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Chen M, Yang C, Zhai X, Wang C, Liu M, Zhang B, Guo X, Wang Y, Li H, Liu Y, Han J, Wang X, Li J, Jia L, Li L. Comprehensive Identification and Characterization of HML-9 Group in Chimpanzee Genome. Viruses 2024; 16:892. [PMID: 38932184 PMCID: PMC11209481 DOI: 10.3390/v16060892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Endogenous retroviruses (ERVs) are related to long terminal repeat (LTR) retrotransposons, comprising gene sequences of exogenous retroviruses integrated into the host genome and inherited according to Mendelian law. They are considered to have contributed greatly to the evolution of host genome structure and function. We previously characterized HERV-K HML-9 in the human genome. However, the biological function of this type of element in the genome of the chimpanzee, which is the closest living relative of humans, largely remains elusive. Therefore, the current study aims to characterize HML-9 in the chimpanzee genome and to compare the results with those in the human genome. Firstly, we report the distribution and genetic structural characterization of the 26 proviral elements and 38 solo LTR elements of HML-9 in the chimpanzee genome. The results showed that the distribution of these elements displayed a non-random integration pattern, and only six elements maintained a relatively complete structure. Then, we analyze their phylogeny and reveal that the identified elements all cluster together with HML-9 references and with those identified in the human genome. The HML-9 integration time was estimated based on the 2-LTR approach, and the results showed that HML-9 elements were integrated into the chimpanzee genome between 14 and 36 million years ago and into the human genome between 18 and 49 mya. In addition, conserved motifs, cis-regulatory regions, and enriched PBS sequence features in the chimpanzee genome were predicted based on bioinformatics. The results show that pathways significantly enriched for ERV LTR-regulated genes found in the chimpanzee genome are closely associated with disease development, including neurological and neurodevelopmental psychiatric disorders. In summary, the identification, characterization, and genomics of HML-9 presented here not only contribute to our understanding of the role of ERVs in primate evolution but also to our understanding of their biofunctional significance.
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Affiliation(s)
- Mingyue Chen
- National 111 Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering, Hubei University of Technology, Wuhan 430068, China;
| | - Caiqin Yang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Xiuli Zhai
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Chunlei Wang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Mengying Liu
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Bohan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Xing Guo
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Yanglan Wang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hanping Li
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Yongjian Liu
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Jingwan Han
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Xiaolin Wang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Jingyun Li
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Lei Jia
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Lin Li
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
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Liang B, Yan T, Wei H, Zhang D, Li L, Liu Z, Li W, Zhang Y, Jiang N, Meng Q, Jiang G, Hu Y, Leng J. HERVK-mediated regulation of neighboring genes: implications for breast cancer prognosis. Retrovirology 2024; 21:4. [PMID: 38388382 PMCID: PMC10885364 DOI: 10.1186/s12977-024-00636-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 02/18/2024] [Indexed: 02/24/2024] Open
Abstract
Human endogenous retroviruses (HERVs) are the remnants of ancient retroviral infections integrated into the human genome. Although most HERVs are silenced or rendered inactive by various regulatory mechanisms, they retain the potential to influence the nearby genes. We analyzed the regulatory map of 91 HERV-Ks on neighboring genes in human breast cancer and investigated the impact of HERV-Ks on the tumor microenvironment (TME) and prognosis of breast cancer. Nine RNA-seq datasets were obtained from GEO and NCBI SRA. Differentially expressed genes and HERV-Ks were analyzed using DESeq2. Validation of high-risk prognostic candidate genes using TCGA data. These included Overall survival (multivariate Cox regression model), immune infiltration analysis (TIMER), tumor mutation burden (maftools), and drug sensitivity analysis (GSCA). A total of 88 candidate genes related to breast cancer prognosis were screened, of which CD48, SLAMF7, SLAMF1, IGLL1, IGHA1, and LRRC8A were key genes. Functionally, these six key genes were significantly enriched in some immune function-related pathways, which may be associated with poor prognosis for breast cancer (p = 0.00016), and the expression levels of these genes were significantly correlated with the sensitivity of breast cancer treatment-related drugs. Mechanistically, they may influence breast cancer development by modulating the infiltration of various immune cells into the TME. We further experimentally validated these genes to confirm the results obtained from bioinformatics analysis. This study represents the first report on the regulatory potential of HERV-K in the neighboring breast cancer genome. We identified three key HERV-Ks and five neighboring genes that hold promise as novel targets for future interventions and treatments for breast cancer.
