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Transposable elements contribute to activation of maize genes in response to abiotic stress

Irina Makarevitch, Amanda J. Waters, Patrick T. West, Michelle C. Stitzer, Jeffrey Ross-Ibarra, Nathan M. Springer
doi: https://doi.org/10.1101/008052
Irina Makarevitch
1Department of Biology, Hamline University, Saint Paul, MN USA
2Department of Plant Biology, University of Minnesota, Saint Paul, MN USA
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Amanda J. Waters
2Department of Plant Biology, University of Minnesota, Saint Paul, MN USA
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Patrick T. West
2Department of Plant Biology, University of Minnesota, Saint Paul, MN USA
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Michelle C. Stitzer
3Department of Plant Sciences, University of California-Davis, Davis, CA USA
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Jeffrey Ross-Ibarra
3Department of Plant Sciences, University of California-Davis, Davis, CA USA
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Nathan M. Springer
2Department of Plant Biology, University of Minnesota, Saint Paul, MN USA
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  • For correspondence: springer@umn.edu
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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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted August 15, 2014.
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Transposable elements contribute to activation of maize genes in response to abiotic stress
Irina Makarevitch, Amanda J. Waters, Patrick T. West, Michelle C. Stitzer, Jeffrey Ross-Ibarra, Nathan M. Springer
bioRxiv 008052; doi: https://doi.org/10.1101/008052
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Transposable elements contribute to activation of maize genes in response to abiotic stress
Irina Makarevitch, Amanda J. Waters, Patrick T. West, Michelle C. Stitzer, Jeffrey Ross-Ibarra, Nathan M. Springer
bioRxiv 008052; doi: https://doi.org/10.1101/008052

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