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

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.

Keywords: Genomics; Model Organisms; Molecular Biology; Plant Sciences; RNAseq.