Translatomics for 3’UTRs, CRISPR, and YebC
Recent Publications Harnessing the Power of Translatomics
Every week we provide a digest of a small number of recent interesting papers in the field of translatomics.
In this week’s Sunday papers,
- West et al. used a massively parallel reporter assay with RNA-seq and polysome profiling to show how human 3′UTRs fine-tune gene expression through combined effects on mRNA stability, translation, and promoter context.
- Nugent et al. developed ReLiC, an RNA-linked CRISPR screening platform that integrates RNA reporters with CRISPR knockouts to map how RNA-associated proteins regulate splicing, translation, and decay.
- Ignatov et al. identify YebC as a conserved bacterial RNA-binding protein that transiently interacts with rRNA to promote translation, preventing ribosome stalling at proline-rich motifs.
The quantitative impact of 3′UTRs on gene expression
Nucleic Acids Research, 2025
West, J. D., Smith, H. J., Vu, L. T., Fogarty, E. A., Matreyek, K. A., Fowler, D. M. & Grimson, A.
In this paper, West et al. systematically quantified how human 3′ untranslated regions (3′UTRs) shape gene expression by applying a massively parallel reporter assay to over 1,400 full-length 3′UTRs. By integrating measurements of RNA abundance, RNA stability, ribosome loading, and protein output, the study provided a comprehensive view of post-transcriptional regulation encoded within 3′UTRs.
The study showed that numerous 3′UTRs control gene output by coordinating effects on both transcript stability and translational efficiency. Sequence-encoded features such as length and GC content were predictive of these regulatory effects, while specific motifs suggested regulation by RNA-binding proteins. Interestingly, 3′UTR activity was not fixed but could vary depending on the promoter driving expression, revealing crosstalk between transcriptional and post-transcriptional layers.
The authors employed RNA-seq, which quantified reporter transcript levels and enabled assessment of 3′UTR effects on mRNA stability. In parallel, polysome profiling was used to measure ribosome association, providing a direct readout of translational regulation mediated by different 3′UTRs. Together, these approaches allowed dissection of the relative contributions of transcription, decay, and translation to final protein expression.
Overall, this work delivers the most detailed quantitative characterization to date of full-length human 3′UTRs. It highlights translation as a major, nuanced regulatory axis and demonstrates how promoter context and encoded sequence features combine to fine-tune gene expression outcomes.
Learn more about EIRNABio’s ribosome profiling and polysome profiling services here.
Decoding post-transcriptional regulatory networks by RNA-linked CRISPR screening in human cells
Nature Methods, 2025
Nugent, P.J., Park, H., Wladyka, C.L., Yelland, J.N., Sinha, S., Chen, K.Y., Bynum, C., Quarterman, G., Lee, S.C., Hsieh, A.C. & Subramaniam, A.R.
In this paper, the authors present ReLiC, an RNA-linked CRISPR platform designed to systematically dissect post-transcriptional regulation in human cells. The method integrates Cas9, sgRNAs, and barcoded RNA reporters into a defined genomic locus, allowing scalable measurement of RNA metabolism after gene knockout. The authors generated a library targeting 2,092 human genes encoding all known RNA-associated proteins.
Applying ReLiC to translation, the team coupled the platform with polysome profiling. Using a β-globin reporter, they separated RNAs by ribosome occupancy and identified over 300 genes whose knockout reduced polysome association, including ribosomal proteins and translation factors. This demonstrated ReLiC’s ability to map regulators of ribosome loading and link them to proteostasis pathways.
The platform also captured isoform-specific regulation, distinguishing intron retention from exon skipping events. This enabled the authors to dissect roles of SF3B spliceosome subunits in controlling distinct splicing outcomes.
Finally, chemogenomic ReLiC identified regulators of translation under drug stress. In particular, the ribosome collision sensor GCN1 was required for cellular adaptation to the anti-leukemic drug homoharringtonine, as shown by RNA-seq, polysome analysis, and ribosome profiling.
Overall, the work demonstrates that ReLiC is a robust and scalable framework to map RNA regulatory networks. It provides new insights into how RNA-associated proteins govern the balance between RNA processing, translation, and decay, and establishes a foundation for studying post-transcriptional control in both basic biology and therapeutic contexts.
Learn more about EIRNABio’s ribosome profiling and polysome profiling services here.
RNA-binding protein YebC enhances translation of proline-rich amino acid stretches in bacteria
Nature Communications, 2025
Ignatov, D., Shanmuganathan, V., Ahmed-Begrich, R., Alagesan, K., Hahnke, K., Wang, C., Krause, K., Cornejo, F.A., Funke, K., Erhardt, M., Frese, C.K. & Charpentier, E.
This paper investigates the role of YebC, a conserved bacterial RNA-binding protein, in protein synthesis. Using proteomic approaches in Streptococcus pyogenes, the authors identified 30 previously uncharacterized RNA-binding proteins, among them YebC. Crosslinking experiments revealed that YebC transiently interacts with 23S rRNA near the peptidyl-transferase centre of the ribosome. Functional studies showed that deleting yebC only mildly affected bacterial growth and virulence but had notable consequences for translation. Ribosome profiling indicated that loss of YebC causes increased ribosome pausing at proline-rich motifs, particularly at stretches containing consecutive prolines. This suggests YebC facilitates peptide bond formation under structurally challenging conditions.
Further experiments in S. pyogenes, Salmonella Typhimurium, and in vitro reconstituted systems demonstrated that YebC enhances efficient translation of proline-rich proteins and rescues ribosome stalling. Site-directed mutagenesis pinpointed key amino acid residues essential for RNA binding and activity, with positively charged surfaces and a conserved tyrosine (Y84) being crucial. While YebC does not stably associate with ribosomes, its transient binding appears sufficient to promote translation. Comparisons with elongation factor P (EF-P) showed overlapping but distinct roles, with some redundancy in function.
The findings also highlight evolutionary parallels: YebC shares functional similarity with its mitochondrial homolog TACO1, required for translation of polyproline motifs in eukaryotic mitochondria. Overall, the study identifies YebC as a novel bacterial translation factor that alleviates ribosome stalling at proline-rich motifs, expanding our understanding of how cells ensure efficient protein synthesis in the face of difficult amino acid sequences.
Learn more about EIRNABio’s ribosome profiling services here.
