deltaTE: detection of translationally regulated genes by integrative analysis of Ribo-seq and RNA-seq data.
Publication available at
Author(s)
Type
Journal Article
Abstract
Ribosome profiling quantifies the genome-wide ribosome occupancy of transcripts. With the integration of matched RNA sequencing data, the translation efficiency (TE) of genes can be calculated to reveal translational regulation. This layer of gene-expression regulation is otherwise difficult to assess on a global scale and generally not well understood in the context of human disease. Current statistical methods to calculate differences in TE have low accuracy, cannot accommodate complex experimental designs or confounding factors, and do not categorize genes into buffered, intensified, or exclusively translationally regulated genes. This article outlines a method [referred to as deltaTE (ΔTE), standing for change in TE] to identify translationally regulated genes, which addresses the shortcomings of previous methods. In an extensive benchmarking analysis, ΔTE outperforms all methods tested. Furthermore, applying ΔTE on data from human primary cells allows detection of substantially more translationally regulated genes, providing a clearer understanding of translational regulation in pathogenic processes. In this article, we describe protocols for data preparation, normalization, analysis, and visualization, starting from raw sequencing files. © 2019 The Authors.
Date Issued
2019-12
Online Publication Date
2022-07-27T14:09:01Z
Date Acceptance
2019-10-01
ISSN
1934-3639
Publisher
Wiley
Start Page
1
End Page
22
Journal / Book Title
Current Protocols in Molecular Biology
Volume
129
Issue
1
Copyright Statement
© 2019 The Authors.
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
License URI
Sponsor
Heart Research UK
FONDATION LEDUCQ
Identifier
https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cpmb.108
https://www.ncbi.nlm.nih.gov/pubmed/31763789
Grant Number
RG2657/17/19
16CVD03
Subjects
RNA-seq
Ribo-seq
deltaTE
translation efficiency
translational regulation
Databases, Genetic
Genome
High-Throughput Nucleotide Sequencing
Humans
Protein Biosynthesis
RNA
RNA-Seq
Ribosomes
Sequence Analysis, RNA
Software
Transcriptome
Ribosomes
Humans
RNA
Sequence Analysis, RNA
Protein Biosynthesis
Genome
Software
Databases, Genetic
High-Throughput Nucleotide Sequencing
Transcriptome
RNA-Seq
RNA-seq
Ribo-seq
deltaTE
translation efficiency
translational regulation
Databases, Genetic
Genome
High-Throughput Nucleotide Sequencing
Humans
Protein Biosynthesis
RNA
RNA-Seq
Ribosomes
Sequence Analysis, RNA
Software
Transcriptome
Biochemistry & Molecular Biology
Publication Status
Published online
Country
United States
Date Publish Online
2019-10-17