Nomenclature for endogenous retrovirus (ERV) loci.-猫眼课题宝

DOI：

10.1186/s12977-018-0442-1

发表时间：

2018-08-28

期刊：

Retrovirology

影响因子：

3.3

通讯作者：

中科院分区：

医学2区

文献类型：

作者：

Gifford RJ;Blomberg J;Coffin JM;Fan H;Heidmann T;Mayer J;Stoye J;Tristem M;Johnson WE

来源链接：

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6114882/

逆转录病毒整合到生殖系DNA中可导致形成垂直遗传的前病毒序列，称为内源性逆转录病毒（ERV）。在它们的进化过程中，脊椎动物基因组已经积累了数千个ERV基因座。这些序列提供了关于古老逆转录病毒的有用的回顾性信息，并且在塑造脊椎动物基因组的进化中也发挥了重要作用。目前迫切需要一个统一的ERV基因座命名系统，不仅有助于基因组注释，而且有助于ERV及其对基因组生物学和进化的影响的研究。在这篇综述中，我们研究了如何ERV命名法的发展，并考虑实施一个系统的方法命名ERV基因座的可能性。我们建议，这样的命名法不仅应提供独特的标识符为个别位点，但也表示在不同物种的ERVs之间的直系亲属关系。此外，我们建议，在可能的情况下，记忆链接到以前的，完善的名称ERV基因座和组应予以保留。我们展示了这种方法可以如何应用和整合到现有的逆转录病毒，ERVs和转座因子的分类和命名方案。

Retroviral integration into germline DNA can result in the formation of a vertically inherited proviral sequence called an endogenous retrovirus (ERV). Over the course of their evolution, vertebrate genomes have accumulated many thousands of ERV loci. These sequences provide useful retrospective information about ancient retroviruses, and have also played an important role in shaping the evolution of vertebrate genomes. There is an immediate need for a unified system of nomenclature for ERV loci, not only to assist genome annotation, but also to facilitate research on ERVs and their impact on genome biology and evolution. In this review, we examine how ERV nomenclatures have developed, and consider the possibilities for the implementation of a systematic approach for naming ERV loci. We propose that such a nomenclature should not only provide unique identifiers for individual loci, but also denote orthologous relationships between ERVs in different species. In addition, we propose that—where possible—mnemonic links to previous, well-established names for ERV loci and groups should be retained. We show how this approach can be applied and integrated into existing taxonomic and nomenclature schemes for retroviruses, ERVs and transposable elements.