May 25th, 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,
- Cao et al. employ polysome profiling to uncover the mechanism by which circMYLK4 alters energy metabolism in skeletal muscle.
- Cheng et al. utilize ribosome profiling to demonstrate how a small nucleolar RNA influences cell senescence and ribosome subunit biogenesis.
- He et al. identify a novel protein encoded by circular RNA that regulates intramuscular fat content in pigs.
Circular RNA circMYLK4 shifts energy metabolism from glycolysis to OXPHOS by binding to the calcium channel auxiliary subunit CACNA2D2
Journal of Biological Chemistry, 2024
Haigang Cao, Chenchen Li, Xiaohui Sun, Jinjin Yang, Xiao Li, Gongshe Yang, Jianjun Jin, Xine Shi
This study demonstrates the critical role that the circular RNA circMYLK4 plays in skeletal muscle energy metabolism, by directly shifting the balance from glycolysis to oxidative phosphorylation (OXPHOS). Mechanistically, circMYLK4 was shown to bind to CACNA2D2—calcium channel auxiliary subunit—, inhibiting release of calcium from the sarcoplasmic reticulum, and therefore reducing cytoplasmic calcium levels, suppressing glycogen breakdown and limiting glycolysis. Despite this, mitochondrial function is enhanced, with increased mitochondrial area, DNA copy number, and ATP production observed.
Using polysome profiling and other techniques, the authors set out to determine whether circMYLK4 encodes non-annotated peptides, or directly regulates translation. circMYLK4 was found associated exclusively with monosome fractions, and not polysomes, which, in combination with appropriate transcriptomics and proteomics data, indicates that it is not actively translated. RNA pull-down followed by mass spectrometry and Western blotting subsequently identified the protein CACNA2D2 as a direct binding partner of circMYLK4. These findings not only deepen our understanding of circRNA functions beyond miRNA sponging or translation, but also offer new insights into metabolic regulation and muscle plasticity. Given the central role of metabolic flexibility in health and disease, circMYLK4 presents a potential therapeutic target for metabolic disorders, muscular dystrophies, and performance optimization in muscle function and regeneration.
Learn more about EIRNA Bio’s polysome profiling service here.
A non-canonical role for a small nucleolar RNA in ribosome biogenesis and senescence
Cell, 2024
Yujing Cheng, Siwen Wang, He Zhang, Jong-Sun Lee, Chunyang Ni, Jason Guo, Eric Chen, Shenming Wang, Asha Acharya, Tsung-Cheng Chang, Michael Buszczak, Hao Zhu, and Joshua T. Mendell
This study identifies a novel function of the small nucleolar RNA SNORA13 in promoting cellular senescence. In addition to its canonical role in RNA modification – pseudouridylation of the 18S rRNA-, SNORA13 was shown to directly bind to ribosomal protein RPL23, inhibiting 60S ribosome subunit assembly, with subsequent accumulation of free ribosomal proteins, activation of the p53 pathway, and initiation of senescence via the nucleolar stress response.
Combined analyses by Ribosome profiling and RNA-seq were employed on a SNORA13 knockout model, to assess whether senescence is driven by its rRNA modification activity, impacting translation efficiency. This revealed only minimal changes in translation efficiency, ruling out a SNORA13-driven translational mechanism for senescence. Additionally, sucrose gradient fractionation and polysome profiling showed that SNORA13 knockout cells exhibited a significant increase in free 60S subunits and 80S monosomes. Rescue experiments confirmed that this regulatory effect on ribosome assembly was independent of SNORA13’s pseudouridylation function but dependent on its direct interaction with RPL23. Thus, SNORA13’s role in regulating 60S assembly was shown to be genetically separable from its pseudouridylation function , supporting a model in which SNORA13 directly modulates ribosome biogenesis—but not translation—to promote p53-mediated senescence. This work positions SNORA13 as a potential therapeutic target: inhibiting SNORA13 could enhance ribosome biogenesis and reduce p53 activation in ribosomopathies, while preserving SNORA13 activity may suppress tumor progression by enforcing senescence.
Learn more about EIRNA Bio’s ribosome profiling and polysome profiling service here.
A novel protein encoded by porcine circANKRD17 activates the PPAR pathway to regulate intramuscular fat metabolism
Journal of Animal Science and Biotechnology, 2025
Xiao He, Fang Xie, Ying Nie, Xuefeng Wang, Junyi Luo, Ting Chen, Qianyun Xi, Yongliang Zhang and Jiajie Sun
In this study, the authors demonstrate that the circular RNA circANKRD17 regulates fatty acid transport, synthesis, and oxidation via activation of the PPAR signaling pathway through production of a novel protein, thus linking circRNA translation to functional metabolic regulation in pigs. Functional assays in 3T3-L1 cells and C57BL/6 mice show that this circANKRD17-derived protein significantly promotes lipid droplet formation, triglyceride accumulation, and expression of genes involved in the PPAR pathway.
Ribosome profiling (Ribo-seq) played a central role in identifying the translational potential of circANKRD17. The back-splice junction of circANKRD17 showed strong ribosome occupancy, and further experimental validation confirmed the circular structure and cytoplasmic localization of this RNA. To confirm translation, the open reading frame of circANKRD17 was cloned into a vector with a 3×Flag tag. Western blot using anti-Flag antibodies detected the expected 571-amino-acid protein in transfected 3T3-L1 cells, demonstrating successful translation. The detection of non-annotated ORFs made possible by ribosome profiling, paired with protein expression and functional assays, provided strong evidence of the role of circANKRD17 as a key regulator of lipid metabolism by means of its encoded protein.
These findings not only enhance understanding of intramuscular fat regulation in livestock, with implications for meat quality improvement, but also open avenues for exploring circRNA-derived proteins in metabolic disease models.
Learn more about EIRNA Bio’s ribosome profiling services here.