title: 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.
authors.affiliation: Department of Biology, Hamline University, Saint Paul, Minnesota, United States of America; Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota, United States of America.
authors.forename: Irina
authors.initials: I
authors.lastname: Makarevitch
authors.affiliation: Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota, United States of America.
authors.forename: Amanda J
authors.initials: AJ
authors.lastname: Waters
authors.affiliation: Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota, United States of America.
authors.forename: Patrick T
authors.initials: PT
authors.lastname: West
authors.affiliation: Department of Plant Sciences and Center for Population Biology, University of California Davis, Davis, California, United States of America.
authors.forename: Michelle
authors.initials: M
authors.lastname: Stitzer
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota, United States of America.
authors.forename: Candice N
authors.initials: CN
authors.lastname: Hirsch
authors.affiliation: Department of Plant Sciences and Center for Population Biology, University of California Davis, Davis, California, United States of America; Genome Center, University of California Davis, Davis, California, United States of America.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Ross-Ibarra
authors.affiliation: Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota, United States of America.
authors.forename: Nathan M
authors.initials: NM
authors.lastname: Springer
mesh_terms: D004251:DNA Transposable Elements / Q000235:genetics*; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D023281:Genomics; D036226:Seedlings / Q000235:genetics; D014158:Transcription, Genetic; D003313:Zea mays / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements