Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
Methods Mol Biol. 2021;2298:15-27. doi: 10.1007/978-1-0716-1374-0_2.
While over 150 distinct types of chemical modifications are known to occur on various cellular RNAs and can be dynamically controlled, the function of most of these modifications remains poorly defined. Collectively, these RNA modifications have been recently termed the "epitranscriptome". Identification and annotation of individual RNA modifications throughout the transcriptome are key for studying the role of the epitranscriptome in the regulation of gene expression and for elucidating the functional relevance of particular RNA modifications in diverse physiological and disease processes. In this protocol, we demonstrate how to identify and annotate RNA modifications based on the informatic analysis of methylated RNA immunoprecipitation and sequencing (MeRIP-seq) data, using RNAmod, a convenient one-stop online interactive platform for the annotation, analysis, and visualization of mRNA modifications.
虽然已知在各种细胞 RNA 上发生了超过 150 种不同类型的化学修饰，并且这些修饰可以被动态调控，但这些修饰的大多数功能仍未被明确界定。这些 RNA 修饰共同被称为“转录后修饰组”。在转录组中识别和注释单个 RNA 修饰对于研究转录后修饰组在基因表达调控中的作用以及阐明特定 RNA 修饰在不同生理和疾病过程中的功能相关性至关重要。在本方案中，我们将展示如何基于甲基化 RNA 免疫沉淀测序 (MeRIP-seq) 数据的信息学分析，使用 RNAmod，一个方便的一站式在线交互式平台，对 mRNA 修饰进行注释、分析和可视化，来识别和注释 RNA 修饰。
