A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package.
A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package.
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使用 MeRIP-Seq 数据和 exomePeak R/Bioconductor Package 进行 RNA 甲基化差异分析的方案
DOI：
10.1016/j.ymeth.2014.06.008
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发表时间：
2014-10-01
期刊：
影响因子：
4.8
通讯作者：
Huang, Yufei
中科院分区：
文献类型：
--
作者：
Meng, Jia;Lu, Zhiliang;Liu, Hui;Zhang, Lin;Zhang, Shaowu;Chen, Yidong;Rao, Manjeet K.;Huang, Yufei
尽管对DNA/染色质相关表观遗传学（如组蛋白修饰和DNA甲基化）的研究非常普遍，但RNA表观遗传学并没有引起足够的重视，直到一种新的基于亲和的测序方法MeRIP-Seq被开发出来并应用于研究哺乳动物细胞中mRNA n6 -甲基腺苷（m6A）。作为ChIP-Seq和RNA- seq的结合，MeRIP-Seq具有研究各种转录后RNA修饰的转录组分布的潜力。我们之前开发了R/Bioconductor软件包exomePeak，用于在特定实验条件下检测RNA甲基化位点，或从MeRIP-Seq数据中识别病例对照研究中的差异RNA甲基化位点。与ChIP-Seq和RNA-Seq等其他研究相对较好的数据类型相比，MeRIP-Seq数据的研究还处于非常早期的阶段，现有的协议没有优化处理MeRIP-Seq数据的内在特征。我们在这里提供了一个详细和易于使用的协议，使用exomePeak R/Bioconductor软件包以及其他软件程序来分析MeRIP-Seq数据，包括原始reads比对，RNA甲基化位点检测，motif发现，差异RNA甲基化分析和功能分析。特别是，简要讨论了每个处理步骤背后的基本原理以及所使用的特定方法、最佳实践和可能的替代策略。
Despite the prevalent studies of DNA/Chromatin related epigenetics, such as, histone modifications and DNA methylation, RNA epigenetics has not drawn deserved attention until a new affinity-based sequencing approach MeRIP-Seq was developed and applied to survey the global mRNA N6-methyladenosine (m6A) in mammalian cells. As a marriage of ChIP-Seq and RNA-Seq, MeRIP-Seq has the potential to study the transcriptome-wide distribution of various post-transcriptional RNA modifications. We have previously developed an R/Bioconductor package ‘exomePeak’ for detecting RNA methylation sites under a specific experimental condition or the identifying the differential RNA methylation sites in a case control study from MeRIP-Seq data. Compared with other relatively well studied data types such as ChIP-Seq and RNA-Seq, the study of MeRIP-Seq data is still at very early stage, and existing protocols are not optimized for dealing with the intrinsic characteristic of MeRIP-Seq data. We therein provide here a detailed and easy-to-use protocol of using exomePeak R/Bioconductor package along with other software programs for analysis of MeRIP-Seq data, which covers raw reads alignment, RNA methylation site detection, motif discovery, differential RNA methylation analysis, and functional analysis. Particularly, the rationales behind each processing step as well as the specific method used, the best practice, and possible alternative strategies are briefly discussed.
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