Research

Biomedical Genomics of Transposable Elements

‣ TEs are a heterogeneous crowd of repeated DNA sequences ubiquitous in eukaryotes, amounting to millions of copies in the human genome. Their mobilization is a major source of structural variation linked to numerous pathologies such as genetic diseases, cancer, neurodegeneration, and aging. In addition, TE “jumps” spread their embedded regulatory sequences throughout the genomes, eventually rewiring the hosts’ genetic programs. 

‣ In spite of occupying 50% of the human genome and causing a new insertion every 50th births on average, the repeatome remains largely overlooked – if not excluded – in most genomic analyses. The technical challenges raised by repetitive DNA (genome assembly fragmentation, multiple mapping) are more often avoided than tackled, in spite of TEs’ evolutionary relevance.

‣ Taking advantage of both molecular biology and bioinformatics, my research directly investigates the contribution of TEs to regulatory variation. By implementing and promoting original methods in genomics, I am particularly interested in answering how much, and through which mechanisms TEs influence modern human health.

You can read more about the role of segregating TE in human population on this blog post

Highlights

2020 - Goubert, C., Zevallos, N. A., & Feschotte, C. Contribution of unfixed transposable element insertions to human regulatory variation. Philosophical Transactions of the Royal Society B: Biological Sciences, 375(1795). https://doi.org/10.1098/rstb.2019.0331

 

2020 - Goubert, C., Thomas, J., Payer, L. M., Kidd, J. M., Feusier, J., Watkins, W. S., Burns, K. H., Jorde, L. B., & Feschotte, C. (2020). TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data. Nucleic Acids Research, 48(6), e36–e36. https://doi.org/10.1093/nar/gkaa074

2020 - Watkins, W. S., Feusier, J. E., Thomas, J., Goubert, C., Mallick, S., Jorde, L. B., & Schaack, S. The Simons Genome Diversity Project: A Global Analysis of Mobile Element Diversity. Genome Biology and Evolution, 12(6), 779–794. https://doi.org/10.1093/gbe/evaa086

2017 - Feusier, J., Witherspoon, D. J., Scott Watkins, W., Goubert, C., Sasani, T. A., & Jorde, L. B.  Discovery of rare, diagnostic AluYb8/9 elements in diverse human populations. Mobile DNA, 8(1), 9. https://doi.org/10.1186/s13100-017-0093-0