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.

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.

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.

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.

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.

The rapid degradation of translated upstream regions points to an inefficient translation initiation process

The paper shows that upstream translations are often degraded, suggesting inefficient initiation and implications for protein annotation.

The Integration of Proteogenomics and Ribosome Profiling Circumvents Key Limitations to Increase the Coverage and Confidence of Novel Microproteins

This paper introduces RP3, a pipeline combining proteogenomics and ribosome profiling to identify microprotein-encoding smORFs missed by Ribo-Seq alone, improving detection and confidence.

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

This study introduces RiboGL, a model combining graph and recurrent neural networks to predict ribosome density from mRNA secondary structure, outperforming existing methods.

GRASPS: a simple-to-operate translatome technology reveals omics-hidden disease-associated pathways in TDP-43-related amyotrophic lateral sclerosis

GRASPS identifies more differentially expressed transcripts with higher fold changes and significance in TDP-43 ALS models, revealing previously missed disease pathways.

Small proteome of the nitrogen-fixing plant symbiont Sinorhizobium meliloti

The paper expands the known proteome of Sinorhizobium meliloti by identifying 48 novel small proteins using Ribo-seq and proteogenomics.

Genome-wide ribosome profiling uncovers the role of iron in the control of protein translation

The paper uses ribosome profiling to show how iron deficiency affects protein translation in yeast by altering gene expression and RNA-binding protein activity.

High-Throughput Translational Profiling with riboPLATE-seq

This study introduces riboPLATE-seq, a method for generating paired libraries of ribosome-associated and total mRNA, and demonstrates its use in detecting translational changes caused by kinase inhibitors.

Trans control of cardiac mRNA translation in a protein length-dependent fashion

The paper identifies a trans locus in rats that causes a protein length-dependent shift in translational efficiency, affecting cardiac hypertrophy and sarcomere protein stoichiometry.

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.

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.

A protein-RNA interaction atlas of the ribosome biogenesis factor AATF

The paper presents a comprehensive analysis of AATF's RNA interactions, revealing its role in ribosome biogenesis through binding to pre-rRNA and mRNAs of ribosome factors.

Global ribosome profiling reveals that mutant huntingtin stalls ribosomes and represses protein synthesis independent of fragile X mental retardation protein

This study shows mutant huntingtin (mHtt) stalls ribosomes and suppresses protein synthesis independently of FMRP, using ribosome profiling in HD cells and mouse models.

Retapamulin-assisted ribosome profiling reveals the alternative bacterial proteome

The paper uses retapamulin-assisted ribosome profiling to identify alternative translation start sites in E. coli, revealing new proteins and regulatory roles.

Experience-dependent translational state defined by cell type-specific ribosome profiling

The paper introduces TRiP, a method for cell type-specific ribosome profiling, and shows experience-induced changes in translation in mouse CA1 pyramidal cells.

Translational contributions to tissue-specificity in rhythmic and constitutive gene expression.

The paper investigates how translation efficiency contributes to tissue-specific rhythmic and constitutive gene expression in kidney and liver, revealing translational control mechanisms and compensation effects.

ROSE: a deep learning based framework for predicting ribosome stalling

ROSE predicts ribosome stalling from ribosome profiling data, showing better performance than conventional models and revealing regulatory factors and functional interactions.