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Genes Devoid of Full-Length Transposable Element Insertions are Involved in Development and in the Regulation of Transcription in Human and Closely Related Species

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Abstract

Transposable elements (TEs) are major components of mammalian genomes, and their impact on genome evolution is now well established. In recent years several findings have shown that they are associated with the expression level and function of genes. In this study, we analyze the relationships between human genes and full-length TE copies in terms of three factors (gene function, expression level, and selective pressure). We classified human genes according to their TE density, and found that TE-free genes are involved in important functions such as development, transcription, and the regulation of transcription, whereas TE-rich genes are involved in functions such as transport and metabolism. This trend is conserved through evolution. We show that this could be explained by a stronger selection pressure acting on both the coding and non-coding regions of TE-free genes than on those of TE-rich genes. The higher level of expression found for TE-rich genes in tumor and immune system tissues suggests that TEs play an important role in gene regulation.

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Acknowledgments

We would like to thank Christian Biémont for his comments and his critical reading of this manuscript, and Monika Ghosh for English correction.

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Authors and Affiliations

  1. Université de Lyon, F-69000, Lyon, France

    Hussein Mortada, Cristina Vieira & Emmanuelle Lerat

  2. Laboratoire de Biométrie et Biologie Evolutive, Université Claude Bernard—Lyon 1, CNRS, UMR 5558, F-69622, Villeurbanne, France

    Hussein Mortada, Cristina Vieira & Emmanuelle Lerat

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Correspondence to Emmanuelle Lerat.

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Mortada, H., Vieira, C. & Lerat, E. Genes Devoid of Full-Length Transposable Element Insertions are Involved in Development and in the Regulation of Transcription in Human and Closely Related Species. J Mol Evol 71, 180–191 (2010). https://doi.org/10.1007/s00239-010-9376-5

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