5-Methylcytosine RNA Methylation in &ITArabidopsis Thaliana&IT
5-Methylcytosine RNA Methylation in &ITArabidopsis Thaliana&IT
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DOI：
10.1016/j.molp.2017.09.013
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发表时间：
2017-11-06
期刊：
影响因子：
27.5
通讯作者：
Yu, Hao
中科院分区：
文献类型：
--
作者：
Cui, Xuean;Liang, Zhe;Yu, Hao
5-甲基胞嘧啶（m(5)C）是一种特征明显的DNA修饰，在原核生物和真核生物中也有大量的非编码rna被报道。然而，m(5)C在植物mrna中的分布和生物学功能在很大程度上仍然未知。在这里，我们通过应用m(5)C RNA免疫沉淀和深度测序方法（m(5)C- rip -seq）报道了拟南芥中RNA m(5)C的转录组全谱分析。LC-MS/MS和dot blot分析揭示了不同组织和不同发育阶段m(5)C mRNA修饰的动态模式。m(5)C- rip -seq分析鉴定出幼苗中4465个表达基因中6045个m(5)C峰。我们发现m(5)C富含编码序列，其两个峰位于开始密码子之后和停止密码子之前，并且与低翻译活性的mrna相关。我们进一步证明了RNA（胞嘧啶-5）-甲基转移酶，trna特异性甲基转移酶4B (TRM4B)，具有m(5)C RNA甲基转移酶活性。TRM4B突变表现出根系发育缺陷和m(5)C峰降低。TRM4B影响根系发育相关基因的转录水平，与这些基因的mRNA稳定性和m(5)C水平呈正相关。我们的研究结果表明，在拟南芥中，mRNA中的m(5)C是一个新的表转录组标记，并且这种修饰的调控是植物发育中基因调控网络的一个组成部分。
5-Methylcytosine (m(5)C) is a well-characterized DNA modification, and is also predominantly reported in abundant non-coding RNAs in both prokaryotes and eukaryotes. However, the distribution and biological functions of m(5)C in plant mRNAs remain largely unknown. Here, we report transcriptome-wide profiling of RNA m(5)C in Arabidopsis thaliana by applying m(5)C RNA immunoprecipitation followed by a deep-sequencing approach (m(5)C-RIP-seq). LC-MS/MS and dot blot analyses reveal a dynamic pattern of m(5)C mRNA modification in various tissues and at different developmental stages. m(5)C-RIP-seq analysis identified 6045 m(5)C peaks in 4465 expressed genes in young seedlings. We found that m(5)C is enriched in coding sequences with two peaks located immediately after start codons and before stop codons, and is associated with mRNAs with low translation activity. We further demonstrated that an RNA (cytosine-5)-methyl-transferase, tRNA-specific methyltransferase 4B (TRM4B), exhibits m(5)C RNA methyltransferase activity. Mutations in TRM4B display defects in root development and decreased m(5)C peaks. TRM4B affects the transcript levels of the genes involved in root development, which is positively correlated with their mRNA stability and m(5)C levels. Our results suggest that m(5)C in mRNA is a new epitranscriptome marker in Arabidopsis, and that regulation of this modification is an integral part of gene regulatory networks underlying plant development.