Identification of the distribution of human endogenous retroviruses K (HML-2) by PCR-based target enrichment sequencing
Abstract Background Human endogenous retroviruses (HERVs), suspected to be transposition-defective, may reshape the transcriptional network of the human genome by regulatory elements distributed in their long terminal repeats (LTRs). HERV-K (HML-2), the most preserved group with the least number of...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-05-01
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| Series: | Retrovirology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12977-020-00519-z |
| _version_ | 1831791896323686400 |
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| author | Bei Xue Tiansheng Zeng Lisha Jia Dongsheng Yang Stanley L. Lin Leonardo A. Sechi David J. Kelvin |
| author_facet | Bei Xue Tiansheng Zeng Lisha Jia Dongsheng Yang Stanley L. Lin Leonardo A. Sechi David J. Kelvin |
| author_sort | Bei Xue |
| collection | DOAJ |
| description | Abstract Background Human endogenous retroviruses (HERVs), suspected to be transposition-defective, may reshape the transcriptional network of the human genome by regulatory elements distributed in their long terminal repeats (LTRs). HERV-K (HML-2), the most preserved group with the least number of accumulated of mutations, has been associated with aberrant gene expression in tumorigenesis and autoimmune diseases. Because of the high sequence similarity between different HERV-Ks, current methods have limitations in providing genome-wide mapping specific for individual HERV-K (HML-2) members, a major barrier in delineating HERV-K (HML-2) function. Results In an attempt to obtain detailed distribution information of HERV-K (HML-2), we utilized a PCR-based target enrichment sequencing protocol for HERV-K (HML-2) (PTESHK) loci, which not only maps the presence of reference loci, but also identifies non-reference loci, enabling determination of the genome-wide distribution of HERV-K (HML-2) loci. Here we report on the genomic data obtained from three individuals. We identified a total of 978 loci using this method, including 30 new reference loci and 5 non-reference loci. Among the 3 individuals in our study, 14 polymorphic HERV-K (HML-2) loci were identified, and solo-LTR330 and N6p21.32 were identified as polymorphic for the first time. Conclusions Interestingly, PTESHK provides an approach for the identification of the genome-wide distribution of HERV-K (HML-2) and can be used for the identification of polymorphic loci. Since polymorphic HERV-K (HML-2) integrations are suspected to be related to various diseases, PTESHK can supplement other emerging techniques in accessing polymorphic HERV-K (HML-2) elements in cancer and autoimmune diseases. |
| first_indexed | 2024-12-22T15:02:39Z |
| format | Article |
| id | doaj.art-4e8a4bb2e7994845b9da5d93f39d2d0d |
| institution | Directory Open Access Journal |
| issn | 1742-4690 |
| language | English |
| last_indexed | 2024-12-22T15:02:39Z |
| publishDate | 2020-05-01 |
| publisher | BMC |
| record_format | Article |
| series | Retrovirology |
| spelling | doaj.art-4e8a4bb2e7994845b9da5d93f39d2d0d2022-12-21T18:22:05ZengBMCRetrovirology1742-46902020-05-0117111510.1186/s12977-020-00519-zIdentification of the distribution of human endogenous retroviruses K (HML-2) by PCR-based target enrichment sequencingBei Xue0Tiansheng Zeng1Lisha Jia2Dongsheng Yang3Stanley L. Lin4Leonardo A. Sechi5David J. Kelvin6Division of Immunology, Shantou University Medical CollegeDivision of Immunology, Shantou University Medical CollegeDivision of Immunology, Shantou University Medical CollegeDivision of Immunology, Shantou University Medical CollegeDivision of Immunology, Shantou University Medical CollegeDepartment of Biomedical Sciences, University of SassariDivision of Immunology, Shantou University Medical CollegeAbstract Background Human endogenous retroviruses (HERVs), suspected to be transposition-defective, may reshape the transcriptional network of the human genome by regulatory elements distributed in their long terminal repeats (LTRs). HERV-K (HML-2), the most preserved group with the least number of accumulated of mutations, has been associated with aberrant gene expression in tumorigenesis and autoimmune diseases. Because of the high sequence similarity between different HERV-Ks, current methods have limitations in providing genome-wide mapping specific for individual HERV-K (HML-2) members, a major barrier in delineating HERV-K (HML-2) function. Results In an attempt to obtain detailed distribution information of HERV-K (HML-2), we utilized a PCR-based target enrichment sequencing protocol for HERV-K (HML-2) (PTESHK) loci, which not only maps the presence of reference loci, but also identifies non-reference loci, enabling determination of the genome-wide distribution of HERV-K (HML-2) loci. Here we report on the genomic data obtained from three individuals. We identified a total of 978 loci using this method, including 30 new reference loci and 5 non-reference loci. Among the 3 individuals in our study, 14 polymorphic HERV-K (HML-2) loci were identified, and solo-LTR330 and N6p21.32 were identified as polymorphic for the first time. Conclusions Interestingly, PTESHK provides an approach for the identification of the genome-wide distribution of HERV-K (HML-2) and can be used for the identification of polymorphic loci. Since polymorphic HERV-K (HML-2) integrations are suspected to be related to various diseases, PTESHK can supplement other emerging techniques in accessing polymorphic HERV-K (HML-2) elements in cancer and autoimmune diseases.http://link.springer.com/article/10.1186/s12977-020-00519-zHERV-K (HML-2)PTESHKGenome-wide distributionPolymorphic loci |
| spellingShingle | Bei Xue Tiansheng Zeng Lisha Jia Dongsheng Yang Stanley L. Lin Leonardo A. Sechi David J. Kelvin Identification of the distribution of human endogenous retroviruses K (HML-2) by PCR-based target enrichment sequencing Retrovirology HERV-K (HML-2) PTESHK Genome-wide distribution Polymorphic loci |
| title | Identification of the distribution of human endogenous retroviruses K (HML-2) by PCR-based target enrichment sequencing |
| title_full | Identification of the distribution of human endogenous retroviruses K (HML-2) by PCR-based target enrichment sequencing |
| title_fullStr | Identification of the distribution of human endogenous retroviruses K (HML-2) by PCR-based target enrichment sequencing |
| title_full_unstemmed | Identification of the distribution of human endogenous retroviruses K (HML-2) by PCR-based target enrichment sequencing |
| title_short | Identification of the distribution of human endogenous retroviruses K (HML-2) by PCR-based target enrichment sequencing |
| title_sort | identification of the distribution of human endogenous retroviruses k hml 2 by pcr based target enrichment sequencing |
| topic | HERV-K (HML-2) PTESHK Genome-wide distribution Polymorphic loci |
| url | http://link.springer.com/article/10.1186/s12977-020-00519-z |
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