Ribo-seq

Profiling of terminating ribosomes reveals translational control at stop codons

The paper profiles terminating ribosomes to show sequence-dependent pausing at stop codons and its impact on translation fidelity and protein diversity.

Virus-driven tRNA competition universally represses host genes with similar codon usage

The paper shows viral infection represses host genes with codon usage similar to viruses, supporting multiple hypotheses about tRNA competition during infection.

Activity-dependent synthesis of translational machinery through dynamic remodeling of ribonucleoprotein granules

The paper uses optogenetic stimulation and Ribo-seq in Drosophila to show that neuronal activity triggers two phases of translation: one for synaptic factors and another for ribosomal proteins, regulated by TOP motifs and La-related protein.

seq2ribo: Structure-aware integration of machine learning and simulation to predict ribosome location profiles from RNA sequences

seq2ribo predicts ribosome location profiles from RNA sequences using a hybrid simulation and machine learning approach, achieving high correlation with experimental data.

Label-Free Live Cell Type Prediction by Integrating Raman Spectroscopy and Machine Learning

This paper uses Raman spectroscopy and machine learning to classify brain tumor cell types at single-cell resolution, achieving high accuracy in distinguishing IDH1 mutation status and histological subtypes.

Developmental and transcriptional programs that define the initiation of the forelimb

The paper identifies four stages of forelimb initiation in mouse embryos using scRNA-seq and other sequencing methods, revealing TBX5-target genes involved in limb development.

Decoding universal principles of codon-mediated regulation of gene expression

The paper develops a regression-based model to predict mRNA and protein abundance using codon weights derived from transcriptomic data, validated across multiple species.

Cytosolic and ER-associated ribosomes share rRNA 2'-O-methylation landscapes across human cell types

The paper compares 2'-O-methylation patterns of cytosolic and ER-associated ribosomes across human cell types and finds minimal compartment-specific differences.

Translatome and translation dynamics analysis of a RiboCancer cell line panel reveals that leukemia-associated Rps15 mutations rewire translation through codon-specific tRNA accommodation defects.

The paper analyzes translatome and translation dynamics in RiboCancer cell lines to show that Rps15 mutations disrupt tRNA accommodation, affecting translation efficiency and transcriptional regulation in CLL.

Ribo-seq reveals IsrR-mediated translational repression of SAOUHSC_02924 (gabT) during iron limitation in Staphylococcus aureus

The paper uses Ribo-seq to show IsrR represses gabT translation during iron limitation in S. aureus, preventing TCA cycle precursor accumulation and metabolic imbalance.

In vivo single-cell ribosome profiling reveals cell-type-specific translational programs during aging

The paper uses in vivo single-cell ribosome profiling to study translational changes in mouse epidermal stem cells during aging, finding cell-type-specific translational reprogramming in aged stem cells.

Identification of a large class of cancer-germline microproteins as a source of immunotherapeutic targets

The paper identifies a large class of non-canonical cancer-germline antigens (ncCGAs) from lncRNAs and mRNA untranslated regions, showing their potential as immunotherapeutic targets.

Ribosome profiling to study translation in cortical synaptoneurosomes on group 1 mGluR activation

The paper uses ribosome profiling to study translation changes in synaptoneurosomes from rat cortical tissue after group 1 mGluR activation, showing increased translation of synaptic and ribosomal protein mRNAs.

RiboPipe: efficient per-transcript codon-resolution ribo-seq coverage imputation for low-coverage transcripts

RiboPipe imputes codon-resolution Ribo-seq coverage for low-coverage transcripts using a unified framework that improves accuracy and efficiency.

Suppression of upstream ORF translation is not a widespread mechanism of translational stimulation by yeast helicase Ded1

The paper shows that Ded1 in yeast primarily stimulates translation by unwinding 5' UTR structures, not by suppressing upstream ORF translation.

Ribosome profiling reveals widespread translational control across developmental stages in the brown alga Ectocarpus

The paper uses ribosome profiling to analyze translational regulation in Ectocarpus across developmental stages, finding widespread stage- and sex-specific control and post-transcriptional buffering.

5-Azacytidine incorporation into mRNAs disrupts translation and induces ribosome collisions

This study shows 5-AzaC incorporation into mRNAs disrupts translation, causes ribosome collisions, and activates stress responses, contributing to its cytotoxicity beyond DNA hypomethylation.

The use of Benzonase to produce ribosome footprints simplifies translational levels quantification by Ribo-seq

This paper introduces using Benzonase to generate ribosome footprints for Ribo-seq, simplifying the protocol and reducing time, cost, and bias.

Data-driven design of LNA-blockers for efficient contaminant removal in Ribo-seq libraries

The paper presents a computational workflow to design LNA-blockers for removing contaminants from Ribo-seq libraries, improving sequencing yield and reducing costs.

Evolutionary emergence and preservation of microproteins encoded by upstream ORFs

The paper identifies conserved microproteins from upstream ORFs in yeast using Ribo-Seq and Nanopore data, showing they are subject to purifying selection.

Translational buffering tunes gene expression in mice and humans

The paper analyzes translational buffering across human and mouse datasets, finding conserved patterns and highlighting the role of cellular context in gene expression regulation.

Integrative multiomics analysis and CRISPR screening identify functional noncanonical translation loci in the mouse immune system.

Ribosome profiling reveals extensive translational alterations in steatohepatitis-associated hepatocellular carcinoma

This study uses ribosome profiling to show that steatohepatitis-associated HCC has extensive translational alterations affecting hundreds of genes and revealing novel translated regions.

Translational regulation of GAD1 identified by circadian and light-responsive ribosome-bound transcriptome analysis in the mouse hypothalamic suprachiasmatic nucleus

The paper identifies translational regulation of GAD1 in the mouse SCN using Ribo-seq and RNA-seq, showing light-induced ribosome binding without mRNA changes.

Ribosome profiling reveals distinct translational programs underlying Arabidopsis seed dormancy and germination

This study uses ribosome profiling to show that translational regulation, including ribosome positioning and uORF activity, controls Arabidopsis seed dormancy and germination.

Translational Downregulation of 5' TOP mRNAs During T Cell Exhaustion

The paper identifies translational repression of 5' TOP mRNAs in exhausted human CD8+ T cells despite elevated mTOR activity.

eIF3d and eIF3e mediate selective translational control of hypoxia that can be inhibited by novel small molecules

The paper identifies eIF3d and eIF3e as mediators of hypoxia-induced translational control and shows that small molecules can inhibit this process.

The impact of common variants on gene expression in the human brain: from RNA to protein to schizophrenia risk

The paper identifies eQTLs, rQTLs, and pQTLs in the human brain and shows that many eQTL effects are attenuated post-transcriptionally, yet still correlate with schizophrenia GWAS signals.

Conditional Deep Learning Model Reveals Translation Elongation Determinants during Amino Acid Deprivation

The paper introduces Riboclette, a conditional deep learning model that predicts ribosome footprints under amino acid deprivation and identifies key codons and motifs driving translation stalling.

Axon-specific mRNA translation shapes dopaminergic circuit development

The paper identifies axon-specific mRNA translation in dopaminergic neurons and shows how it regulates axon development and connectivity.