Publications

 Publications

1. Nam, Hye J.† , Han, Jun H.†, Yu, J.†, Cho, Chang S., Kim, D., Kim, Young E., Kim, Min J., Kim, Jeong H., Jo, Dong H., and Bae, S. (2025). Autophagy induction enhances homologous recombination-associated CRISPR–Cas9 gene editing. Nucleic Acids Research 53. 10.1093/nar/gkaf258.

2. Yu, J., Lee, H., Cho, S.M., Lee, Y., Kim, D., Hong, S.G., Park, S.-J., Kim, S.-G., Jin, H., and Lee, J. (2024). Life under the snow: A year-round transcriptome analysis of Antarctic mosses in natural habitats provides insight into the molecular adaptation of plants under extreme environment. Plant, Cell & Environment 47, 976-991. https://doi.org/10.1111/pce.14793.

3. Kim, J.H., Yu, J., Kim, J.Y., Park, Y.J., Bae, S., Kang, K.K., and Jung, Y.J. (2024). Phenotypic characterization of pre-harvest sprouting resistance mutants generated by the CRISPR/Cas9-geminiviral replicon system in rice. BMB Rep. 57, 79-85. 10.5483/BMBRep.2023-0210.

4. Kim, H., Lee, Y., Yu, J., Park, J.-Y., Lee, J., Kim, S.-G., and Hyun, Y. (2024). Production of the antimalarial drug precursor amorphadiene by microbial terpene synthase-like from the moss Sanionia uncinata. Planta 260, 145. 10.1007/s00425-024-04558-0.

5. Choi, Y.J., Nam, Y.A., Hyun, J.Y., Yu, J., Mun, Y., Yun, S.H., Lee, W., Park, C.J., Han, B.W., and Lee, B.A.-O. (2024). Impaired chaperone-mediated autophagy leads to abnormal SORT1 (sortilin 1) turnover and CES1-dependent triglyceride hydrolysis. Autophagy.

6. Kim, J.Y., Kim, J.H., Jang, Y.H., Yu, J., Bae, S., Kim, M.-S., Cho, Y.-G., Jung, Y.J., and Kang, K.K. (2023). Transcriptome and Metabolite Profiling of Tomato SGR-Knockout Null Lines Using the CRISPR/Cas9 System. International Journal of Molecular Sciences 24, 109.

7. Kim, H.K., Kim, J.Y., Kim, J.H., Go, J.Y., Jung, Y.-S., Lee, H.J., Ahn, M.-J., Yu, J., Bae, S., Kim, H.S., et al. (2023). Biochemical Characterization of Orange-Colored Rice Calli Induced by Target Mutagenesis of OsOr Gene. Plants 12, 56.

8. Jin, H.†, Yu, J.†, Kaleku, J., Lee, Y., Park, E., Lee, H., Kim, H.-W., and Lee, J. (2023). High-Quality Genome Resource of a Novel Venturiaceae sp. KMAF11, Isolated from Diseased Colobanthus quitensis, an Antarctic Flowering Plant. Plant Disease 107, 911-914. 10.1094/pdis-03-22-0706-a.

9. Choi, Y.-J., Yun, S.H., Yu, J., Mun, Y., Lee, W., Park, C.J., Han, B.W., and Lee, B.-H. (2023). Chaperone-mediated autophagy dysregulation during aging impairs hepatic fatty acid oxidation via accumulation of NCoR1. Molecular Metabolism 76, 101784. https://doi.org/10.1016/j.molmet.2023.101784.

10. Kim, N.-S., Yu, J., Bae, S., Kim, H.S., Park, S., Lee, K., Lee, S.I., and Kim, J.A. (2022). Identification and Characterization of PSEUDO-RESPONSE REGULATOR (PRR) 1a and 1b Genes by CRISPR/Cas9-Targeted Mutagenesis in Chinese Cabbage (Brassica rapa L.). International Journal of Molecular Sciences 23, 6963.

11. Kim, J.H., Yu, J., Kim, H.K., Kim, J.Y., Kim, M.-S., Cho, Y.-G., Bae, S., Kang, K.K., and Jung, Y.J. (2022). Genome Editing of Golden SNP-Carrying Lycopene Epsilon-Cyclase (LcyE) Gene Using the CRSPR-Cas9/HDR and Geminiviral Replicon System in Rice. International Journal of Molecular Sciences 23, 10383.

12. Kim, E.J.†, Chae, H.†, Koo, M.H., Yu, J., Kim, H., Cho, S.M., Hong, K.W., Lee, J.Y., Youn, U.J., Kim, S., et al. (2022). Statistical optimization of phytol and polyunsaturated fatty acid production in the Antarctic microalga Micractinium variabile KSF0031. Algae 37, 175-183. 10.4490/algae.2022.37.4.1.

13. Hong, S.-A.†, Seo, J.H.†, Wi, S., Jung, E.S., Yu, J., Hwang, G.-H., Yu, J.H., Baek, A., Park, S., Bae, S., and Cho, S.-R. (2022). In vivo gene editing via homology-independent targeted integration for adrenoleukodystrophy treatment. Molecular Therapy 30, 119-129. https://doi.org/10.1016/j.ymthe.2021.05.022.

