Chyuan-Chuan Wu
Associate Professor

Expertise and Research

Fields of Study

• Biochemistry
• Structural biology
• Macromolecular X-ray crystallography
• Molecular biology
• Molecular structure of protein-DNA complexes
• Molecular structure of protein-ligand/substrate complexes
• Multi-protein complex structure

Research Interests

Our lab mainly uses X-ray protein crystallography and single-particle cryo-EM to determine the molecular structures of biological macromolecules, in order to elucidate the relationship between molecular structure and function. Our research interests and expertise include protein–nucleic acid interactions, protein conformational changes and functional regulation, the assembly of macromolecular complexes, and interactions between proteins and small-molecule drugs. Our current main research topics are as follows:

1. Degradation mechanism of the human mitochondrial genome (mtDNA)

Damaged mtDNA must be cleared promptly to maintain its integrity and function; otherwise, mutations accumulate and mitochondrial function declines, which is positively correlated with aging, neurodegenerative diseases, and acute and chronic inflammatory diseases. Human mitochondria contain a complex responsible for degrading damaged mtDNA, referred to here as the mtDNA degradation machinery. This complex includes DNA polymerase γ, the DNA helicase Twinkle, and the exonuclease MGME1, but how these molecules assemble into the mtDNA degradation machinery, and how their individual functions are carried out and regulated, remain largely unresolved. By understanding the structural mechanisms of the mtDNA degradation machinery, our lab hopes to elucidate how damaged mtDNA is cleared and how this relates to the development of associated diseases, with the aim of contributing to the treatment of cellular aging and related diseases.

2. Substrate recognition by RNA methyltransferases

RNA:m⁵C methyltransferases participate in post-transcriptional RNA modification and thereby regulate gene expression and protein synthesis. How these enzymes specifically recognize their target RNAs at the molecular structural level is still unclear. This project therefore aims to determine the structures of human RNA:m⁵C methyltransferases in complex with RNA, in order to elucidate the molecular mechanism by which these enzymes act in post-transcriptional modification.

3. Structural mechanism of RNA/DNA hybrid recognition by DDX41

The DDX family of RNA helicases is widely involved in RNA biogenesis and function. Although they share the same enzymatic activity, each member has its own functional specificity in the cell. DDX41 can recognize foreign nucleic acids in the cytoplasm to activate immune responses, and in the nucleus it regulates the formation and resolution of R-loops during gene expression. In both functions, DDX41 specifically binds RNA/DNA hybrid regions, yet the structural mechanism underlying this property remains unknown. This project therefore aims to determine the structure of human DDX41 in complex with an RNA/DNA hybrid, in order to understand the molecular mechanism of this RNA helicase.

Publications

1. Wang, H.Y., Lee, Y.Y., Chien, P.J., Tsai, W.A., Sun, P.J., Wang, L.T., Wu, C.C.*, Fan, H.F.* (2025) Single-molecule fluorescence reveals the DNA unwinding mechanism of mitochondrial helicase TWINKLE and its interplay with single-stranded DNA-binding proteins. Nucleic Acids Res. 53(16):gkaf803. doi: 10.1093/nar/gkaf803
2. Chiu, H.P., Shen, C.H., Wu, J.K., Mao, E.Y.C., Yen, H.Y., Chang, Y.P., Wu, C.C.*, Fan, H.F.* (2024) Nuclease-induced stepwise photodropping (NISP) to precisely investigate single-stranded DNA degradation behaviors of exonucleases and endonucleases. Nucleic Acids Res. 52(20):e97. doi: 10.1093/nar/gkae822
3. Mao, E.Y.C., Yen, H.Y., Wu, C.C.* (2024) Structural basis of how MGME1 processes DNA 5' ends to maintain mitochondrial genome integrity. Nucleic Acids Res. 52(7):4067-4078. doi: 10.1093/nar/gkae186
4. Wu, C.C., Lin, J.L.J., Yuan H.S.* (2020) Structures, Mechanisms, and Functions of His-Me Finger Nucleases. Trends Biochem Sci 45(11):935-946. doi: 10.1016/j.tibs.2020.07.002
5. Wu, C.C., Lin, J.L.J., Yang-Yen, H.F., and Yuan, H.S.* (2019) A unique exonuclease ExoG cleaves between RNA and DNA in mitochondrial DNA replication. Nucleic Acids Research 47:5405-5419. doi: 10.1093/nar/gkz241
6. Chen, S.F., Huang, N.L., Lin, J.H., Wu, C.C., Wang, Y.R., Yu, Y.J., Gilson, M.K.*, and Chan, N.L.* (2018) Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate. Nature Communications 9:3085. doi: 10.1038/s41467-018-05406-y
7. Wu, C.C.¹, Baiga, T.J.¹, Downes, M.¹, La Clair, J.J., Atkins, A.R., Richard, S.B., Fan, W., Stockley-Noel, T.A., Bowman, M.E., Noel, J.P.*, and Evans, R.M.* (2017) Structural basis for specific ligation of the peroxisome proliferator-activated receptor delta. Proceedings of the National Academy of Sciences of the United States of America 114:E2563-E2570. doi: 10.1073/pnas.1621513114
   (¹These three authors contribute equally to this work)
8. Wang, Y.R., Chen, S.F., Wu, C.C., Liao, Y.W., Lin, T.S., Liu, K.T., Chen, Y.S., Li, T.K., Chien, T.C., and Chan, N.L.* (2017) Producing irreversible topoisomerase II-mediated DNA breaks by site-specific Pt(II)-methionine coordination chemistry. Nucleic Acids Research 45:10861-10871. doi: 10.1093/nar/gkx742
9. Lin, J.L., Wu, C.C., Yang, W.Z., and Yuan, H.S.* (2016) Crystal structure of endonuclease G in complex with DNA reveals how it nonspecifically degrades DNA as a homodimer. Nucleic Acids Research 44:10480-10490. doi: 10.1093/nar/gkw931