Chien-Hung Yu
Associate Professor

Associate Professor Chien-Hung Yu

中文頁面

Address:
No.1, University Road, Tainan City 701, Taiwan (R.O.C.)
TEL (ext.):
5540 (Office), 5525 (Lab)
E-mail:
chienhung_yu@mail.ncku.edu.tw

Education

Ph. D., Leiden University, The Netherlands (2011)

Portrait of Associate Professor Chien-Hung Yu

Expertise and Research

Areas of Expertise

  • Molecular Biology
  • Protein Translation
  • RNA Biology

Research Interests

Codons are the bridge that carries genetic information to amino acids and then to proteins, and lie at the heart of the central dogma of molecular biology. Most amino acids can be encoded by two or more synonymous codons, but these synonymous codons are not used with equal frequency, a phenomenon known as codon usage bias. Interestingly, codon usage bias exists in almost all known genomes, yet it is unclear why it has been preserved throughout long-term evolution. Our previous studies showed that, although codon usage bias does not change the amino acid sequence, it can regulate protein folding as well as the expression levels of messenger RNA and protein. In clinical settings, with advances in sequencing technology, an increasing number of diseases have been found to be associated with mutations in synonymous codons. In the future, our lab will use molecular biology, biochemistry, genetics, and bioinformatics approaches to investigate the mechanisms by which codon usage bias affects gene expression. We also hope that a deeper understanding of these mechanisms will lead to treatments for diseases associated with synonymous codon mutations.