14. Yu, J.†, Tu, L.†, Subburaj, S.†, Bae, S., and Lee, G.-J. (2021). Simultaneous targeting of duplicated genes in Petunia protoplasts for flower color modification via CRISPR-Cas9 ribonucleoproteins. Plant Cell Reports 40, 1037-1045. 10.1007/s00299-020-02593-1.

15. Song, B., Yang, S., Hwang, G.-H., Yu, J., and Bae, S. (2021). Analysis of NHEJ-Based DNA Repair after CRISPR-Mediated DNA Cleavage. International Journal of Molecular Sciences 22, 6397.

16. Lee, K., Park, O.-S., Go, J.Y., Yu, J., Han, J.H., Kim, J., Bae, S., Jung, Y.J., and Seo, P.J. (2021). Arabidopsis ATXR2 represses de novo shoot organogenesis in the transition from callus to shoot formation. Cell Reports 37, 109980. https://doi.org/10.1016/j.celrep.2021.109980.

17. Lee, H.G., Kim, D.H., Choi, Y.-R., Yu, J., Hong, S.-A., Seo, P.J., and Bae, S. (2021). Enhancing plant immunity by expression of pathogen-targeted CRISPR-Cas9 in plants. Gene and Genome Editing 1, 100001. https://doi.org/10.1016/j.ggedit.2021.100001.

18. Kyung, J., Jeon, M., Jeong, G., Shin, Y., Seo, E., Yu, J., Kim, H., Park, C.-M., Hwang, D., and Lee, I. (2021). The two clock proteins CCA1 and LHY activate VIN3 transcription during vernalization through the vernalization-responsive cis-element. The Plant Cell 34, 1020-1037. 10.1093/plcell/koab304.

19. Kim, Y.†, Hong, S.-A.†, Yu, J.†, Eom, J., Jang, K., Yoon, S., Hong, D.H., Seo, D., Lee, S.-N., Woo, J.-S., et al. (2021). Adenine base editing and prime editing of chemically derived hepatic progenitors rescue genetic liver disease. Cell Stem Cell 28, 1614-1624.e1615. https://doi.org/10.1016/j.stem.2021.04.010.

20. Kim, E.J., Chae, H., Yu, J., Kim, H., Cho, S.M., Shin, S.C., Choi, H.-G., Kim, S., and Han, S.J. (2021). Mitochondrial genome of the Antarctic microalga Micractinium simplicissimum KSF0127 (Chlorellaceae, Trebouxiophyceae). Mitochondrial DNA Part B 6, 878-879. 10.1080/23802359.2021.1886010.

21. Kim, C.†, Jeong, Y.K.†, Yu, J., Shin, H.J., Ku, K.B., Cha, H.J., Han, J.H., Hong, S.-A., Kim, B.-T., Kim, S.-J., et al. (2021). Efficient Human Cell Coexpression System and Its Application to the Production of Multiple Coronavirus Antigens. Advanced Biology 5, 2000154. https://doi.org/10.1002/adbi.202000154.

22. Jung, Y.J., Lee, H.J., Yu, J., Bae, S., Cho, Y.-G., and Kang, K.K. (2021). Transcriptomic and physiological analysis of OsCAO1 knockout lines using the CRISPR/Cas9 system in rice. Plant cell reports 40, 1013-1024. 10.1007/s00299-020-02607-y.

23. Jang, H.-K.†, Jo, D.H.†, Lee, S.-N., Cho, C.S., Jeong, Y.K., Jung, Y., Yu, J., Kim, J.H., Woo, J.-S., and Bae, S. (2021). High-purity production and precise editing of DNA base editing ribonucleoproteins. Science advances 7, eabg2661. doi:10.1126/sciadv.abg2661.

24. Hur, J.H., Kang, C.Y., Lee, S., Parveen, N., Yu, J., Shamim, A., Yoo, W., Ghosh, A., Bae, S., Park, C.-J., and Kim, Kyeong K. (2021). AC-motif: a DNA motif containing adenine and cytosine repeat plays a role in gene regulation. Nucleic Acids Research 49, 10150-10165. 10.1093/nar/gkab728.

25. Yun, Y.†, Hong, S.-A.†, Kim, K.-K., Baek, D., Lee, D., Londhe, A.M., Lee, M., Yu, J., McEachin, Z.T., Bassell, G.J., et al. (2020). CRISPR-mediated gene correction links the ATP7A M1311V mutations with amyotrophic lateral sclerosis pathogenesis in one individual. Communications Biology 3, 33. 10.1038/s42003-020-0755-1.

26. Yu, J.†, Cho, E.†, Choi, Y.-G.†, Jeong, Y.K., Na, Y., Kim, J.-S., Cho, S.-R., Woo, J.-S., and Bae, S. (2020). Purification of an Intact Human Protein Overexpressed from Its Endogenous Locus via Direct Genome Engineering. ACS Synthetic Biology 9, 1591-1598. 10.1021/acssynbio.0c00090.

