Further varieties of ancient endogenous retrovirus in human DNA.

IF 3.1 2区 生物学 Q1 GENETICS & HEREDITY
Martin C Frith
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Abstract

A retrovirus inserts its genome into the DNA of a cell, occasionally a germ-line cell that gives rise to descendants of the host organism: it is then called an endogenous retrovirus (ERV). The human genome contains relics from many kinds of ancient ERV. Some relics contributed new genes and regulatory elements. This study finds further kinds of ancient ERV, in the thoroughly-studied human genome version hg38: ERV-Hako, ERV-Saru, ERV-Hou, ERV-Han, and ERV-Goku. It also finds many relics of ERV-V, previously known from just two copies on chromosome 19 with placental genes. It finds a type of ERV flanked by MER41E long terminal repeats (LTRs), with surprisingly little similarity to the known MER41 ERV. ERV-Hako has subtypes that contain sequence from host genes SUSD6 and SPHKAP: the SUSD6 variant was transferred between catarrhine and platyrrhine primates. A retrovirus uses tRNA to prime reverse transcription: Hako is the only human ERV relic that used tRNA-Trp (tryptophan, symbol W), and HERV-W is misnamed because it used tRNA-Arg, based on the Genomic tRNA Database. One ERV-Saru LTR is the previously-described enhancer of AIM2 in innate immunity. This study contributes to understanding primate ERV history, but also shows that related ERVs can have drastic differences, challenging the goal of clearly annotating all ERV relics in genomes.

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人类DNA中远古内源性逆转录病毒的进一步变种。
逆转录病毒将其基因组插入细胞的DNA,有时是生殖系细胞,产生宿主生物的后代:然后称为内源性逆转录病毒(ERV)。人类基因组中含有多种古代ERV的遗迹。一些遗迹贡献了新的基因和调控元件。本研究在被彻底研究的人类基因组版本hg38中发现了更多的古代ERV: ERV- hako, ERV- saru, ERV- hou, ERV- han和ERV- goku。它还发现了许多ERV-V的遗迹,以前只知道在19号染色体上有胎盘基因的两个拷贝。它发现了一种由MER41E长末端重复序列(LTRs)组成的ERV,与已知的MER41 ERV几乎没有什么相似之处。ERV-Hako的亚型包含宿主基因SUSD6和SPHKAP的序列:SUSD6变异在长鼻猴和长鼻猴灵长类动物之间转移。逆转录病毒使用tRNA启动逆转录:Hako是唯一使用tRNA- trp(色氨酸,符号W)的人类ERV遗迹,HERV-W因使用tRNA- arg而被错误命名,基于基因组tRNA数据库。一种ERV-Saru LTR是先前描述的先天性免疫中AIM2的增强子。这项研究有助于了解灵长类动物ERV的历史,但也表明相关ERV可能存在巨大差异,这对明确注释基因组中所有ERV遗迹的目标提出了挑战。
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来源期刊
Mobile DNA
Mobile DNA GENETICS & HEREDITY-
CiteScore
8.20
自引率
6.10%
发文量
26
审稿时长
11 weeks
期刊介绍: Mobile DNA is an online, peer-reviewed, open access journal that publishes articles providing novel insights into DNA rearrangements in all organisms, ranging from transposition and other types of recombination mechanisms to patterns and processes of mobile element and host genome evolution. In addition, the journal will consider articles on the utility of mobile genetic elements in biotechnological methods and protocols.
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