Transposable elements contribute to activation of maize genes in response to abiotic stress
By I. Makarevitch, Amanda J. Waters, P. T. West, Michelle C. Stitzer, J. Ross-Ibarra, Nathan M. Springer. bioRxiv, 2014
340 citations recorded by the source corpus.
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.
Subfields: Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/92e4578f88a55bafbe25611409891430eb4e5acf
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Citations in the corpus
- Genetics and genomics of moso bamboo (Phyllostachys edulis): Current status, future challenges, and biotechnological opportunities toward a sustainable bamboo industry (2020, background): “Recent advancements in molecular diagnostics recruit TEs as tools for studying genome-level variation, evolution, gene tagging, and targeted gene silencing, which overall can facilitate crop improvement (Cho, 2018; Joly-Lopez et al., 2017; Makarevitch et al., 2015).”
- LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons1[OPEN] (2017, background): “…shaped genome landscapes, such as genome organization (Ammiraju et al., 2007, 2010) and epigenetic status of the insertion sites (Fedoroff, 2012), thereby affecting the expression of adjacent genes (Hollister and Gaut, 2009; Hollister et al., 2011; Vonholdt et al., 2012; Makarevitch et al., 2015).”