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Nearby transposable elements impact plant stress gene regulatory networks: a meta-analysis in A. thaliana and S. lycopersicum by Jan Deneweth; Yves Van de Peer; Vanessa Vermeirssen is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

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## Abstract ## Background Transposable elements (TE) make up a large portion of many plant genomes and are playing innovative roles in genome evolution. Several TEs can contribute to gene regulation by influencing expression of nearby genes as stress-responsive regulatory motifs. To delineate TE-mediated plant stress regulatory networks, we took a 2-step computational approach consisting of identifying TEs in the proximity of stress-responsive genes, followed by searching for cis-regulatory motifs in these TE sequences and linking them to known regulatory factors. Through a systematic meta-analysis of RNA-seq expression profiles and genome annotations, we investigated the relation between the presence of TE superfamilies upstream, downstream or within introns of nearby genes and the differential expression of these genes in various stress conditions in the TE-poor Arabidopsis thaliana and the TE-rich Solanum lycopersicum. ## Results We found that stress conditions frequently expressed genes having members of various TE superfamilies in their genomic proximity, such as SINE upon proteotoxic stress and Copia and Gypsy upon heat stress in A. thaliana, and EPRV and hAT upon infection,

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Author

Jan Deneweth; Yves Van de Peer; Vanessa Vermeirssen

Publisher

Springer Science and Business Media LLC

Published

2022

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)