Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome
Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome
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DOI：
10.1038/nchembio.2040
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发表时间：
2016-05-01
影响因子：
14.8
通讯作者：
Yi, Chengqi
中科院分区：
文献类型：
--
作者：
Li, Xiaoyu;Xiong, Xushen;Yi, Chengqi
N-1-甲基腺苷（m（1）A）是一种普遍存在的RNA转录后修饰，但其在mRNA中的丰度、拓扑结构和动力学尚不清楚。在这里，我们发现m（1）A在智人mRNA中普遍存在，其显示m（1）A/A比率为-0.02%。我们基于m（1）A免疫沉淀和m（1）A阻止逆转录的固有能力开发了m（1）A-ID-seq技术，作为转录组范围m（1）A谱分析的手段。m（1）A-ID-seq在mRNA和非编码RNA中鉴定了901个m（1）A峰（来自600个基因），并揭示了一个突出的特征，即在mRNA转录物的5'非翻译区富集，这与N-6-甲基腺苷的模式不同，N-6-甲基腺苷是最丰富的哺乳动物内部mRNA修饰。此外，mRNA中的m（1）A可被ALKBH 3（一种已知的DNA/RNA去甲基化酶）逆转。最后，我们发现m（1）A甲基化对刺激有动态反应，并且我们鉴定了数百个应激诱导的m（1）A位点。总的来说，我们的方法允许全面分析m（1）A修饰，并通过可逆和动态m（1）A甲基化为潜在的表观遗传调控的功能研究提供工具。
N-1-Methyladenosine (m(1)A) is a prevalent post-transcriptional RNA modification, yet little is known about its abundance, topology and dynamics in mRNA. Here, we show that m(1)A is prevalent in Homo sapiens mRNA, which shows an m(1)A/A ratio of -0.02%. We develop the m(1)A-ID-seq technique, based on m(1)A immunoprecipitation and the inherent ability of m(1)A to stall reverse transcription, as a means for transcriptome-wide m(1)A profiling. m(1)A-ID-seq identifies 901 m(1)A peaks (from 600 genes) in mRNA and noncoding RNA and reveals a prominent feature, enrichment in the 5' untranslated region of mRNA transcripts, that is distinct from the pattern for N-6-methyladenosine, the most abundant internal mammalian mRNA modification. Moreover, m(1)A in mRNA is reversible by ALKBH3, a known DNA/RNA demethylase. Lastly, we show that m(1)A methylation responds dynamically to stimuli, and we identify hundreds of stress-induced m(1)A sites. Collectively, our approaches allow comprehensive analysis of m(1)A modification and provide tools for functional studies of potential epigenetic regulation via the reversible and dynamic m(1)A methylation.