Frith Martin C
Department of Computational Biology and Medical Sciences, University of Tokyo, Chiba, Japan.
Artificial Intelligence Research Center, AIST, Tokyo, Japan.
Mob DNA. 2025 Mar 13;16(1):11. doi: 10.1186/s13100-025-00348-x.
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.
逆转录病毒将其基因组插入细胞的DNA中，偶尔也会插入生殖系细胞，后者会产生宿主生物体的后代：此时它被称为内源性逆转录病毒（ERV）。人类基因组包含许多种古代ERV的遗迹。一些遗迹贡献了新的基因和调控元件。本研究在经过充分研究的人类基因组版本hg38中发现了更多种类的古代ERV：ERV-Hako、ERV-Saru、ERV-Hou、ERV-Han和ERV-Goku。研究还发现了许多ERV-V的遗迹，此前仅在19号染色体上带有胎盘基因的两个拷贝中发现过。研究发现一种ERV两侧是MER41E长末端重复序列（LTR），与已知的MER41 ERV惊人地相似性很低。ERV-Hako有一些亚型包含宿主基因SUSD6和SPHKAP的序列：SUSD6变体在旧世界猴和新世界猴灵长类动物之间转移。逆转录病毒利用tRNA启动逆转录：根据基因组tRNA数据库，Hako是唯一使用tRNA-Trp（色氨酸，符号W）的人类ERV遗迹，而HERV-W的命名有误，因为它使用的是tRNA-Arg。一个ERV-Saru LTR是先前描述的先天免疫中AIM2的增强子。这项研究有助于理解灵长类ERV的历史，但也表明相关的ERV可能有巨大差异，这对在基因组中清晰注释所有ERV遗迹的目标构成了挑战。