27. Jung, Y.J., Kim, J.H., Lee, H.J., Kim, D.H., Yu, J., Bae, S., Cho, Y.-G., and Kang, K.K. (2020). Generation and Transcriptome Profiling of Slr1-d7 and Slr1-d8 Mutant Lines with a New Semi-Dominant Dwarf Allele of SLR1 Using the CRISPR/Cas9 System in Rice. International Journal of Molecular Sciences 21, 5492.

28. Hwang, G.-H.†, Yu, J.†, Yang, S., Son, W.J., Lim, K., Kim, H.S., Kim, J.-S., and Bae, S. (2020). CRISPR-sub: Analysis of DNA substitution mutations caused by CRISPR-Cas9 in human cells. Computational and Structural Biotechnology Journal 18, 1686-1694. https://doi.org/10.1016/j.csbj.2020.06.026.

29. Lee, C., Hyun Jo, D., Hwang, G.-H., Yu, J., Kim, J.H., Park, S.-e., Kim, J.-S., Kim, J.H., and Bae, S. (2019). CRISPR-Pass: Gene Rescue of Nonsense Mutations Using Adenine Base Editors. Molecular Therapy 27, 1364-1371. 10.1016/j.ymthe.2019.05.013.

30. Kim, D.-H., Yu, J., Park, J.C., Jeong, C.-B., Bae, S., and Lee, J.-S. (2019). Targeted cytochrome P450 3045C1 (CYP3045C1) gene mutation via CRISPR-Cas9 ribonucleoproteins in the marine rotifer Brachionus koreanus. Hydrobiologia 844, 117-128. 10.1007/s10750-018-3854-y.

31. Jeong, Y.K.†, Yu, J.†, and Bae, S. (2019). Construction of non-canonical PAM-targeting adenosine base editors by restriction enzyme-free DNA cloning using CRISPR-Cas9. Scientific Reports 9, 4939. 10.1038/s41598-019-41356-1.

32. Jeon, Y., Choi, Y.H., Jang, Y., Yu, J., Goo, J., Lee, G., Jeong, Y.K., Lee, S.H., Kim, I.-S., Kim, J.-S., et al. (2018). Direct observation of DNA target searching and cleavage by CRISPR-Cas12a. Nature Communications 9, 2777. 10.1038/s41467-018-05245-x.

33. Hwang, G.-H., Park, J., Lim, K., Kim, S., Yu, J., Yu, E., Kim, S.-T., Eils, R., Kim, J.-S., and Bae, S. (2018). Web-based design and analysis tools for CRISPR base editing. BMC Bioinformatics 19, 542. 10.1186/s12859-018-2585-4.

34. Baek, K., Yu, J., Jeong, J., Sim, S.J., Bae, S., and Jin, E. (2018). Photoautotrophic production of macular pigment in a Chlamydomonas reinhardtii strain generated by using DNA-free CRISPR-Cas9 RNP-mediated mutagenesis. Biotechnology and Bioengineering 115, 719-728. https://doi.org/10.1002/bit.26499.

35. Yu, J.†, Baek, K.†, Jin, E., and Bae, S. (2017). DNA-free Genome Editing of Chlamydomonas reinhardtii Using CRISPR and Subsequent Mutant Analysis. Bio-protocol 7, e2352. 10.21769/BioProtoc.2352.

36. Lee, S.H.†, Yu, J.†, Hwang, G.H., Kim, S., Kim, H.S., Ye, S., Kim, K., Park, J., Park, D.Y., Cho, Y.K., et al. (2017). CUT-PCR: CRISPR-mediated, ultrasensitive detection of target DNA using PCR. Oncogene 36, 6823-6829. 10.1038/onc.2017.281.

37. Lee, J.-H., Park, S.-J., Hariharasudhan, G., Kim, M.-J., Jung, S.M., Jeong, S.-Y., Chang, I.-Y., Kim, C., Kim, E., Yu, J., et al. (2017). ID3 regulates the MDC1-mediated DNA damage response in order to maintain genome stability. Nature Communications 8, 903. 10.1038/s41467-017-01051-z.

38. Jeong, J.†, Baek, K.†, Yu, J.†, Kirst, H., Betterle, N., Shin, W., Bae, S., Melis, A., and Jin, E. (2017). Deletion of the chloroplast LTD protein impedes LHCI import and PSI–LHCI assembly in Chlamydomonas reinhardtii. Journal of Experimental Botany 69, 1147-1158. 10.1093/jxb/erx457.

39. Seo, E., Yu, J., Ryu, K.H., Lee, M.M., and Lee, I. (2011). WEREWOLF, a Regulator of Root Hair Pattern Formation, Controls Flowering Time through the Regulation of FT mRNA Stability. Plant Physiology 156, 1867-1877. 10.1104/pp.111.176685.

40. Hyun, Y., Choi, S., Hwang, H.-J., Yu, J., Nam, S.-J., Ko, J., Park, J.-Y., Seo, Y.S., Kim, E.Y., Ryu, S.B., et al. (2008). Cooperation and Functional Diversification of Two Closely Related Galactolipase Genes for Jasmonate Biosynthesis. Developmental Cell 14, 183-192. https://doi.org/10.1016/j.devcel.2007.11.010.\