INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors

• Published in: Nucleic acids research Vol. 50; no. 22; p. e128
• Main Authors: Hör, Jens, Jung, Jakob, Ðurica-Mitić, Svetlana, Barquist, Lars, Vogel, Jörg
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 09-12-2022
• Subjects: Methods Online; Peptide Chain Initiation, Translational; Peptide Nucleic Acids - pharmacology; Protein Biosynthesis; Proteomics - methods; Ribosomes - genetics; Ribosomes - metabolism; RNA, Messenger - genetics; RNA, Messenger - metabolism; Transcriptome
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkac838

Ribosome profiling (Ribo-seq) is a powerful method for the transcriptome-wide assessment of protein synthesis rates and the study of translational control mechanisms. Yet, Ribo-seq also has limitations. These include difficulties with the analysis of translation-modulating molecules such as antibiotics, which are often toxic or challenging to deliver into living cells. Here, we have developed in vitro Ribo-seq (INRI-seq), a cell-free method to analyze the translational landscape of a fully customizable synthetic transcriptome. Using Escherichia coli as an example, we show how INRI-seq can be used to analyze the translation initiation sites of a transcriptome of interest. We also study the global impact of direct translation inhibition by antisense peptide nucleic acid (PNA) to analyze PNA off-target effects. Overall, INRI-seq presents a scalable, sensitive method to study translation initiation in a transcriptome-wide manner without the potentially confounding effects of extracting ribosomes from living cells.