Abstract
BackgroundTransposable 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.ResultsWe 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, and Harbinger, LINE and Retrotransposon upon light stress in S. lycopersicum. These stress-specific gene-proximal TEs were mostly located within introns and more detected near upregulated than downregulated genes. Similar stress conditions were often related to the same TE superfamily. Additionally, we detected both novel and known motifs in the sequences of those TEs pointing to regulatory cooption of these TEs upon stress. Next, we constructed the regulatory network of TFs that act through binding these TEs to their target genes upon stress and discovered TE-mediated regulons targeted by TFs such as BRB/BPC, HD, HSF, GATA, NAC, DREB/CBF and MYB factors in Arabidopsis and AP2/ERF/B3, NAC, NF-Y, MYB, CXC and HD factors in tomato.ConclusionsOverall, we map TE-mediated plant stress regulatory networks using numerous stress expression profile studies for two contrasting plant species to study the regulatory role TEs play in the response to stress. As TE-mediated gene regulation allows plants to adapt more rapidly to new environmental conditions, this study contributes to the future development of climate-resilient plants.
Highlights
Transposable elements (TE) make up a large portion of many plant genomes and are playing innovative roles in genome evolution
We focused on gene-proximal TEs that are implicated in differential gene regulation upon stress and their contribution to regulatory motifs that are bound by stress-responsive transcription factor (TF)
Positioning of TEs relative to genes in A. thaliana and S. lycopersicum Inspired by the work of Makarevitch for maize abiotic stress and Jouffroy for tomato ripening [8, 27], we aimed to investigate genome-wide the association of TE families with stress-responsive expression of nearby genes in various stress conditions in Arabidopsis and tomato
Summary
Transposable elements (TE) make up a large portion of many plant genomes and are playing innovative roles in genome evolution. Transposable elements (TEs) form the major part of ‘junk DNA’ in all eukaryotic genomes. Transposable elements of class II, known as DNA transposons, replicate by a ‘cut and paste’ mechanism in the case of Terminal Inverted Repeats (TIR), or rolling circle in the case of Helitrons. Many of them contain Miniature Inverted-repeat Transposable Elements (MITEs), which are small non-autonomous TIRs that are present in high copies in genomes. Both classes of TEs can have autonomous and non-autonomous elements, where autonomous TEs encode all necessary products required for transposition [1, 5]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
