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A revised nomenclature for transcribed human endogenous retroviral loci

Jens Mayer1, Jonas Blomberg2 and Ruth L Seal3*

Author Affiliations

1 Department of Human Genetics, Theoretical Medicine and Biosciences, Centre for Human and Molecular Biology, Saarland University, D-66421 Homburg, Germany

2 Section of Virology, Department of Medical Sciences, Uppsala University, SE-751 85 Uppsala, Sweden

3 HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK

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Mobile DNA 2011, 2:7  doi:10.1186/1759-8753-2-7

Published: 4 May 2011

Abstract

Background

Endogenous retroviruses (ERVs) and ERV-like sequences comprise 8% of the human genome. A hitherto unknown proportion of ERV loci are transcribed and thus contribute to the human transcriptome. A small proportion of these loci encode functional proteins. As the role of ERVs in normal and diseased biological processes is not yet established, transcribed ERV loci are of particular interest. As more transcribed ERV loci are likely to be identified in the near future, the development of a systematic nomenclature is important to ensure that all information on each locus can be easily retrieved.

Results

Here we present a revised nomenclature of transcribed human endogenous retroviral loci that sorts loci into groups based on Repbase classifications. Each symbol is of the format ERV + group symbol + unique number. Group symbols are based on a mixture of Repbase designations and well-supported symbols used in the literature. The presented guidelines will allow newly identified loci to be easily incorporated into the scheme.

Conclusions

The naming system will be employed by the HUGO Gene Nomenclature Committee for naming transcribed human ERV loci. We hope that the system will contribute to clarifying a certain aspect of a sometimes confusing nomenclature for human endogenous retroviruses. The presented system may also be employed for naming transcribed loci of human non-ERV repeat loci.