March 23rd, 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,
- Chen et al. use ribosome profiling to reveal the importance of ac4c-mediated translational regulation in the maturation of oocytes.
- Yu et al. employ ribosome profiling and suggest that OLA1, a conserved GTPase, plays a role in resolution of D/E-induced ribosome stalling.
- Labaronne et al. apply ribosome profiling to find that non-canonical initiation events in the HIV mRNA contribute towards immune response and CDS regulation.
NAT10-mediated mRNA N4-acetylation is essential for the translational regulation during oocyte meiotic maturation in mice
Science Advances, 2024
Chen, L., Wang, W.J., Liu, S.Y., Su, R.B., Wu, Y.K., Wu, X., Zhang, S.Y., Qiao, J., Sha, Q.Q. and Fan, H.Y.
Mammalian oocyte maturation is tightly regulated by posttranscriptional mRNA modifications, including N4-acetylcytidine (ac4C), which influences mRNA stability and translation. While ac4C has been studied in various RNAs, its role in oocyte maturation remains unclear. Traditional ac4C detection methods have limitations, particularly for low-input samples like oocytes. To address this, researchers developed ac4C LACE-seq, a high-sensitivity, low-input sequencing method that enables single-nucleotide resolution mapping of ac4C. Using this approach, they profiled ac4C in mouse germinal vesicle (GV) oocytes and generated Nat10 knockout models to investigate ac4C’s role in oocyte development and maturation.
Deleting Nat10 in mouse oocytes significantly reduced ac4C RNA modifications, leading to defects in meiotic maturation and infertility. Immunofluorescence and Western blotting confirmed the loss of NAT10 and ac4C signals in Nat10-deleted oocytes. Using ac4C LACE-seq, researchers mapped ac4C modifications primarily to the 5’UTR and CDS regions, and found that such sites were CU enriched. Oocytes lacking Nat10 showed spindle assembly defects, increased chromosomal aneuploidy, and reduced fertilization potential. Comparison against RNA sequencing data, in combination with an online translational database, revealed that Nat10 deletion did not significantly alter transcript stability but impaired translation efficiency. Key maternal mRNAs, including Msy2, Btg4, and Ccnb1, showed reduced ac4C modifications and lower protein expression. Translation reporter assays confirmed that Nat10 deletion impaired translation activation during oocyte maturation. Mutating predicted ac4C sites reduced protein levels, while incorporating ac4C into mRNAs enhanced translation efficiency. These results demonstrate that ac4C modifications, mediated by NAT10, are essential for the translational regulation of maternal mRNAs and proper oocyte development.
Learn more about EIRNA Bio’s ribosome profiling and RNA-seq services here.
Conserved GTPase OLA1 promotes efficient translation on D/E-rich mRNA
Nature Communications, 2025
Yu, T., Li, X., Dong, W., Zhou, Q., Li, Q., Du, Z. and Zeng, F.
GTPases are essential regulatory proteins involved in key cellular processes, including translation. OLA1 and its bacterial homolog YchF belong to the TRAFAC class of GTPases but uniquely hydrolyze ATP instead of GTP. These proteins play roles in stress responses, cancer progression, and translation regulation. OLA1 influences HSP70 stability, interacts with BRCA1, and affects translation initiation under stress. It binds ribosomes across species, potentially regulating ribosome biogenesis and function. However, key molecular details, including its precise ribosome interactions and translation regulation mechanisms, remain unclear due to the absence of structural data on OLA1/YchF-ribosome complexes. Here, the authors utilise structural analysis in conjunction with ribosome profiling to shed more light in this area.
Sucrose cushion assays showed that YchF weakly binds the ribosome, preferentially associating with the 50S subunit rather than the assembled 70S ribosome. Cryo-electron microscopy (cryo-EM) at 2.37 Å resolution revealed that YchF primarily contacts ribosomal proteins uL14, bL19, and rRNA H62 through its helical and ATPase domains. Structural comparisons with ribosome-free YchF showed conformational shifts upon binding, suggesting a role in ribosome remodeling. Functional assays demonstrated that YchF promotes ribosomal subunit dissociation in chloramphenicol-treated E. coli cells. Ribosome profiling (Ribo-seq) in human OLA1-deficient cells revealed increased ribosome stalling at D/E-rich sequences, leading to mRNA degradation and altered translation efficiency. These findings suggest OLA1/YchF helps resolve stalled ribosomes, maintaining translation balance. Loss of OLA1 disrupts ribosome composition, impacting cellular stress responses and migration, highlighting its role in translation regulation.
Learn more about EIRNA Bio’s polysome profiling and ribosome profiling services here.
Non-AUG HIV-1 uORF translation elicits specific T cell immune response and regulates viral transcript expression
Nature Communications, 2025
Labaronne, E., Décimo, D., Bertrand, L., Guiguettaz, L., Sohier, T.J., Cluet, D., Vivet-Boudou, V., Chaves Valadão, A.L., Dahoui, C., François, P., Hatin, I, Lambotte, O., Samri, A., Autran, B., Etienne, L., Goujon, C., Paillart, J., Namy, O., Ramirez, B.C., Ohlmann, T., Moris, A. and Ricci, E.P.
HIV-1 is a positive-sense, single-stranded RNA virus that undergoes reverse transcription into DNA, which integrates into the host genome or remains unintegrated. Viral RNA is transcribed by host RNA polymerase II and undergoes alternative splicing to generate regulatory and structural proteins. Translation of HIV-1 transcripts is highly regulated via cap-dependent and cap-independent mechanisms, including IRES-mediated initiation and protease-driven inhibition of host translation factors. This regulation influences immune recognition by T cells. While in vitro studies have revealed key mechanisms, a comprehensive view of HIV-1 translation dynamics remains incomplete. Here, mass spectrometry, ribosome profiling, and RNA sequencing are used to analyse viral translation in infected CD4+ cells.
Gene expression analysis integrating RNA-seq and Ribo-seq data revealed early, mild transcriptomic changes, but by 24–36 hours post-infection (hpi), thousands of host transcripts were differentially expressed, with most changes driven by transcript abundance rather than translational control. Ribosome occupancy measurements showed that while global host translation remained relatively stable, a subset of 423 genes exhibited translational regulation, influenced by GC content and codon usage. Unexpectedly, incoming viral genomic RNA was actively translated at 1hpi, with shifts in translation patterns for viral proteins over time. Mass spectrometry tracked protein abundance, identifying post-translational regulation independent of transcript levels, particularly in mitochondrial and translation-related proteins. Ribosome profiling following harringtonine treatment was used to map translation start sites, confirming both canonical AUG and non-AUG initiation in viral 5’UTRs. Luciferase reporter assays validated the role of uORFs in inhibiting main ORF translation, with the DDX3 helicase mitigating this effect. T-cell assays in HIV-infected individuals detected immune responses to uORF-derived peptides, confirming their translation during infection. These findings highlight the complex, multi-layered regulatory strategies HIV-1 employs to control host and viral protein expression.
Learn more about EIRNA Bio’s ribosome profiling and RNA-seq services here.