Mouse mammary tumor virus integration site selection in human and mouse genomes

Abstract

Based on integration site preferences, retroviruses can be placed into three groups. Viruses that comprise the first group, murine leukemia virus and foamy virus, integrate preferentially near transcription start sites. The second group, notably human immunodeficiency virus and simian immunodeficiency virus, preferentially targets transcription units. Avian sarcoma-leukosis virus (ASLV) and human T-cell leukemia virus (HTLV), forming the third group, show little preference for any genomic feature. We have previously shown that some human cells sustain mouse mammary tumor virus (MMTV) infection; therefore, we infected a susceptible human breast cell line, Hs578T, and, without introducing a species-specific bias, compared the MMTV integration profile to those of other retroviruses. Additionally, we infected a mouse cell line, NMuMG, and thus we could compare MMTV integration site selection in human and mouse cells. In total, we examined 468 unique MMTV integration sites. Irrespective of whether human or mouse cells were infected, no integration bias favoring transcription start sites was detected, a profile that is reminiscent of that of ASLV and HTLV. However, in contrast to ASLV and HTLV, not even a modest tendency in favor of integration within genes was observed. Similarly, repetitive sequences and genes that are frequently tagged by MMTV in mammary tumors were not preferentially targeted in cell culture either in mouse or in human cells; hence, we conclude that MMTV displays the most random dispersion of integration sites among retroviruses determined so far.

FIG. 1.

Frequency of retroviral integration (MMTV in human [MMTV h] and mouse [MMTV m] genomes, HTLV, ASLV, HIV, SIV, MLV, and FV) within and around transcription units, transcription start sites, and CpG islands. (A) Integration sites of the retroviruses were mapped relative to RefSeq transcription units divided into eight bins and plotted as the percentage of all integrations within each bin. (B) Integration frequencies near transcription start sites of RefSeq genes. Percentages of all integrations per kb for each interval near the transcription start sites of RefSeq genes were plotted for each virus. (C) Integration near CpG islands. Regions upstream and downstream of CpG islands were scored for the percentages of integrations per kb for each virus. The scattered line represents a mean random value calculated using the computer-generated random sites. The random value for the mouse genome is omitted.

FIG. 2.

Phylogenetic tree constructed by the neighbor-joining method based on an alignment of amino acid sequences of the integrase proteins of MMTV, HTLV, ASLV, HIV, SIV, MLV, and FV. Bootstrap values adjacent to each node represent percentages of 1,000 trees supporting the clustering. The length of duplication generated by each virus during integration and the preferential targeting of each virus are shown. The total branch lengths between the two species are proportional to the distance for each pair of species. The scale bar shows the distance.