May 18th, 2025
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,
- Schaefer et al. document a novel function of SOX2 in translational regulating extracellular matrix and developmental gene transcripts.
- Boraas et al. uncover a role of G3BP1 in assisting in localised translational recruitment.
- Meurs et al. delve deeper into the mechanics of reinitiation, uncovering a novel role for MCTS2.
Nuclear and cytosolic fractions of SOX2 synergize as transcriptional and translational co-regulators of cell fate
Cell Reports, 2024
Schaefer, T., Mittal, N., Wang, H., Ataman, M., Candido, S., Lötscher, J., Velychko, S., Tintignac, L., Bock, T., Börsch, A., Baßler, J. et al
SOX2 is a key transcription factor (TF) that maintains stemness and pluripotency in embryonic, germ, and adult stem cells. Along with TFs like OCT4 and c-MYC, ectopic SOX2 expression can reprogram differentiated cells to a stem-like state. Sustained SOX2 is crucial for tissue homeostasis, while its dysregulation is linked to cancers, especially epithelial and neuronal types. Structurally, SOX2 has an N-terminal HMG domain for DNA binding and nuclear transport, and a C-terminal transactivation domain for co-factor interaction. Beyond gene regulation, SOX2 also binds RNA and associates with nuclear pore proteins. However, its nuclear entry is tightly controlled, while its cytosolic pool is under investigation for independent functionality.
This study systematically demonstrates that SOX2, classically known as a transcription factor, also directly modulates translation. Using correlation analysis and siRNA knockdown in cancer cells, the authors observed that SOX2 expression inversely regulates RPS6 phosphorylation, independent of mTOR/S6K1 signalling or stress responses. Polysome profiling showed that SOX2 alters ribosome activity, increasing 80S monosomes and reducing active translation. Furthermore, immunoprecipitation-mass spectrometry (IP-MS) and proximity labelling (BioID) confirmed that SOX2 physically associates with mature ribosomes, especially via its C-terminal domain. Additionally, RNA-seq and Ribo-seq analyses revealed that SOX2 selectively modulates translation of genes linked to metabolism, extracellular matrix interactions, and development. Functional assays validated these effects, showing that SOX2 promotes glucose uptake, enhances glycolysis, and drives spheroid formation in cancer cells. Importantly, a disease-associated SOX2 mutant (L97P) lost the ability to regulate translation, confirming functional relevance. Altogether, this paper redefines SOX2 as a bifunctional regulator of transcription and translation.
Learn more about EIRNA Bio’s ribosome profiling service here.
G3BP1 ribonucleoprotein complexes regulate focal adhesion protein mobility and cell migration
Cell Reports, 2025
Boraas, L.C., Hu, M., Martino, P., Thornton, L., Vejnar, C.E., Zhen, G., Zeng, L., Parker, D.M., Cox, A.L., Giraldez, A.J., Su, X. et al
Cell migration relies on dynamic focal adhesions (FAs), where proteins like paxillin (PXN) and vinculin link the actin cytoskeleton to the extracellular matrix. FA assembly and disassembly are critical for movement, but the molecular mechanisms regulating FA protein dynamics remain unclear. β-actin mRNA (ACTB) localizes to FAs and supports their stability via local translation, while other mRNAs similarly regulate migration at the leading edge. However, the full extent of mRNA localization to FAs had not been previously resolved. To address this, the authors used an unbiased approach and discovered hundreds of mRNAs, and several RNA-binding proteins, enriched at FAs in unstressed cells.
Using hydromechanical isolation and poly(A) RNA-seq, the authors identified hundreds of mRNAs enriched at focal adhesions (FAs) in human fibroblasts and endothelial cells, validated by smFISH and MERFISH imaging. Proteomic analysis following RNase treatment revealed that the RNA-binding protein G3BP1 localizes to FAs in an RNA-dependent manner. Co-immunoprecipitation confirmed G3BP1’s interactions with FA proteins like TLN1 and ACTN1, which were disrupted by RNA degradation or FA disassembly. In-vitro and in-cellulo assays showed G3BP1 forms RNPs with FA-enriched mRNAs (e.g., TRAK2, KIF1C), crucial for mRNA localization at FAs. Loss of G3BP1 reduced FA-mRNA enrichment, decreased cell migration (tracked by live-cell imaging), and led to smaller, less dynamic FAs (measured via fluorescence recovery after photobleaching (FRAP) of PXN). Protein synthesis assays showed that G3BP1’s effects were independent of global translation. Functional rescue with G3BP1 mutants demonstrated that RNA-binding and dimerization domains are essential for regulating FA dynamics and migration.
Learn more about EIRNA Bio’s ribosome profiling service here.
MCTS2 and distinct eIF2D roles in uORF-dependent translation regulation revealed by in vitro re-initiation assays
EMBO Press, 2025
Meurs, R., De Matos, M., Bothe, A., Guex, N., Weber, T., Teleman, A.A., Ban, N. and Gatfield, D.
Upstream open reading frames (uORFs) regulate protein translation by reducing ribosome access to downstream coding sequences, typically acting as inhibitors. However, downstream initiation can occur via mechanisms like leaky scanning or post-uORF reinitiation by ribosomes. The non-canonical initiation factor MCTS1-DENR facilitates reinitiation by aiding tRNA recycling and delivery, particularly after short or start-stop uORFs. Its activity is selective and may depend on specific uORF sequences. eIF2D, a similar factor, shows overlapping but distinct functions, and its precise role in reinitiation remains unclear. This study uses ribosome profiling and cell-based assays to dissect the contributions of both factors to uORF-dependent re-initiation.
Here, the authors identify Klhdc8a and Asb8 as DENR-dependent re-initiation targets. Reporter constructs reveal that DENR strongly promotes reinitiation, particularly after short uORFs. Reinitiation remains largely unaffected by eIF2α phosphorylation, suggesting ternary complex availability is not a key limiting factor in this context. While eIF2D can partially compensate for DENR loss in vitro, it plays a minimal role in reinitiation in vivo and likely has broader, uORF-independent regulatory functions. Notably, MCTS2, previously considered a pseudogene, forms functional reinitiation complexes with DENR, equivalent to MCTS1-DENR. The study confirms the direct role of MCTS1-DENR in reinitiation and introduces MCTS2-DENR as a redundant, active complex.
Learn more about EIRNA Bio’s ribosome profiling services here.