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The role of retrotransposons in gene family expansions in the human and mouse genomes

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    0461699 - ÚBO 2017 RIV GB eng J - Journal Article
    Janoušek, Václav - Laukaitis, C. M. - Yanchukov, Alexey - Karn, R. C.
    The role of retrotransposons in gene family expansions in the human and mouse genomes.
    Genome Biology and Evolution. Roč. 8, č. 9 (2016), s. 2632-2650. ISSN 1759-6653
    R&D Projects: GA MŠk EE2.3.20.0303
    Institutional support: RVO:68081766
    Keywords : gene families * transposable elements * retrotransposons * LINE * LTR * SINE
    Subject RIV: EB - Genetics ; Molecular Biology
    Impact factor: 3.979, year: 2016

    Retrotransposons comprise a large portion of mammalian genomes. They contribute to structural changes and more importantly to gene regulation. The expansion and diversification of gene families have been implicated as sources of evolutionary novelties. Given the roles retrotransposons play in genomes, their contribution to the evolution of gene families warrants further exploration. In this study we found a significant association between two major retrotransposon classes, LINEs and LTRs, and lineage-specific gene family expansions in both the human and mouse genomes. The distribution and diversity differs between LINEs and LTRs, suggesting that each has a distinct involvement in gene family expansion. LTRs are associated with open chromatin sites surrounding the gene families, supporting their involvement in gene regulation, whereas LINEs may play a structural role promoting gene duplication. Our findings also suggest that gene family expansions, especially in the mouse genome, undergo two phases. The first phase is characterized by elevated deposition of LTRs and their utilization in reshaping gene regulatory networks. The second phase is characterized by rapid gene family expansion due to continuous accumulation of LINEs and it appears that, in some instances at least, this could become a runaway process. We provide an example in which this has happened and we present a simulation supporting the possibility of the runaway process. Altogether we provide evidence of the contribution of retrotransposons to the expansion and evolution of gene families. Our findings emphasize the putative importance of these elements in diversification and adaptation in the human and mouse lineages.
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