Episo: quantitative estimation of RNA 5-methylcytosine at isoform level by high-throughput sequencing of RNA treated with bisulfite
Episo: quantitative estimation of RNA 5-methylcytosine at isoform level by high-throughput sequencing of RNA treated with bisulfite
复制标题
Episo：通过对经亚硫酸氢盐处理的 RNA 进行高通量测序，在异构体水平上定量估计 RNA 5-甲基胞嘧啶
DOI：
10.1093/bioinformatics/btz900
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发表时间：
2020-04-01
期刊：
影响因子：
5.8
通讯作者：
Zhang, Zhihua
中科院分区：
文献类型：
--
作者：
Liu, Junfeng;An, Ziyang;Zhang, Zhihua
动机：RNA 5-甲基胞嘧啶（m（5）C）是一种转录后修饰，可能参与许多生物学过程和肿瘤发生。RNA m（5）C可以通过亚硫酸氢盐处理的RNA的高通量测序（RNA-BisSeq）以单核苷酸分辨率进行分析。然而，由于缺乏m（5）C异构体水平的定量工具，m（5）C在转录组范围内的分布及其在剪接中的潜在功能的探索仍有待阐明。结果：我们开发了一个计算软件包，用于在转录异构体水平上定量表位转录组RNA m（5）C（命名为Episo）。Episo由三个工具组成：mapper，quant和Bisulfite fq，分别用于映射，量化和模拟RNA-BisSeq数据。Episo的高准确度使用改进的m（5）C特异性甲基化RNA免疫沉淀（meRIP）方案以及一组计算机实验进行了验证。通过将Episo应用于公开的人类和小鼠RNA-BisSeq数据，我们发现RNA m（5）C在转录异构体中的分布并不均匀，这意味着m（5）C可能在异构体水平上受到调控。
Motivation: RNA 5-methylcytosine (m(5)C) is a type of post-transcriptional modification that may be involved in numerous biological processes and tumorigenesis. RNA m(5)C can be profiled at single-nucleotide resolution by high-throughput sequencing of RNA treated with bisulfite (RNA-BisSeq). However, the exploration of transcriptome-wide profile and potential function of m(5)C in splicing remains to be elucidated due to lack of isoform level m(5)C quantification tool.Results: We developed a computational package to quantify Epitranscriptomal RNA m(5)C at the transcript isoform level (named Episo). Episo consists of three tools: mapper, quant and Bisulfitefq, for mapping, quantifying and simulating RNA-BisSeq data, respectively. The high accuracy of Episo was validated using an improved m(5)C-specific methylated RNA immunoprecipitation (meRIP) protocol, as well as a set of in silico experiments. By applying Episo to public human and mouse RNA-BisSeq data, we found that the RNA m(5)C is not evenly distributed among the transcript isoforms, implying the m(5)C may subject to be regulated at isoform level.