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LERAT Emmanuelle

  • BIométrie et Biologie Evolutive, CNRS - Université Lyon 1, Villeurbanne, France
  • Bioinformatics, Evolutionary genomics, Viruses and transposable elements
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Recommendation:  1

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Educational and work
PhD in Bioinformatics Major research interest in the evolution of genomes in the light of their repeat content and more particularly the transposable elements (TEs). Strong background in molecular biology, in evolution, and in bioinformatics, with a long history in the annotation and analysis of TEs in various eukaryotic genomes, especially in Drosophila.

Recommendation:  1

06 Jul 2021
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A pipeline to detect the relationship between transposable elements and adjacent genes in host genomes

Recommended by based on reviews by 2 anonymous reviewers

A new tool to cross and analyze TE and gene annotations

Transposable elements (TEs) are important components of genomes. Indeed, they are now recognized as having a major role in gene and genome evolution (Biémont 2010). In particular, several examples have shown that the presence of TEs near genes may influence their functioning, either by recruiting particular epigenetic modifications (Guio et al. 2018) or by directly providing new regulatory sequences allowing new expression patterns (Chung et al. 2007; Sundaram et al. 2014). Therefore, the study of the interaction between TEs and their host genome requires tools to easily cross-annotate both types of entities. In particular, one needs to be able to identify all TEs located in the close vicinity of genes or inside them. Such task may not always be obvious for many biologists, as it requires informatics knowledge to develop their own script codes.

In their work, Meguerdichian et al. (2021) propose a command-line pipeline that takes as input the annotations of both genes and TEs for a given genome, then detects and reports the positional relationships between each TE insertion and their closest genes. The results are processed into an R script to provide tables displaying some statistics and graphs to visualize these relationships. 

This tool has the potential to be very useful for performing preliminary analyses before studying the impact of TEs on gene functioning, especially for biologists. Indeed, it makes it possible to identify genes close to TE insertions. These identified genes could then be specifically considered in order to study in more detail the link between the presence of TEs and their functioning. For example, the identification of TEs close to genes may allow to determine their potential role on gene expression.

References

Biémont C (2010). A brief history of the status of transposable elements: from junk DNA to major players in evolution. Genetics, 186, 1085–1093. https://doi.org/10.1534/genetics.110.124180

Chung H, Bogwitz MR, McCart C, Andrianopoulos A, ffrench-Constant RH, Batterham P, Daborn PJ (2007). Cis-regulatory elements in the Accord retrotransposon result in tissue-specific expression of the Drosophila melanogaster insecticide resistance gene Cyp6g1. Genetics, 175, 1071–1077. https://doi.org/10.1534/genetics.106.066597

Guio L, Vieira C, González J (2018). Stress affects the epigenetic marks added by natural transposable element insertions in Drosophila melanogaster. Scientific Reports, 8, 12197. https://doi.org/10.1038/s41598-018-30491-w

Meguerditchian C, Ergun A, Decroocq V, Lefebvre M, Bui Q-T (2021). A pipeline to detect the relationship between transposable elements and adjacent genes in host genomes. bioRxiv, 2021.02.25.432867, ver. 4 peer-reviewed and recommended by Peer Community In Genomics. https://doi.org/10.1101/2021.02.25.432867

Sundaram V, Cheng Y, Ma Z, Li D, Xing X, Edge P, Snyder MP, Wang T (2014). Widespread contribution of transposable elements to the innovation of gene regulatory networks. Genome Research, 24, 1963–1976. https://doi.org/10.1101/gr.168872.113

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LERAT Emmanuelle

  • BIométrie et Biologie Evolutive, CNRS - Université Lyon 1, Villeurbanne, France
  • Bioinformatics, Evolutionary genomics, Viruses and transposable elements
  • recommender

Recommendation:  1

Reviews:  0

Educational and work
PhD in Bioinformatics Major research interest in the evolution of genomes in the light of their repeat content and more particularly the transposable elements (TEs). Strong background in molecular biology, in evolution, and in bioinformatics, with a long history in the annotation and analysis of TEs in various eukaryotic genomes, especially in Drosophila.