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Research article - Peer-reviewed, 2021

Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell culture

Mahboubi, Amir; Delhomme, Nicolas; Haggstrom, Sara; Hanson, Johannes;

Abstract

Background Translation is a tightly regulated process, controlling the rate of protein synthesis in cells. Ribosome sequencing (Ribo-Seq) is a recently developed tool for studying actively translated mRNA and can thus directly address translational regulation. Ribo-Seq libraries need to be sequenced to a great depth due to high contamination by rRNA and other contaminating nucleic acid fragments. Deep sequencing is expensive, and it generates large volumes of data, making data analysis complicated and time consuming. Methods and results Here we developed a platform for Ribo-Seq library construction and data analysis to enable rapid quality assessment of Ribo-Seq libraries with the help of a small-scale sequencer. Our data show that several qualitative features of a Ribo-Seq library, such as read length distribution, P-site distribution, reading frame and triplet periodicity, can be effectively evaluated using only the data generated by a benchtop sequencer with a very limited number of reads. Conclusion Our pipeline enables rapid evaluation of Ribo-Seq libraries, opening up possibilities for optimization of Ribo-Seq library construction from difficult samples, and leading to better decision making prior to more costly deep sequencing.

Keywords

Ribosomal profiling; Translation; Evaluation of sequencing library quality; Translational profiling; Ribo-Seq

Published in

Plant Methods

2021, volume: 17, number: 1, article number: 92
Publisher: BMC

Authors' information

Mahboubi, Amir
Umea University
Swedish University of Agricultural Sciences, Department of Forest Genetics and Plant Physiology
Haggstrom, Sara
Umea University
Hanson, Johannes
Umea University

UKÄ Subject classification

Bioinformatics (Computational Biology)

Publication Identifiers

DOI: https://doi.org/10.1186/s13007-021-00791-w

URI (permanent link to this page)

https://res.slu.se/id/publ/113413