Ribo-seq

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.

Changes in the translational landscape during red clover necrotic mosaic virus infection

This study uses ribosome profiling and RNA-seq to analyze how RCNMV infection alters translational control in Arabidopsis, identifying immune-related gene enrichment and novel viral translation features.

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.

Ribo-ITP expands the translatome of limited input samples

Ribo-ITP identifies thousands of translons from low-input samples, revealing their regulatory roles and impact on cell growth.

Evaluating Limits of Machine Learning-Assisted Raman Spectroscopy in Classification of Biological Samples

This study evaluates how experimental factors affect ML-assisted Raman spectroscopy classification accuracy, finding that data quality and spectral similarity are key limitations.

Mitochondrial translation termination, recycling, reinitiation, and rescue for in-frame and out-of-frame contexts

The paper investigates mitochondrial translation termination, recycling, and quality control mechanisms using Ribo-Seq and Disome-Seq, revealing roles of release factors and rescue mechanisms.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Dynamic Ribosomal RNA Methylation Regulates Translation in the Hematopoietic System and is Essential for Stem Cell Fitness

The paper identifies rRNA methylation dynamics as a mechanism regulating translation efficiency and HSC fitness during hematopoietic differentiation.

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.

Spatiotemporal dynamics and selectivity of mRNA translation during mouse pre-implantation development

This study investigates mRNA translation dynamics during mouse pre-implantation development, revealing novel mechanisms of translational selectivity and the role of Eif1ad3 in ribosome biogenesis.

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.

A simple, fast and cost-efficient protocol for ultra-sensitive ribosome profiling

This paper introduces a new ribosome profiling protocol that is faster, cheaper, and more sensitive, enabling use with minimal RNA input.

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.

Predicting the translation efficiency of messenger RNA in mammalian cells

The paper predicts translation efficiency (TE) of mRNA in mammalian cells using a deep learning model trained on ribosomal profiling data across multiple cell types.

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.

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.