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Retroviruses integrate into a shared, non-palindromic DNA motif

Nature Microbiology volume 2, Article number: 16212 (2017) Cite this article

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Abstract

Many DNA-binding factors, such as transcription factors, form oligomeric complexes with structural symmetry that bind to palindromic DNA sequences1. Palindromic consensus nucleotide sequences are also found at the genomic integration sites of retroviruses2–6 and other transposable elements7–9, and it has been suggested that this palindromic consensus arises as a consequence of the structural symmetry in the integrase complex2,3. However, we show here that the palindromic consensus sequence is not present in individual integration sites of human T-cell lymphotropic virus type 1 (HTLV-1) and human immunodeficiency virus type 1 (HIV-1), but arises in the population average as a consequence of the existence of a non-palindromic nucleotide motif that occurs in approximately equal proportions on the plus strand and the minus strand of the host genome. We develop a generally applicable algorithm to sort the individual integration site sequences into plus-strand and minus-strand subpopulations, and use this to identify the integration site nucleotide motifs of five retroviruses of different genera: HTLV-1, HIV-1, murine leukaemia virus (MLV), avian sarcoma leucosis virus (ASLV) and prototype foamy virus (PFV). The results reveal a non-palindromic motif that is shared between these retroviruses.

Integration of a cDNA copy of the viral RNA genome is essential to establish infection by retroviruses. This process (see, for example, ref. 10 for a review) is catalysed by the virus-encoded enzyme integrase (IN) and is composed of two steps: (1) the 3′ processing reaction and (2) strand transfer. During the 3′ processing reaction, a di- or tri-nucleotide is removed from the 3′ ends of the viral long terminal repeats (LTRs) to expose the nucleophilic 3′OH groups, which consequently attack the phosphodiester backbone of the target DNA during strand transfer. Strand transfer results in single-stranded DNA gaps that are filled in and repaired by host cellular enzymes. Depending on the retrovirus, the strand transfer reaction takes place with a four (for example, murine leukaemia virus (MLV) and prototype foamy virus (PFV)), five (for example, human immunodeficiency virus type 1 (HIV-1)) or six (for example, human T-cell lymphotropic virus (HTLV-1 and 2)) base pair stagger, giving rise to a duplication of the respective number of nucleotides at the integration site.

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Figure 1: Palindromic HTLV-1 and HIV-1 target integration site consensus sequences and position probability matrices (PPMs), calculated from 4,521 HTLV-1 and 13,442 HIV-1 InS sequences.
Figure 2: Distribution of adjusted palindrome index (API) scores.
Figure 3: Summary of results from fitting the two-component mixture model by maximum likelihood.

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  • 14 July 2017

    In the PDF version of this article previously published, the year of publication provided in the footer of each page and in the 'How to cite' section was erroneously given as 2017, it should have been 2016. This error has now been corrected. The HTML version of the article was not affected.

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Acknowledgements

This work was supported by the Wellcome Trust UK (Senior Investigator Award 100291 to C.R.M.B.; Investigator Award 107005 to G.N.M.) and the MRC (project reference MC_UP_0801/1). The authors thank the following individuals for providing materials: A. Zhyvoloup and A. Fassati (Division of Infection and Immunity, University College London) and H. Niederer (Division of Infectious Diseases, Imperial College London). The authors also thank L. Game and M. Dore at the Medical Research Council Clinical Sciences Centre Genomics Laboratory at Hammersmith Hospital, London, UK.

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Authors and Affiliations

  1. MRC Biostatistics Unit, Cambridge Institute for Public Health, Cambridge, CB2 0SR, UK

    Paul D. W. Kirk

  2. Department of Life Sciences, Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London, SW7 2AZ, UK

    Maxime Huvet

  3. Division of Infectious Diseases, Section of Virology, Imperial College London, London, SW7 2AZ, UK

    Anat Melamed, Goedele N. Maertens & Charles R. M. Bangham

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  1. Paul D. W. Kirk
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Contributions

P.K. and C.B. conceived the project. A.M. and G.M. performed the experiments. P.K. and M.H. performed the statistical analysis and modelling. P.K. and C.B. co-wrote the paper.

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Correspondence to Charles R. M. Bangham.

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Kirk, P., Huvet, M., Melamed, A. et al. Retroviruses integrate into a shared, non-palindromic DNA motif. Nat Microbiol 2, 16212 (2017). https://doi.org/10.1038/nmicrobiol.2016.212

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