Decoding the epitranscriptional landscape from native RNA sequences.
Decoding the epitranscriptional landscape from native RNA sequences.
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从天然RNA序列解读表观转录组图谱
DOI：
10.1093/nar/gkaa620
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发表时间：
2021-01-25
影响因子：
14.9
通讯作者：
Nookaew I
中科院分区：
文献类型：
--
作者：
Jenjaroenpun P;Wongsurawat T;Wadley TD;Wassenaar TM;Liu J;Dai Q;Wanchai V;Akel NS;Jamshidi-Parsian A;Franco AT;Boysen G;Jennings ML;Ussery DW;He C;Nookaew I
传统的表观转录组学依赖于通过抗体或化学处理来捕获单一的RNA修饰，并结合短读长测序来确定其在转录组中的位置。这种方法劳动强度大，可能会引入实验假象。使用牛津纳米孔技术（ONT）对天然RNA进行直接测序可以直接检测RNA碱基修饰，尽管这些修饰可能表现为测序错误。天然RNA的特定碱基错误百分比（%ESB）比未修饰的RNA高，这使得核糖核苷酸修饰位点的检测成为可能。基于%ESB的差异，我们开发了一种生物信息学工具，即从ONT信号故障推断表观转录图谱（ELIGOS），它基于各种类型的合成修饰RNA，并应用于rRNA和mRNA。ELIGOS能够使用未修饰的体外转录RNA或模拟直接RNA测序系统误差的背景误差模型作为参考，准确预测大肠杆菌、酵母和人类细胞的rRNA中已知类别的RNA甲基化位点（曲线下面积>0.93）。通过对ELIGOS进行差异分析，比较酵母和小鼠细胞中的野生型和敲除型，研究RNA m6A甲基转移酶的影响，定位并识别了众所周知的DRACH/RRACH基序，这与先前的研究一致。最后，在三个人类细胞系的mRNA中也可以识别出DRACH基序。ELIGOS鉴定的mRNA修饰达到了单个碱基分辨率的水平。总之，我们开发了一个生物信息学软件包来揭示天然RNA修饰。
Traditional epitranscriptomics relies on capturing a single RNA modification by antibody or chemical treatment, combined with short-read sequencing to identify its transcriptomic location. This approach is labor-intensive and may introduce experimental artifacts. Direct sequencing of native RNA using Oxford Nanopore Technologies (ONT) can allow for directly detecting the RNA base modifications, although these modifications might appear as sequencing errors. The percent Error of Specific Bases (%ESB) was higher for native RNA than unmodified RNA, which enabled the detection of ribonucleotide modification sites. Based on the %ESB differences, we developed a bioinformatic tool, epitranscriptional landscape inferring from glitches of ONT signals (ELIGOS), that is based on various types of synthetic modified RNA and applied to rRNA and mRNA. ELIGOS is able to accurately predict known classes of RNA methylation sites (AUC > 0.93) in rRNAs from Escherichiacoli, yeast, and human cells, using either unmodified in vitro transcription RNA or a background error model, which mimics the systematic error of direct RNA sequencing as the reference. The well-known DRACH/RRACH motif was localized and identified, consistent with previous studies, using differential analysis of ELIGOS to study the impact of RNA m6A methyltransferase by comparing wild type and knockouts in yeast and mouse cells. Lastly, the DRACH motif could also be identified in the mRNA of three human cell lines. The mRNA modification identified by ELIGOS is at the level of individual base resolution. In summary, we have developed a bioinformatic software package to uncover native RNA modifications.
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影响因子：
48
作者：
Linder, Bastian;Grozhik, Anya V.;Olarerin-George, Anthony O.;Meydan, Cem;Mason, Christopher E.;Jaffrey, Samie R.
通讯作者：
Jaffrey, Samie R.
影响因子：
14.9
作者：
Hansen KD;Brenner SE;Dudoit S
通讯作者：
Dudoit S
影响因子：
48
作者：
Flusberg, Benjamin A.;Webster, Dale R.;Lee, Jessica H.;Travers, Kevin J.;Olivares, Eric C.;Clark, Tyson A.;Korlach, Jonas;Turner, Stephen W.
通讯作者：
Turner, Stephen W.
影响因子：
10.5
作者：
Ke S;Alemu EA;Mertens C;Gantman EC;Fak JJ;Mele A;Haripal B;Zucker-Scharff I;Moore MJ;Park CY;Vågbø CB;Kusśnierczyk A;Klungland A;Darnell JE Jr;Darnell RB
通讯作者：
Darnell RB
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng