Stress Induced Activation of LTR Retrotransposons in the Drosophila melanogaster Genome

Abstract

Background: Retrotransposons with long terminal repeats (LTR retrotransposons) are widespread in all groups of eukaryotes and are often both the cause of new mutations and the source of new sequences. Apart from their high activity in generative and differentiation-stage tissues, LTR retrotransposons also become more active in response to different stressors. The precise causes of LTR retrotransposons’ activation in response to stress, however, have not yet been thoroughly investigated. Methods: We used RT-PCR to investigate the transcriptional profile of LTR retrotransposons and piRNA clusters in response to oxidative and chronic heat stresses. We used Oxford Nanopore sequencing to investigate the genomic environment of new insertions of the retrotransposons. We used bioinformatics methods to find the stress-induced transcription factor binding sites in LTR retrotransposons. Results: We studied the transposition activity and transcription level of LTR retrotransposons in response to oxidative and chronic heat stress and assessed the contribution of various factors that can affect the increase in their expression under stress conditions: the state of the piRNA-interference system, the influence of the genomic environment on individual copies, and the presence of the stress-induced transcription factor binding sites in retrotransposon sequences. Conclusions: The main reason for the activation of LTR retrotransposons under stress conditions is the presence of transcription factor binding sites in their regulatory sequences, which are triggered in response to stress and are necessary for tissue regeneration processes. Stress-induced transposable element activation can function as a trigger mechanism, triggering multiple signal pathways and resulting in a polyvariant cell response.

Structural variants contribute to phenotypic variation in maize

“…TEs often activate (i.e. express and/or mobilize) in response to stress in many eukaryotes, including maize (Makarevitch et al ., 2015; Liang et al ., 2021), Arabidopsis (Wang et al ., 2022; Sun et al ., 2020), and Drosophila melanogaster (de Oliveira et al ., 2021; Milyaeva et al ., 2023), suggesting that they may contribute to trait variation in stressful environments. However, we lack systematic studies of how TEs in general affect phenotypic variation or how TEs may contribute to genotype-by-environment interactions outside of the context of stress.…”