到脉冲场凝胶电泳分离的染色体带。亚端粒序列结构差异很大，主要是由于编码表面蛋白（TS 和 DGF-1）、逆转录转座子热点基因（RHS）、逆转录转座子元件、RNA 解旋酶和 N-乙酰转移酶基因的相对丰度和组织的差异。虽然亚端粒区富含假基因，但它们也包含与已知和未知表达基因匹配的完整基因序列，表明这些区域不是无功能的 DNA，而是表达基因组的功能部分。亚端粒区的大小从 5 到 182kb 不等；这些较小的区域可能是由最近的染色体断裂和端粒愈合事件产生的。
亚端粒区的非同源性表明，位于这些区域的基因易发生重组，从而增加了它们的变异性，即使在同源染色体之间也是如此。典型的亚端粒基因的存在可以增加同源重组机制或微同源介导的末端连接的可能性，这可能利用这些区域进行游离末端的配对和重组。
