Mapping the non-standardized biases of ribosome profiling

Biological Chemistry
Alexander BartholomäusZoya Ignatova

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.

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Citations

Sep 18, 2016·Nucleic Acids Research·Maxim V Gerashchenko, Vadim N Gladyshev
Oct 30, 2016·RNA Biology·Luis Enrique Cabrera-QuioAndrea Pauli
Dec 8, 2016·Nucleic Acids Research·Dmitry E AndreevIvan N Shatsky
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Jun 1, 2021·NAR Genomics and Bioinformatics·Katarzyna ChyżyńskaEivind Valen
Jun 15, 2021·Nucleic Acids Research·Alexander BartholomäusZoya Ignatova

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Methods Mentioned

BETA
RNA-Seq
PCR
footprinting
RNAseq

Software Mentioned

Maq
baySeq
RefSeq
TopHat
DESeq
EdgeR
Bowtie
ensembl

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