Ribo-seq

Anisomycin-induced ribosome collisions follow a dose-dependent positional rule, distinct from the UV-induced collision landscape

Low- and high-dose anisomycin confine ribosome collisions to a dose-shifted zone just past the start codon, whereas 30 min after UV, collisions appear more dispersed and favor highly translated mRNAs.

sORF-Trans2MS: a two-module deep learning framework for sORF translation and MS-supported microprotein prediction

sORF-Trans2MS is a two-module deep learning framework that predicts Ribo-supported sORFs and MS-supported microproteins, improving prediction and extending discovery to underrepresented candidates.

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.

Unveiling the small protein landscape of uropathogenic E. coli

This study identifies 338 previously unannotated small open reading frames in UPEC strain CFT073, with functional evidence for nine intergenic sORFs and potential roles in stress response.

RNA Structure Coordinates Translation Across the Meiotic Program

In yeast meiosis, flexibly folded mRNAs are preferentially translated while cytoplasmic RNA helicase levels dip; raising Ded1p or breaking CCW22 UTR pairing mistimes translation and disrupts meiotic progression.

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.

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.

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

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.

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.

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.

A pan-cancer atlas of therapeutic T cell targets

ImmunoVerse integrates RNA-Seq and immunopeptidomes to catalog 28,446 tumor-specific HLA-presented antigens across 21 cancers, including a splicing-derived PMEL peptide with T cell expansion support.

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.

Improved Super-Resolution Ribosome Profiling Revealed Prevalent Translation of Upstream ORFs and Small ORFs in Arabidopsis

The paper improves super-resolution Ribo-seq in Arabidopsis to identify prevalent translation of upstream and small ORFs, revealing new translation events and regulatory mechanisms.

What can Ribo-seq and proteomics tell us about the non-canonical proteome?

This paper discusses the current state of research on non-canonical open reading frames (ORFs) and proposes standards for their investigation and reporting using Ribo-seq and proteomics.

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.

An Improved Human smORF Annnotation Workflow Combining De Novo Transcriptome Assembly and Ribo-Seq

The paper improves smORF annotation by integrating de novo transcriptome assembly and Ribo-Seq, identifying thousands of novel translated smORFs in human cell lines and highlighting their functional potential.

Quantifying multi-layered expression regulation in response to stress of the endoplasmic reticulum

The paper quantifies gene expression regulation at multiple layers in response to ER stress in cervical cancer cells over time, identifying shared and stress-specific regulatory events.

Integrative analysis of RNA, translation and protein levels reveals distinct regulatory variation across humans

The paper integrates RNA, translation, and protein data to show genetic variation affects translation and protein levels in humans.