Comprehensive identification and characterization of the HERV-K (HML-9) group in the human genome.

IF 2.7 3区医学 Q3 VIROLOGY

Retrovirology Pub Date : 2022-06-08 DOI:10.1186/s12977-022-00596-2

Lei Jia, Mengying Liu, Caiqin Yang, Hanping Li, Yongjian Liu, Jingwan Han, Xiuli Zhai, Xiaolin Wang, Tianyi Li, Jingyun Li, Bohan Zhang, Changyuan Yu, Lin Li

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引用次数: 0

Abstract

Background: Human endogenous retroviruses (HERVs) result from ancestral infections caused by exogenous retroviruses that became incorporated into the germline DNA and evolutionarily fixed in the human genome. HERVs can be transmitted vertically in a Mendelian fashion and be stably maintained in the human genome, of which they are estimated to comprise approximately 8%. HERV-K (HML1-10) transcription has been confirmed to be associated with a variety of diseases, such as breast cancer, lung cancer, prostate cancer, melanoma, rheumatoid arthritis, and amyotrophic lateral sclerosis. However, the poor characterization of HML-9 prevents a detailed understanding of the regulation of the expression of this family in humans and its impact on the host genome. In light of this, a precise and updated HERV-K HML-9 genomic map is urgently needed to better evaluate the role of these elements in human health.

Results: We report a comprehensive analysis of the presence and distribution of HERV-K HML-9 elements within the human genome, with a detailed characterization of the structural and phylogenetic properties of the group. A total of 23 proviruses and 47 solo LTR elements were characterized, with a detailed description of the provirus structure, integration time, potential regulated genes, transcription factor binding sites (TFBS), and primer binding site (PBS) features. The integration time results showed that the HML-9 elements found in the human genome integrated into the primate lineage between 17.5 and 48.5 million years ago (mya).

Conclusion: The results provide a clear characterization of HML-9 and a comprehensive background for subsequent functional studies.

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人类基因组中 HERV-K (HML-9) 组的全面鉴定和特征描述。

背景：人类内源性逆转录病毒（HERVs）源于外源性逆转录病毒引起的祖先感染，这些病毒被整合到种系 DNA 中，并在进化过程中固定在人类基因组中。HERVs 可以以孟德尔方式垂直传播，并在人类基因组中稳定存在，估计约占人类基因组的 8%。HERV-K（HML1-10）转录已被证实与多种疾病相关，如乳腺癌、肺癌、前列腺癌、黑色素瘤、类风湿性关节炎和肌萎缩侧索硬化症。然而，由于对 HML-9 的特征描述不清，因此无法详细了解该家族在人体内的表达调控及其对宿主基因组的影响。有鉴于此，我们迫切需要一个精确的、最新的 HERV-K HML-9 基因组图谱，以更好地评估这些元件在人类健康中的作用：结果：我们报告了对人类基因组中 HERV-K HML-9 元粒的存在和分布的全面分析，并详细描述了该组元粒的结构和系统发育特性。共鉴定了 23 个前病毒和 47 个单独的 LTR 元件，并详细描述了前病毒的结构、整合时间、潜在调控基因、转录因子结合位点（TFBS）和引物结合位点（PBS）特征。整合时间结果表明，人类基因组中发现的 HML-9 元子是在 1750 万年前至 4850 万年前整合到灵长类血统中的：结论：研究结果明确了 HML-9 的特征，为后续功能研究提供了全面的背景资料。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Retrovirology 医学-病毒学

CiteScore

5.80

自引率

3.00%

发文量

审稿时长

>0 weeks

期刊介绍： Retrovirology is an open access, online journal that publishes stringently peer-reviewed, high-impact articles on host-pathogen interactions, fundamental mechanisms of replication, immune defenses, animal models, and clinical science relating to retroviruses. Retroviruses are pleiotropically found in animals. Well-described examples include avian, murine and primate retroviruses. Two human retroviruses are especially important pathogens. These are the human immunodeficiency virus, HIV, and the human T-cell leukemia virus, HTLV. HIV causes AIDS while HTLV-1 is the etiological agent for adult T-cell leukemia and HTLV-1-associated myelopathy/tropical spastic paraparesis. Retrovirology aims to cover comprehensively all aspects of human and animal retrovirus research.