Volume 10 Supplement 1

Frontiers of Retrovirology: Complex retroviruses, retroelements and their hosts

Open Access

Identification and analysis of HML2 sequences in human genome assembly GRCh37/hg19

  • Marta Cadeddu1,
  • Laura Vargiu1, 2,
  • Patricia Rodriguez-Tomé2,
  • Göran O Sperber3,
  • Jonas Blomberg4 and
  • Enzo Tramontano1
Retrovirology201310(Suppl 1):P9

https://doi.org/10.1186/1742-4690-10-S1-P9

Published: 19 September 2013

Background

Human endogenous retroviruses (HERVs) originated from exogenous retroviral infections of the human germ line cells and spread in the human population through vertical transmission over millions of years. Among HERVs, the HML2 proviruses [1] are the most recently integrated and show the most intact proviral genomes. HML-2 expression has tentatively been associated with different pathological conditions, including Hodgkin’s lymphoma, melanoma, breast and testicular cancer. A comprehensive recent study identified 91 HML2 proviruses [2].

Material and methods

Human genome (assembly GRCh 37/hg19) was analyzed with RetroTector (ReTe) version 1.01 [3]. ReTe was run on a machine with 4 6-core Xeon processors, 2.66Ghz each, 256 Gb of RAM and 4 Tb of disks, with an estimated execution time of 1-2 days. BLASTN, using HML consensuses (Blikstad et al, unpublished) and the May 2013 Repeatmasker library, ENSEMBL and MEGA5 were used, in successive steps, for classification and identification of locus position and phylogenetic inference. Time since integration was inferred using a neutral substitution rate between cognate LTRs of 0.2 mutations per million years.

Results

ReTe [2] identified more than 120 HML2 proviruses, many of which were not previously reported, accounting for roughly 0.01% of the total human genome. Among the identified HML2 proviruses more than 50% are ≥ 8000 bp in length and more than 50% have both LTRs. HML2 proviruses bordering to HML1, HML3, HML9 and HML10, as well as recombinant proviruses containing HML2 sequences were detected. HML2 proviruses were present in all chromosomes and showed to form clusters, particularly in chromosomes 1, 4, 8 and 19. Open reading frames (ORFs) predicted by ReTe revealed that 21 proviruses have at least 1 ORFs in gag, pro, pol and env genes, while 6 had ORFs in 3 genes. Age analysis versus reductions of ORFs and proviral length was performed. Phylogenetic analyses were performed with whole element DNA, concatenated Gag, Pro and Pol amino acid sequences, and Pol amino acid sequences.

Conclusions

In an attempt to establish a comprehensive catalog of HML2 proviruses that could set the basis for further research, we detected over 120 HML2 proviruses and performed a first characterization of them.

Authors’ Affiliations

(1)
Dept. of Life and Environmental Sciences
(2)
Center for Advanced Studies, Research and Development
(3)
Dept of Neuroscience, Physiology Unit
(4)
Dept. of Medical Sciences, Section of Virology

References

  1. Andersson ML, Lindeskog M, Medstrand P, Westley B, May F, Blomberg J: Diversity of human endogenous retroviral class II-like sequences. J Gen Virol. 1999, 80: 255-260.View ArticlePubMedGoogle Scholar
  2. Subramanian RP, Wildschutte JH, Russo C, Coffin JM: Identification, characterization and comparative genomic distribution of the HERV-K (HML2) group of endogenous retroviruses. Retrovirology. 2011, 8: 90-10.1186/1742-4690-8-90.PubMed CentralView ArticlePubMedGoogle Scholar
  3. Sperber GO, Airola T, Jern P, Blomberg J: Automated recognition of retroviral sequences in genomic data-RetroTector. Nucleic acids research. 2007, 35:Google Scholar

Copyright

© Cadeddu et al; licensee BioMed Central Ltd. 2013

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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