Ribo-seq

A ribosomal pseudouridine drives an oncogenic translation program

The paper shows that SNORA81-guided pseudouridylation at a specific 28S rRNA site influences selective translation and ovarian cancer cell proliferation.

Discovery of the TGCB microprotein translated from the lncRNA CHASERR

The paper identifies a microprotein, TGCB, encoded by the lncRNA CHASERR, and shows its deletion is linked to neurodevelopmental disorders.

RiboBA: a bias-aware probabilistic framework for robust ORF identification across diverse ribosome profiling protocols

RiboBA improves ncORF identification by accounting for protocol-induced biases in ribosome profiling data.

Alternative splicing expands and remodels the breast cancer proteoform landscape

The paper develops 3DisoGalaxy to study alternative splicing in breast cancer, finding that many transcripts produce translation-supported proteins and that functional divergence is concentrated in specific regions.

Sequence-intrinsic barriers define a class of translation-restricted uORFs in the human genome

The paper identifies translation-restricted uORFs in the human genome that act as sequence-intrinsic barriers to protein production, showing they are under purifying selection as cis-regulatory elements.

A revised genome annotation of the model cyanobacterium Synechocystis based on start and stop codon-enriched ribosome profiling and proteogenomics

This paper revises the genome annotation of Synechocystis using ribosome profiling and proteogenomics, identifying new genes and correcting existing annotations.

Novel 4D tensor decomposition-based approach integrating tri-omics profiling data can identify functionally relevant gene clusters

This paper introduces a 4D tensor decomposition method to integrate transcriptome, Ribo-seq, and proteome data, identifying gene clusters related to ribosome stacking and translational buffering.

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.

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.

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.

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.

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

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.

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.

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.

Protein Synthesis Profiling Enables In Vivo Capture of Ribosome-Associated mRNAs in Yeast

This paper introduces PSP, a method to identify actively translated mRNAs in yeast without ribosome isolation, and shows it captures condition-specific translational programs and expands detectable genes.

All-at-once RNA folding with 3D motif prediction framed by evolutionary information

This paper introduces CaCoFold-R3D, a method that jointly predicts RNA 3D motifs and secondary structure using evolutionary information, demonstrating its effectiveness for RNA structure prediction.

Transcriptome-wide mapping of small ribosomal subunits elucidates scanning mechanisms of translation initiation in the mammalian brain

This study uses RCP-seq to analyze translation initiation dynamics in mouse brain tissues, revealing SSU poising and uORF effects on translational efficiency.

Evolutionary remodeling of non-canonical ORF translation in mammals

The paper identifies and characterizes non-canonical ORFs in mammals, showing their evolutionary conservation and functional integration into the proteome.

Investigation of the global translational response to oxidative stress in the model archaeon Haloferax volcanii reveals untranslated small RNAs with ribosome occupancy

This study uses RNA-seq and Ribo-seq in Haloferax volcanii to identify genes and small RNAs with altered translation during oxidative stress, revealing new regulatory mechanisms.

Pervasive translation of short open reading frames and de novo gene emergence in Arabidopsis

The paper identifies de novo translated regions in Arabidopsis by analyzing ribosome profiling data and genome comparisons, showing their role in novel gene emergence.

Ischemic stroke induces staged translational remodeling in mouse cortex independent from transcriptional responses.

This study identifies staged translational remodeling in mouse cortex after ischemic stroke, showing changes in codon usage, ribosome occupancy, and frame-disruption events not captured by transcriptomics.

CRISPR-Cas9 Screening Reveals Microproteins Regulating Adipocyte Proliferation and Lipid Metabolism

This study uses CRISPR-Cas9 screening to identify microproteins regulating adipocyte proliferation and lipid metabolism in mice, revealing a novel mouse-specific microprotein involved in adipocyte differentiation.

Translation efficiency covariation across cell types is a conserved organizing principle of mammalian transcriptomes

The paper analyzes ribosome profiling data to show translation efficiency covariation (TEC) is conserved across human and mouse cells, revealing gene functions not evident from RNA or protein co-expression.

Translational landscape during Seed Germination at Sub-Codon resolution

This study uses ribosome profiling to analyze translational regulation during Arabidopsis seed germination, identifying codon usage patterns and uORFs involved in translational control.

Nuclear Receptor Transcription factors promote axon regeneration in the Adult Corticospinal Tract

This study identifies NR2F1 and NR2F6 as nuclear receptor transcription factors that promote axon regeneration in the corticospinal tract through chromatin remodeling, enhancer redeployment, and translational reprogramming.

Pan-viral ORFs discovery using Massively Parallel Ribosome Profiling

This study uses Massively Parallel Ribosome Profiling to identify thousands of viral ORFs, including non-canonical ones, and shows their impact on HLA-I peptides and protein synthesis regulation.

Sequence features and dynamics of subcellular translation revealed by APEX-Ribo-Seq

APEX-Ribo-Seq maps local translation across organelles and identifies compartment-specific transcripts, revealing sequence features and dynamics of subcellular translation.