Ribo-seq

HRIBO - High-throughput analysis of bacterial ribosome profiling data

HRIBO is a workflow for analyzing bacterial Ribo-seq data to discover novel ORFs, using annotation-independent methods and integrating additional features for prioritization.

The translational landscape of SARS-CoV-2 and infected cells

This study uses ribosome profiling to analyze SARS-CoV-2 and host mRNA translation in infected cells, finding that viral mRNAs are not more efficiently translated than host mRNAs and highlighting unique translational strategies.

Selection of internal references for transcriptomics and RT-qPCR assays in Neurofibromatosis type 1 (NF1) related Schwann cell lines

This study identifies optimal internal reference genes for transcriptomics and RT-qPCR in NF1-related Schwann cell lines, finding that GAPDH is unstable and recommending PPIA/TBP for malignant lines and PPIA/RPLP0 for benign lines.

RiboDiPA: A novel tool for differential pattern analysis in Ribo-seq data

RiboDiPA is a tool for differential pattern analysis of Ribo-seq data, identifying genes with significant changes in ribosome occupancy patterns across conditions.

Chronic Intermittent Ethanol Activates CHOP in Striatal Microglia and Exacerbates Ethanol Withdrawal

This study investigates how chronic intermittent ethanol affects microglial translatome in striatum, identifying CHOP and UPR as key factors in ethanol withdrawal symptoms.

miRNA-mediated loss of m6A increases nascent translation in glioblastoma

The paper shows that miRNA-mediated loss of m6A increases nascent translation in glioblastoma stem cells during differentiation.

Human NMD ensues independently of stable ribosome stalling

This study challenges the prevailing model of NMD by showing that ribosome stalling at stop codons does not occur during NMD activation in vitro or in vivo.

Inferring efficiency of translation initiation and elongation from ribosome profiling

The paper develops a method to infer translation elongation kinetics from ribosome profiling data and finds ribosomal collisions occur at many sites along mRNAs in yeast.

Translation regulation of Japanese encephalitis virus revealed by ribosome profiling

This study uses ribosome profiling to identify translation regulation mechanisms in Japanese encephalitis virus, revealing frameshifting, tRNA dysregulation, and alternative initiation sites that affect viral protein synthesis and neuroinvasiveness.

Quantification of translation uncovers the functions of the alternative transcriptome

ORFquant quantifies translation at the open reading frame level using Ribo-seq, revealing alternative ORFs and gene-specific protein production differences across human cell lines.

Coordination of transcriptional and translational regulations in human cells infected by Listeria monocytogenes

This study investigates how transcriptional and translational regulations coordinate during Listeria monocytogenes infection, finding that translation inhibition specifically targets translation machinery genes.

Selective 40S footprinting reveals that scanning ribosomes remain cap-tethered in human cells

This paper introduces selective 40S footprinting to study translation initiation in human cells, revealing that scanning ribosomes remain cap-tethered and only one ribosome scans a 5UTR at a time.

The mRNA translation landscape in the synaptic neuropil.

The paper identifies and quantifies the transcriptome and translatome in neuronal cell bodies, dendrites, and axons using RNA-seq and Ribo-seq, revealing that local translation is a major source of synaptic proteins.

Nuclease-mediated depletion biases in ribosome footprint profiling libraries

The paper evaluates commercial RNA-seq depletion methods for ribosome footprint profiling and recommends custom biotinylated oligos over nuclease-based approaches due to their impact on data resolution.

Developmental regulation of Canonical and small ORF translation from mRNA

The paper improves Poly-Ribo-Seq to study small ORF translation in Drosophila embryos, revealing both productive and non-productive ribosomal binding patterns across embryonic stages.

Transcriptome and translatome changes in germinated pollen under heat stress uncover roles of transporter genes involved in pollen tube growth.

The paper uses ribosome profiling to analyze transcriptome and translatome changes in Arabidopsis pollen under heat stress, revealing heat-sensitive transporter genes and novel translational dynamics.

Repurposing Ribo-Seq to provide insights into structured RNAs

The paper shows that contaminant RNAs in bacterial Ribo-Seq data can reveal secondary structures of non-coding RNAs, enabling large-scale in vivo RNA structure analysis.

YTHDF1 drives intestinal immune response against bacterial infection

This study identifies YTHDF1 as a key regulator of intestinal immune responses against bacterial infection by modulating TRAF6 mRNA translation through m6A methylation.

Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing

The paper maps ribosomal collisions in mouse liver using disome profiling, revealing that translational pausing is widespread and associated with protein folding and evolutionary conservation.

Ribosome Profiling in Archaea Reveals Leaderless Translation, Novel Translational Initiation Sites, and Ribosome Pausing at Single Codon Resolution

This study uses ribosome profiling in Haloferax volcanii to uncover leaderless translation, novel initiation sites, and ribosome pausing, revealing complex translation mechanisms in Archaea.

Ribosome profiling at isoform level reveals an evolutionary conserved impact of differential splicing on the proteome

The paper introduces ORQAS, a pipeline for quantifying translation of transcript isoforms using ribosome profiling, and finds that differential splicing impacts translation across species.

Cellular senescence and quiescence are associated with altered ribosomal RNA methylation and processing

The paper identifies altered 2-O-methylation patterns in rRNA associated with senescence and quiescence in human fibroblasts using RiboMeth-seq.

Thousands of novel unannotated proteins expand the MHC I immunopeptidome in cancer

The paper identifies thousands of novel unannotated proteins in cancer that contribute to the MHC I immunopeptidome, expanding potential targets for immunotherapy.

XPRESSyourself: Enhancing, Standardizing, and Automating Ribosome Profiling Computational Analyses Yields Improved Insight into Data

XPRESSyourself automates and standardizes ribosome profiling analysis, improving reproducibility and enabling new insights into translation regulation.

A workbench for the translational control of gene expression

The paper introduces a statistical method to identify reproducible Ribo-seq profiles in E. coli, finding only 49 highly reproducible profiles across multiple datasets.

Stop Codon Context Influences Genome-Wide Stimulation of Termination Codon Readthrough by Aminoglycosides

The paper investigates how stop codon context affects genome-wide stop codon readthrough induced by aminoglycosides, showing that both premature and normal termination codons are affected.

Disome-seq reveals widespread ribosome collisions that recruit co-translational chaperones

The paper uses disome-seq to detect ribosome collisions during translation, revealing their role in recruiting co-translational chaperones for protein folding.

RiboFlow, RiboR and RiboPy: An ecosystem for analyzing ribosome profiling data at read length resolution

An Improved Human smORF Annnotation Workflow Combining De Novo Transcriptome Assembly and Ribo-Seq

The paper improves smORF annotation by integrating de novo transcriptome assembly and Ribo-Seq, identifying thousands of novel translated smORFs in human cell lines and highlighting their functional potential.

Improving Bacterial Ribosome Profiling Data Quality

The paper analyzes ribosome profiling data from E. coli to identify optimal parameters for improving data quality and gene annotation.