使用 Ribo-seq 技术测量拟南芥组织中 mRNA 转录本上核糖体密度的方案。

Protocol to measure ribosome density along mRNA transcripts of Arabidopsis thaliana tissues using Ribo-seq.

机构信息

Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan.

Institute of Plant and Microbial Biology, Genomic Technology Core, Academia Sinica, Taipei 11529, Taiwan.

出版信息

STAR Protoc. 2023 Sep 15;4(3):102520. doi: 10.1016/j.xpro.2023.102520. Epub 2023 Aug 18.

DOI:10.1016/j.xpro.2023.102520

PMID:37597190

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10469065/

Abstract

Ribosome profiling (Ribo-seq) measures ribosome density along messenger RNA (mRNA) transcripts and is used to estimate the "translational fitness" of a given mRNA in response to environmental or developmental cues with high resolution. Here, we describe a protocol for Ribo-seq in plants adapted for the model plant Arabidopsis thaliana. We describe steps for lysis and nucleolytic digestion and ribosome footprinting. We then detail library construction, sequencing, and data analysis.

摘要

核糖体图谱（Ribo-seq）沿信使 RNA（mRNA）转录本测量核糖体密度，并用于以高分辨率估计给定 mRNA 对环境或发育信号的“翻译适应性”。在这里，我们为拟南芥等模式植物描述了一种适合植物的 Ribo-seq 方案。我们描述了裂解和核酶消化以及核糖体足迹分析的步骤。然后，我们详细介绍了文库构建、测序和数据分析。