Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses

Retrovirology

John M Coffin¹  Crystal Russo¹  Julia H Wildschutte¹  Ravi P Subramanian¹ 

[1] Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA

关键词: human genome;    endogenous retroviruses;    evolution;   

Others  :  1209388
DOI  :  10.1186/1742-4690-8-90

 received in 2011-09-26, accepted in 2011-11-08,  发布年份 2011

【 摘 要 】

Background

Integration of retroviral DNA into a germ cell may lead to a provirus that is transmitted vertically to that host's offspring as an endogenous retrovirus (ERV). In humans, ERVs (HERVs) comprise about 8% of the genome, the vast majority of which are truncated and/or highly mutated and no longer encode functional genes. The most recently active retroviruses that integrated into the human germ line are members of the Betaretrovirus-like HERV-K (HML-2) group, many of which contain intact open reading frames (ORFs) in some or all genes, sometimes encoding functional proteins that are expressed in various tissues. Interestingly, this expression is upregulated in many tumors ranging from breast and ovarian tissues to lymphomas and melanomas, as well as schizophrenia, rheumatoid arthritis, and other disorders.

Results

No study to date has characterized all HML-2 elements in the genome, an essential step towards determining a possible functional role of HML-2 expression in disease. We present here the most comprehensive and accurate catalog of all full-length and partial HML-2 proviruses, as well as solo LTR elements, within the published human genome to date. Furthermore, we provide evidence for preferential maintenance of proviruses and solo LTR elements on gene-rich chromosomes of the human genome and in proximity to gene regions.

Conclusions

Our analysis has found and corrected several errors in the annotation of HML-2 elements in the human genome, including mislabeling of a newly identified group called HML-11. HML-elements have been implicated in a wide array of diseases, and characterization of these elements will play a fundamental role to understand the relationship between endogenous retrovirus expression and disease.

【 授权许可】

   
2011 Subramanian et al; licensee BioMed Central Ltd.

【 图 表 】

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