DataSheet_1_Comprehensive characterization of ERV-K (HML-8) in the chimpanzee genome revealed less genomic activity than humans.xlsx

Endogenous retroviruses (ERVs) originate from ancestral germline infections caused by exogenous retroviruses. Throughout evolution, they have become fixed within the genome of the animals into which they were integrated. As ERV elements coevolve with the host, they are normally epigenetically silenced and can become upregulated in a series of physiological and pathological processes. Generally, a detailed ERV profile in the host genome is critical for understanding the evolutionary history and functional performance of the host genome. We previously characterized and cataloged all the ERV-K subtype HML-8 loci in the human genome; however, this has not been done for the chimpanzee, the nearest living relative of humans. In this study, we aimed to catalog and characterize the integration of HML-8 in the chimpanzee genome and compare it with the integration of HML-8 in the human genome. We analyzed the integration of HML-8 and found that HML-8 pervasively invaded the chimpanzee genome. A total of 76 proviral elements were characterized on 23/24 chromosomes, including detailed elements distribution, structure, phylogeny, integration time, and their potential to regulate adjacent genes. The incomplete structure of HML-8 proviral LTRs will undoubtedly affect their activity. Moreover, the results indicated that HML-8 integration occurred before the divergence between humans and chimpanzees. Furthermore, chimpanzees include more HML-8 proviral elements (76 vs. 40) and fewer solo long terminal repeats (LTR) (0 vs. 5) than humans. These results suggested that chimpanzee genome activity is less than the human genome and that humans may have a better ability to shape and screen integrated proviral elements. Our work is informative in both an evolutionary and a functional context for ERVs.

内源性逆转录病毒（Endogenous Retroviruses, ERVs）起源于外源性逆转录病毒引发的祖先种系感染。在演化进程中，它们逐步整合并固定于宿主动物的基因组内。由于ERV元件与宿主协同演化，其通常会受到表观遗传沉默调控，并可在一系列生理与病理过程中出现表达上调。

一般而言，解析宿主基因组中的ERV全貌，对于理解宿主基因组的演化历史与功能特性至关重要。此前我们已对人类基因组中的ERV-K亚型HML-8位点完成鉴定与编目，但作为现存与人类亲缘关系最近的物种，黑猩猩的相关研究尚未开展。

本研究旨在对黑猩猩基因组中的HML-8整合位点进行编目与鉴定，并将其与人类基因组中的HML-8整合情况开展对比分析。我们针对HML-8的整合现象展开分析后发现，HML-8曾广泛侵染黑猩猩基因组。最终在23条/24条染色体上共鉴定得到76个前病毒元件，涵盖其详细的分布特征、结构特征、系统发育关系、整合时间，以及其调控邻近基因的潜在能力。

HML-8前病毒长末端重复序列（Long Terminal Repeats, LTR）的不完全结构，无疑会对其活性造成影响。此外，研究结果显示，HML-8的整合事件发生于人类与黑猩猩分化之前。进一步对比发现，黑猩猩基因组中含有的HML-8前病毒元件数量更多（76个 vs 人类的40个），而单独LTR的数量则更少（0个 vs 人类的5个）。

上述结果表明，黑猩猩基因组的ERV活性低于人类基因组，且人类或许具备更强的能力对整合的前病毒元件进行塑造与筛选。本研究可为ERV的演化与功能研究提供具有参考价值的依据。