Publications

  1. Tai, S. Y., Hashimoto, M., Zhuang, Y. F., Liang, H. W., Huang, H. P., Nguyen, T. P., Tu, M. H., Chen, S. C., Wu, W. F., Olsthoorn, R. C. L. & Yu, C. H., (2026) Coordinated translation initiation determines -1 programmed ribosomal frameshifting efficiency of chromosomal genes to impact on cell fitness The FEBS Journal. 293, 14, p. 4374-4396 23 p. [Abstract]
  2. Chen, S. C., Xu, C. T., Chang, C. F., Yang, C. S., Lin, P. H., Liu, W. M., Chen, Y. & Yu, C. H., (2025) Characterization of the binding features between SARS-CoV-2 5’-proximal transcripts of genomic RNA and nucleocapsid proteins RNA Biology. 22, 1, p. 1-16 16 p. [Abstract]
  3. Ku, Y. C., Lee, Y. C., Hong, Y. K., Lo, Y. L., Kuo, C. H., Wang, K. C., Hsu, C. K., Yu, C. H., Lin, S. W. & Wu, H. L., (2025) Deciphering the Dysregulating IGF-1–SP1–CD248 Pathway in Fibroblast Functionality during Diabetic Wound Healing Journal of Investigative Dermatology. 145, 5, p. 1180-1195 16 p. [Abstract]
  4. Das, D., Huang, S. H., Weng, C. L., Yu, C. H., Hsu, C. K., Lee, Y. C., Cheng, H. C. & Chuang, H. S., (2024) Detachable acoustofluidic droplet-sorter Analytica Chimica Acta. 1321, 343043. [Abstract]
  5. Huang, S. H., Chen, S. C., Wu, T. Y., Chen, C. Y. & Yu, C. H., (2023) Programmable modulation of ribosomal frameshifting by mRNA targeting CRISPR-Cas12a system iScience. 26, 12, 108492. [Abstract]
  6. Ku, Y. C., Lin, P. H., Huang, C. Y., Lee, C. W., Yu, C. H., Chen, S. C. & Liu, W. M., (2023) An iminocoumarin based covalent-assembly red-emitting fluorescent probe for detection of β-galactosidase activity in ovarian cancer cells. Dyes and Pigments. 210, 111004.
  7. Chen, S. Y., Chen, K. L., Ding, L. Y., Yu, C. H., Wu, H. Y., Chou, Y. Y., Chang, C. J., Chang, C. H., Wu, Y. N., Wu, S. R., Hou, Y. C., Lee, C. T., Chen, P. C., Shan, Y. S. & Huang, P. H., (2022) RNA bisulfite sequencing reveals NSUN2-mediated suppression of epithelial differentiation in pancreatic cancer Oncogene. 41, 22, p. 3162-3176 15 p. [Abstract]
  8. Yang, T. H., Hsu, C. W., Wang, Y. X., Yu, C. H., Jagat, R., Tseng, Y. Y. & Wu, W. S., (2022) YMLA: A comparative platform to carry out functional enrichment analysis for multiple gene lists in yeast. Computers in Biology and Medicine. 151, 106314. [Abstract]
  9. Chen, S. C., Olsthoorn, R. C. L. and Yu, C. H., (2021) Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2. Virus Evolution. 7, 1, veab021. [Abstract]
  10. Yang, Q., Yu, C. H., Zhao, F., Dang, Y., Wu, C., Xie, P., Sachs, M. S. and Liu, Y., (2019) eRF1 mediates codon usage effects on mRNA translation efficiency through premature termination at rare codons. Nucleic acids research. 47, 17, p. 9243-9258 16 p. [Abstract]
  11. Zhao, F., Yu, C. H., and Liu, Y., (2017) Codon usage regulates protein structure and function by affecting translation elongation speed in Drosophila cells Nucleic acids research. 45, 14, p. 8484-8492 9 p. [Abstract]
  12. Zhou, Z., Dang, Y., Zhou, M., Li, L., Yu, C. H., Fu, J., Chen, S., and Liu, Y., (2016) Codon usage is an important determinant of gene expression levels largely through its effects on transcription. Proc. Natl. Acad. Sci. U.S.A., 113, E6117-E6125. [Abstract]
  13. Yu, C. H.*, Dang, Y.*, Zhou, Z*., Wu, C., Zhao, F., Sachs, M.S., and Liu, Y., (2015) Codon usage influences the local rate of translation elongation to regulate co-translational protein folding. Mol. Cell, 59, 744-754. (*co-first authors) (Cover article and highlighted in TIBS) [Abstract]
  14. Yu, C. H. and Olsthoorn, R.C., (2015) Monitoring ribosomal frameshifting as a platform to screen anti-riboswitch drug candidates. Methods Enzymol., 550, 385-393. [Abstract]
  15. Yu, C. H., Teulade-Fichou, M. P. and Olsthoorn, R.C., (2014) Stimulation of ribosomal frameshifting by RNA G-quadruplex structures. Nucleic Acids Res., 42, 1887-1892. [Abstract]
  16. Luo, J., Wärmländer, S.K., Yu, C. H., Muhammad, K., Gräslund, A., and Abrahams, J.P., (2014) The Aβ peptide forms non-amyloid fibrils in the presence of carbon nanotubes. Nanoscale., 6(12):6720-6. [Abstract]
  17. Luo, J., Otero, J.M., Yu, C. H., Wärmländer, S.K., Gräslund, A., Overhand, M., and Abrahams, J.P., (2013) Inhibiting and reversing amyloid-β peptide (1-40) fibril formation with gramicidin S and engineered analogues. Chemistry, 19, 17338-17348. [Abstract]
  18. Luo, J., Yu, C. H., Yu, H., Borstnar, R., Kamerlin, S.C., Gräslund, A., Abrahams, J.P., and Wärmländer, S.K., (2013) Cellular polyamines promote amyloid-beta (Aβ) peptide fibrillation and modulate the aggregation pathways. ACS Chem. Neurosci., 4, 454-62. [Abstract]
  19. Yu, C. H. Luo J., Iwata-Reuyl, D., and Olsthoorn, R.C., (2013) Exploiting preQ1 riboswitches to regulate ribosomal frameshifting. ACS Chem. Biol., 8, 733-740. [Abstract]
  20. Yu, C. H., Noteborn, M.H., Pleij, C.W., and Olsthoorn, R.C., (2011) Stem-loop structures can effectively substitute for an RNA pseudoknot in -1 ribosomal frameshifting. Nucleic Acids Res., 39, 8952-8959. [Abstract]
  21. Yu, C. H., Noteborn, M.H., and Olsthoorn, R.C., (2010) Stimulation of ribosomal frameshifting by antisense LNA. Nucleic Acids Res., 38, 8277-8283. [Abstract]
  22. Lien, H.Y., Yu, C. H., Liou, C.M., and Wu, W.F., (2009) Regulation of clpQY (hslVU) Gene Expression in Escherichia coli. Open Microbiol. J., 3, 29-39. [Abstract]
  23. Lee, Y.Y., Chang, C.F., Kuo, C.L., Chen, M.C., Yu, C. H., Lin, P.I., and Wu, W.F., (2003) Subunit oligomerization and substrate recognition of the Escherichia coli ClpYQ (HslUV) protease implicated by in vivo protein-protein interactions in the yeast two-hybrid system. J. Bacteriol., 185, 2393-2401. [Abstract]