Stress-induced and epigenetic-mediated maize transcriptome regulation study by means of transcriptome reannotation and differential expression analysis.
Stress-induced and epigenetic-mediated maize transcriptome regulation study by means of transcriptome reannotation and differential expression analysis.
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DOI：
10.1038/srep30446
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发表时间：
2016-07-27
影响因子：
4.6
通讯作者：
Varotto S
中科院分区：
文献类型：
--
作者：
Forestan C;Aiese Cigliano R;Farinati S;Lunardon A;Sanseverino W;Varotto S
植物对非生物胁迫的反应和适应涉及复杂的遗传和表观遗传调控系统。为了全面了解对渗透胁迫（包括基因组非编码部分）的分子反应，我们对遭受长期干旱和盐胁迫的玉米植物进行了全叶转录组分析。对 B73 野生型和表观调节因子突变体 rpd1-1/rmr6 施加压力，可以剖析压力反应的表观遗传成分。将总 RNA 测序和转录组重新组装结合起来，我们注释了数千个新的玉米转录本，以及可能在调节基因表达中发挥关键作用的 13,387 个 lncRNA。差异表达分析揭示了数百个受长期应激施加调节的基因，包括许多由应激特异性诱导的lncRNA和转座子。 B73 和 rpd1-1/rmr6 突变体植物之间的胁迫调节基因组的幅度和动态非常不同，这是由于突变本身对基因组调控产生了类胁迫效应，即使在对照条件下，也会激活许多胁迫相关基因。分析的大量总RNA-Seq数据，加上转录组的改进和转录组非编码部分的鉴定，揭示了玉米分子对非生物胁迫反应的遗传和表观遗传机制。
Plant’s response and adaptation to abiotic stresses involve sophisticated genetic and epigenetic regulatory systems. To obtain a global view of molecular response to osmotic stresses, including the non-coding portion of genome, we conducted a total leaf transcriptome analysis on maize plants subjected to prolonged drought and salt stresses. Stress application to both B73 wild type and the epiregulator mutant rpd1-1/rmr6 allowed dissection of the epigenetic component of stress response. Coupling total RNA-Seq and transcriptome re-assembly we annotated thousands of new maize transcripts, together with 13,387 lncRNAs that may play critical roles in regulating gene expression. Differential expression analysis revealed hundreds of genes modulated by long-term stress application, including also many lncRNAs and transposons specifically induced by stresses. The amplitude and dynamic of the stress-modulated gene sets are very different between B73 and rpd1-1/rmr6 mutant plants, as result of stress-like effect on genome regulation caused by the mutation itself, which activates many stress-related genes even in control condition. The analyzed extensive set of total RNA-Seq data, together with the improvement of the transcriptome and the identification of the non-coding portion of the transcriptome give a revealing insight into the genetic and epigenetic mechanism responsible for maize molecular response to abiotic stresses.