微蛋白编码小开放阅读框发现的综合工作流程。

Integrated workflow for discovery of microprotein-coding small open reading frames.

机构信息

Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92617, USA.

Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92617, USA; Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92617, USA.

出版信息

STAR Protoc. 2023 Dec 15;4(4):102649. doi: 10.1016/j.xpro.2023.102649. Epub 2023 Oct 23.

DOI:10.1016/j.xpro.2023.102649

PMID:37874679

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10618807/

Abstract

Small open reading frame (smORF)-encoded microproteins, proteins containing less than 100-150 amino acids, are an emerging class of functional biomolecules. Here, we present a protocol for identifying translated smORFs in mammalian systems genome wide. We describe steps for generation of ribosome profiling (Ribo-seq) data, in silico translation of a transcriptome assembly to create an ORF database, and computational analysis of Ribo-seq to score individual smORFs for translation. Identification of translated smORFs is the first step to studying the functions of microproteins. For complete details on the use and execution of this protocol, please refer to Martinez et al..

摘要

小分子开放阅读框 (smORF) 编码的微蛋白是一种新兴的功能生物分子类别，其包含的氨基酸数量少于 100-150 个。在这里，我们提供了一个在哺乳动物系统中全面鉴定翻译小分子开放阅读框的方案。我们描述了生成核糖体谱 (Ribo-seq) 数据的步骤，通过对转录组组装进行计算机翻译来创建 ORF 数据库，以及对 Ribo-seq 进行计算分析，以对单个小分子开放阅读框的翻译进行评分。鉴定翻译小分子开放阅读框是研究微蛋白功能的第一步。有关该方案使用和执行的完整详细信息，请参考 Martinez 等人的研究。