Ribo-seq

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.

Transcript-wide m6A methylation defines the efficiency of the cap-independent translation initiation

The paper investigates how global m6A methylation levels affect cap-independent translation efficiency, showing that total m6A levels, not specific localization, determine this process.

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.

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.

Empowering multiplexed ultra-throughout ribosome profiling with RiboWich

RiboWich improves ribosome profiling by eliminating ribosome purification and enabling high-throughput, low-input translatome analysis.

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.

DOTSeq enables genome-wide detection of differential ORF usage

DOTSeq provides a framework to detect differential ORF usage in ribosome profiling data, offering improved sensitivity and FDR control for translational regulation analysis.

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.

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.

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.

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.

Thermoregulation network governing virulence of a critical human fungal pathogen

This study identifies a thermoregulatory network in Cryptococcus neoformans that governs virulence through calcineurin signaling, using genetic, proteomic, and transcriptomic approaches.

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.

Ultra-parallel ribosome profiling platform with RNA-dependent RNA amplification

The paper develops a semi-automated Ribo-Seq and Disome-Seq platform to analyze translation status across many samples, identifying factors regulating translation and revealing links between stop codon readthrough and mitochondrial translation deficiency in COVID-19.

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.

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.

Dorsal Striatum Parvalbumin interneurons translatome unveiled

The paper profiles the translatome of dorsal striatum PV interneurons, identifying molecular signatures and gene expression changes linked to psychostimulant exposure and reward behaviors.

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.

Landscape and regulation of new protein translation in the early C. elegans embryo

The paper measures mRNA translation in C. elegans embryos and identifies stage-specific translational regulation and the role of OMA-1 in repressing and promoting translation of target mRNAs.

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.

A trans-acting enhancer lncRNA modulates androgen-dependent gene expression via sequence-specific interaction with the Androgen Receptor

This paper identifies an enhancer lncRNA that interacts with the Androgen Receptor to regulate gene expression and inhibit prostate cancer cell proliferation.

Ribo-seq guided design of enhanced protein secretion in Komagataella phaffii

This paper uses Ribo-seq to identify bottlenecks in protein secretion in Komagataella phaffii and improves HSA production through targeted gene knockouts.

Rare codon translation regulates growth factor-dependent cell proliferation

The paper shows that growth factor signaling promotes cell proliferation by inducing tRNAs that decode rare codons, enhancing translation of DNA replication factors.

Benchmark of cellular deconvolution methods using a multi-assay reference dataset from postmortem human prefrontal cortex

The paper benchmarks cellular deconvolution methods using a multi-assay dataset from human prefrontal cortex, finding Bisque and hspe to be the most accurate.

The multiomics landscape of small peptides encoded by long non-coding RNA-derived sORFs in rice

This study identifies small peptides encoded by lncRNAs in rice using a multi-omics approach, finding 403 LSEPs across four databases.