Mapping the non-standardized biases of ribosome profiling

Bartholomäus, Alexander
Del Campo, Cristian
Ignatova, Zoya

¹Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, D-20146 Hamburg, Germany

Corresponding author: Zoya Ignatova, Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, D-20146 Hamburg, Germany, e-mail: [email protected]

Received June 20, 2015; accepted August 25, 2015; previously published online January August 29, 2015

Biological Chemistry 397(1):p 23-35, January 1, 2016. | DOI: 10.1515/hsz-2015-0197

Abstract:

Ribosome profiling is a new emerging technology that uses massively parallel amplification of ribosome-protected fragments and next-generation sequencing to monitor translation in vivo with codon resolution. Studies using this approach provide insightful views on the regulation of translation on a global cell-wide level. In this review, we compare different experimental set-ups and current protocols for sequencing data analysis. Specifically, we review the pitfalls at some experimental steps and highlight the importance of standardized protocol for sample preparation and data processing pipeline, at least for mapping and normalization.