Genome-wide profiling of stored mRNA in Arabidopsis thaliana seed germination:: epigenetic and genetic regulation of transcription in seed
Genome-wide profiling of stored mRNA in Arabidopsis thaliana seed germination:: epigenetic and genetic regulation of transcription in seed
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DOI：
10.1111/j.1365-313x.2005.02337.x
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发表时间：
2005-03-01
期刊：
影响因子：
7.2
通讯作者：
Nambara, E
中科院分区：
文献类型：
--
作者：
Nakabayashi, K;Okamoto, M;Nambara, E
为了揭示拟南芥种子的转录组，使用ATH1基因芯片（Affyellow，Santa Clara，CA，USA）进行全面的表达分析。在干种子中，检测到超过12 000种储存的mRNA种类，包括所有本体分类。统计分析表明，野生型干种子中高表达基因的启动子过度表达脱落酸响应元件（ABRE），含有核心基序ACGT。虽然偶联元件和种子特异性增强子RY基序单独在高表达基因中没有显著的过度表达，但这些元件与ABRE组合的存在与特别高的基因表达相关。即使在种子吸胀后6 h，吸胀种子的转录组也不同于干种子的转录组。吸胀后，许多上调和下调的基因在三到五个基因的簇中共调节。表达受abi5突变影响的基因倾向于位于簇中，这表明ABI5的反式激活不限于单个基因，而是影响其他邻近基因。此外，胞嘧啶甲基化不仅在着丝粒区域的大型沉默反转录转座子簇中观察到，而且在种子中的非着丝粒沉默基因簇中也观察到。这些结果表明，这些地区可能是转录沉默甲基化或异染色质结构。我们的分析表明，拟南芥种子转录组的特点是由多种调控机制：表观遗传染色质结构，染色体位置（如共调控基因簇）和顺式作用元件。
To reveal the transcriptomes of Arabidopsis seed, comprehensive expression analysis was performed using ATH1 GeneChips (Affymetrix, Santa Clara, CA, USA). In the dry seed, more than 12 000 stored mRNA species were detected, including all ontological categories. Statistical analysis revealed that promoters of highly expressed genes in wild-type dry seeds overrepresented abscisic acid-responsive elements (ABREs) containing the core motif ACGT. Although the coupling element and seed-specific enhancer RY motif alone were not prominently overrepresented in genes with high expression, the presence of these elements in combination with ABRE was associated with particularly high gene expression. The transcriptome of the imbibed seeds differed from that of the dry seed even at 6 h after seed imbibition. After imbibition many upregulated and downregulated genes were co-regulated in clusters of three to five genes. Genes for which expression was affected by the abi5 mutation tended to be located in clusters, suggesting that transactivation by ABI5 is not restricted to a single gene, but affects other proximal genes. Furthermore, cytosine methylation was observed not only in large silent retrotransposon clusters in centromeric regions, but also in non-centromeric silent gene clusters in the seed. These results suggest that such regions might be transcriptionally silenced by methylation or heterochromatin structures. Our analyses reveal that transcriptomes of Arabidopsis seed are characterized by multiple regulatory mechanisms: epigenetic chromatin structures, chromosomal locations (e.g. co-regulated gene clusters) and cis-acting elements.