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Affiliation(s)
- Boying Liang
- Department of Immunology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, 530021, Guangxi, China
- Guangxi Key Laboratory of Translational Medicine for Treating High-Incidence Infectious Diseases with Integrative Medicine, Nanning, China
| | - Tengyue Yan
- Collaborative Innovation Centre of Regenerative Medicine and Medical Bioresource Development and Application Co-Constructed by the Province and Ministry, Guangxi Medical University, Nanning, China
| | - Huilin Wei
- School of Institute of Life Sciences, Guangxi Medical University, Nanning, China
| | - Die Zhang
- Collaborative Innovation Centre of Regenerative Medicine and Medical Bioresource Development and Application Co-Constructed by the Province and Ministry, Guangxi Medical University, Nanning, China
| | - Lanxiang Li
- Department of Immunology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Zengjing Liu
- Genomic Experimental Center, Guangxi Medical University, Nanning, China
| | - Wen Li
- Genomic Experimental Center, Guangxi Medical University, Nanning, China
| | - Yuluan Zhang
- Genomic Experimental Center, Guangxi Medical University, Nanning, China
| | - Nili Jiang
- School of Institute of Life Sciences, Guangxi Medical University, Nanning, China
| | - Qiuxia Meng
- Genomic Experimental Center, Guangxi Medical University, Nanning, China
| | - Guiyang Jiang
- Genomic Experimental Center, Guangxi Medical University, Nanning, China
| | - Yanling Hu
- Department of Immunology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Collaborative Innovation Centre of Regenerative Medicine and Medical Bioresource Development and Application Co-Constructed by the Province and Ministry, Guangxi Medical University, Nanning, China.
- School of Institute of Life Sciences, Guangxi Medical University, Nanning, China.
- Genomic Experimental Center, Guangxi Medical University, Nanning, China.
| | - Jing Leng
- Department of Immunology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Guangxi Key Laboratory of Translational Medicine for Treating High-Incidence Infectious Diseases with Integrative Medicine, Nanning, China.
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Hirata M, Ichiyanagi T, Katoh H, Hashimoto T, Suzuki H, Nitta H, Kawase M, Nakai R, Imamura M, Ichiyanagi K. Sequence divergence and retrotransposon insertion underlie interspecific epigenetic differences in primates. Mol Biol Evol 2022; 39:msac208. [PMID: 36219870 PMCID: PMC9577543 DOI: 10.1093/molbev/msac208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/27/2022] [Accepted: 09/21/2022] [Indexed: 11/14/2022] Open
Abstract
Changes in the epigenome can affect the phenotype without the presence of changes in the genomic sequence. Given the high identity of the human and chimpanzee genome sequences, a substantial portion of their phenotypic divergence likely arises from epigenomic differences between the two species. In this study, the transcriptome and epigenome were determined for induced pluripotent stem cells (iPSCs) generated from human and chimpanzee individuals. The transcriptome and epigenomes for trimethylated histone H3 at lysine-4 (H3K4me3) and lysine-27 (H3K27me3) showed high levels of similarity between the two species. However, there were some differences in histone modifications. Although such regions, in general, did not show significant enrichment of interspecies nucleotide variations, gains in binding motifs for pluripotency-related transcription factors, especially POU5F1 and SOX2, were frequently found in species-specific H3K4me3 regions. We also revealed that species-specific insertions of retrotransposons, including the LTR5_Hs subfamily in human and a newly identified LTR5_Pt subfamily in chimpanzee, created species-specific H3K4me3 regions associated with increased expression of nearby genes. Human iPSCs have more species-specific H3K27me3 regions, resulting in more abundant bivalent domains. Only a limited number of these species-specific H3K4me3 and H3K27me3 regions overlap with species-biased enhancers in cranial neural crest cells, suggesting that differences in the epigenetic state of developmental enhancers appear late in development. Therefore, iPSCs serve as a suitable starting material for studying evolutionary changes in epigenome dynamics during development.
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Affiliation(s)
- Mayu Hirata
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Tomoko Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Hirokazu Katoh
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Takuma Hashimoto
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Hikaru Suzuki
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Hirohisa Nitta
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Masaki Kawase
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Risako Nakai
- Molecular Biology Section, Department of Cellular and Molecular Biology, Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Masanori Imamura
- Molecular Biology Section, Department of Cellular and Molecular Biology, Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
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