• Title/Summary/Keyword: HERV-K

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Identification and Phylogenetic Analysis of SINE-R Retroposon Family in cDNA Library of Human Fetal Brain

  • Yi, Joo-Mi;Shin, Kyung-Mi;Lee, Ji-Won;Paik, In-Ho;Jang, Kyung-Lib;Kim, Heui-Soo
    • Animal cells and systems
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    • v.5 no.3
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    • pp.231-236
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    • 2001

  • SINE-R retroposons have been derived from human endogenous retrovirus HERV-K family and found to be hominoid specific. Both SINE-R retroposons and HERV-K family are potentially capable of affecting the expression of closely located genes. From cDNA library of human fetal brain, we identified seven SINE-R retroposons and compared them with sequences derived from GenBank database. The SINE-R retroposons from human feta1 brain showed 85∼97% sequence similarities with the human-specific retroposon SINE-R.C2. They also showed 88∼96% sequence similarities with the sequence of the schizo-cDNA clone that derived from postmortem frontal cortex tissue of a schizophrenic patient. Phylogenetic analysis using the neiqhbor-joining method revealed that the seven new SINE-R retroposons from cDNA library of the human feta1 brain have proliferated independently during human evolution. The data indicate that such SINE-R retroposons are expressed in human fetal brain and deserve further investigation as potential leads to understanding of neuropsychiatric diseases.

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Metagenomic analysis of viral genes integrated in whole genome sequencing data of Thai patients with Brugada syndrome

  • Suwalak Chitcharoen;Chureerat Phokaew;John Mauleekoonphairoj;Apichai Khongphatthanayothin;Boosamas Sutjaporn;Pharawee Wandee;Yong Poovorawan;Koonlawee Nademanee;Sunchai Payungporn
    • Genomics & Informatics
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    • v.20 no.4
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    • pp.44.1-44.13
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    • 2022

  • Brugada syndrome (BS) is an autosomal dominant inheritance cardiac arrhythmia disorder associated with sudden death in young adults. Thailand has the highest prevalence of BS worldwide, and over 60% of patients with BS still have unclear disease etiology. Here, we performed a new viral metagenome analysis pipeline called VIRIN and validated it with whole genome sequencing (WGS) data of HeLa cell lines and hepatocellular carcinoma. Then the VIRIN pipeline was applied to identify viral integration positions from unmapped WGS data of Thai males, including 100 BS patients (case) and 100 controls. Even though the sample preparation had no viral enrichment step, we can identify several virus genes from our analysis pipeline. The predominance of human endogenous retrovirus K (HERV-K) viruses was found in both cases and controls by blastn and blastx analysis. This study is the first report on the full-length HERV-K assembled genomes in the Thai population. Furthermore, the HERV-K integration breakpoint positions were validated and compared between the case and control datasets. Interestingly, Brugada cases contained HERV-K integration breakpoints at promoters five times more often than controls. Overall, the highlight of this study is the BS-specific HERV-K breakpoint positions that were found at the gene coding region "NBPF11" (n = 9), "NBPF12" (n = 8) and long non-coding RNA (lncRNA) "PCAT14" (n = 4) region. The genes and the lncRNA have been reported to be associated with congenital heart and arterial diseases. These findings provide another aspect of the BS etiology associated with viral genome integrations within the human genome.

  • https://doi.org/10.5808/gi.22047 인용 PDF KSCI

Expression of Endogenous Retroviruses and Disease (내인성 레트로바이러스의 발현과 질병)

  • Lee, Jae-Yeong
    • Korean Journal of Microbiology
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    • v.43 no.4
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    • pp.237-242
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    • 2007

  • One of the chief characteristics of the retrovirus life cycle is the appearance of provirus caused by integration of viral genome into the host cell genome, and its delivery stably to the next generation as a part of host germ line. This stable form is called endogenous retrovirus (ERV) and expressed by exogenous or endogenous factors. HERVs and MuERVs are present in humans and mice correspondingly, and their expressions frequently cause diseases. Several diseases such as cancer, autoimmunity and neurological disorders are related with HERVs. Therefore, various strategies should be established for the development of effective therapies for the suffering patients.

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