Transposable elements contribute to activation of maize genes in response to abiotic stress
Transposable elements contribute to activation of maize genes in response to abiotic stress
复制标题
DOI：
10.1101/008052
复制
发表时间：
2014-08
期刊：
影响因子：
--
通讯作者：
I. Makarevitch;Amanda J. Waters;P. T. West;Michelle C. Stitzer;J. Ross-Ibarra;Nathan M. Springer
中科院分区：
文献类型：
--
作者：
I. Makarevitch;Amanda J. Waters;P. T. West;Michelle C. Stitzer;J. Ross-Ibarra;Nathan M. Springer
转座因子（Transposable elements，TE）在许多真核生物中占基因组的很大一部分。尽管它们被认为是对宿主有害的“垃圾”DNA或基因组寄生虫，但TE与宿主基因具有复杂的相互作用，并有可能促进基因表达的调控变异。据推测，TE和它们附近插入的基因可能在应激条件下被转录激活。玉米基因组中散布着许多不同类型的TE，为研究TE对基因调控的全基因组影响提供了理想的系统。为了分析TE对基因表达响应环境变化的影响程度，我们分析了暴露于一些非生物胁迫的玉米幼苗中的基因和TE转录水平。许多基因在这些应激条件下表现出上调或下调。插入上游区域内的上调基因的TE家族的分析显示，在这些压力条件下的每一个中，四个和九个不同的TE家族与上调基因表达相关，影响高达20%的基因上调响应于非生物胁迫和多达33%的基因，仅在响应于胁迫表达。许多这些相同的TE家族的表达也响应于相同的胁迫条件。应激诱导的转录本和转座子与基因的接近度的分析表明，这些TE可以提供刺激应激响应基因表达的局部增强子活性。我们的数据显示，这些TE插入的等位基因变异的存在下，TE插入和应激反应的基因表达上调之间的强相关性。我们的研究结果表明，TE提供了一个重要的来源，等位基因调控变异的基因响应非生物胁迫玉米。
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.