Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

Abstract

Transposable elements (TEs) account for a large portion of the genome in many eukaryotic species. Despite their reputation as “junk” DNA or genomic parasites deleterious for the host, TEs have complex interactions with host genes and the potential to contribute to regulatory variation in gene expression. It has been hypothesized that TEs and genes they insert near may be transcriptionally activated in response to stress conditions. The maize genome, with many different types of TEs interspersed with genes, provides an ideal system to study the genome-wide influence of TEs on gene regulation. To analyze the magnitude of the TE effect on gene expression response to environmental changes, we profiled gene and TE transcript levels in maize seedlings exposed to a number of abiotic stresses. Many genes exhibit up- or down-regulation in response to these stress conditions. The analysis of TE families inserted within upstream regions of up-regulated genes revealed that between four and nine different TE families are associated with up-regulated gene expression in each of these stress conditions, affecting up to 20% of the genes up-regulated in response to abiotic stress, and as many as 33% of genes that are only expressed in response to stress. Expression of many of these same TE families also responds to the same stress conditions. The analysis of the stress-induced transcripts and proximity of the transposon to the gene suggests that these TEs may provide local enhancer activities that stimulate stress-responsive gene expression. Our data on allelic variation for insertions of several of these TEs show strong correlation between the presence of TE insertions and stress-responsive up-regulation of gene expression. Our findings suggest that TEs provide an important source of allelic regulatory variation in gene response to abiotic stress in maize.

A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize

“…Differential AS in association with temperature stresses was examined in maize using RNA-Seq data from seedlings (Makarevitch et al, 2015). Analysis of this data identified 1,045 maize genes that exhibit differential splicing between cold treated maize tissues and controls.…”

The Role and Regulation of ABI5 (ABA-Insensitive 5) in Plant Development, Abiotic Stress Responses and Phytohormone Crosstalk

“…An increased activity of TE (Transposable Elements) was observed under unfavorable environmental conditions (McCue et al, 2012; Le et al, 2014; Makarevitch et al, 2015). Recently, the mechanism of the modulation of ABI5 expression via TE has been described.…”

Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation

“…The release of transcriptional and post-transcriptional silencing of TEs can lead to bursts of TE activity, rapidly generating new genetic diversity (Vitte et al, 2014). TEs may carry regulatory information such as promoters and transcription factor binding sites, and their mobilization may lead to the creation or expansion of gene regulatory networks (Hénaff et al, 2014; Bolger et al, 2014; Ito et al, 2011; Makarevitch et al, 2015). Furthermore, the transposase enzymes required and encoded by TEs have frequently been domesticated and repurposed as endogenous proteins, such as the DAYSLEEPER gene in Arabidopsis, derived from a hAT transposase enzyme (Bundock and Hooykaas, 2005).…”