Wang Zegang, Tang Kai, Zhang Dayong, Wan Yizhen, Wen Yan, Lu Quanyou, Wang Lei
College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China.
School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China.
PLoS One. 2017 Nov 13;12(11):e0185612. doi: 10.1371/journal.pone.0185612. eCollection 2017.
This study is the first to comprehensively characterize m6A patterns in the Arabidopsis chloroplast and mitochondria transcriptomes based on our open accessible data deposited in NCBI's Gene Expression Omnibus with GEO Series accession number of GSE72706. Over 86% of the transcripts were methylated by m6A in the two organelles. Over 550 and 350 m6A sites were mapped, with ~5.6 to ~5.8 and ~4.6 to ~4.9 m6A sites per transcript, to the chloroplast and mitochondria genome, respectively. The overall m6A methylation extent in the two organelles was greatly higher than that in the nucleus. The m6A motif sequences in the transcriptome of two organelles were similar to the nuclear motifs, suggesting that selection of the m6A motifs for RNA methylation was conserved between the nucleus and organelle transcriptomes. The m6A patterns of rRNAs and tRNAs in the organelle were similar to those in the nucleus. However, the m6A patterns in coding RNAs were distinct between the nucleus and the organelle, suggesting that that regulation of the m6A methylation patterns may be different between the nuclei and the organelles. The extensively methylated transcripts in the two organelles were mainly associated with rRNA, ribosomal proteins, photosystem reaction proteins, tRNA, NADH dehydrogenase and redox. On average, 64% and 79% of the transcripts in the two organelles showed differential m6A methylation across three organs of the leaves, flowers and roots. The m6A methylation extent in the chloroplast was higher than that in the mitochondria. This study provides deep insights into the m6A methylation topology and differentiation in the plant organelle transcriptomes.
本研究首次基于我们存入NCBI基因表达综合数据库（GEO）且GEO系列登录号为GSE72706的公开可获取数据，全面描述了拟南芥叶绿体和线粒体转录组中的m6A模式。在这两个细胞器中，超过86%的转录本被m6A甲基化。分别在叶绿体和线粒体基因组中定位到了超过550个和350个m6A位点，每个转录本约有5.6至5.8个和4.6至4.9个m6A位点。这两个细胞器中的整体m6A甲基化程度远高于细胞核中的。两个细胞器转录组中的m6A基序序列与细胞核中的基序相似，表明RNA甲基化的m6A基序选择在细胞核和细胞器转录组之间是保守的。细胞器中rRNA和tRNA的m6A模式与细胞核中的相似。然而，细胞核和细胞器中编码RNA的m6A模式不同，这表明m6A甲基化模式的调控在细胞核和细胞器之间可能存在差异。这两个细胞器中广泛甲基化的转录本主要与rRNA、核糖体蛋白、光系统反应蛋白、tRNA、NADH脱氢酶和氧化还原相关。平均而言，这两个细胞器中64%和79%的转录本在叶、花和根三个器官中表现出差异m6A甲基化。叶绿体中的m6A甲基化程度高于线粒体。本研究为植物细胞器转录组中的m6A甲基化拓扑结构和分化提供了深入见解。
