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Yoon Jung Kim, Assistant Professor, Research

Research Focus

The entire human genome is encoded in every cell, but how specific genes are turned on or off is a tightly controlled process that determines the function and fate of each cell. Ninety-eight percent of our genome is comprised of noncoding regions that regulate where and when the protein-coding genes are activated. The regulatory elements that control gene function include enhancers, suppressors, and insulator (CTCF) binding sites. I am interested in understanding how enhancers control target gene transcription in different cell types and how chromosomal 3D structural alterations affect gene regulation.

Over the past decade, I have created innovative functional genomic techniques and approaches to examine enhancer function and regulation during normal development and in cancer. This includes uncovering new insights into cis-regulatory gene regulation of development and disease.

I am also studying how extrachromosomal DNA (ecDNA) amplification drives cancer formation by leveraging my expertise in functional genomics. With Dr. Sihan Wu, I am working to elucidate the functions of ecDNA and how ecDNA drives oncogene amplification in cancer cells with strong drug resistance. I am focusing on unequal ecDNA segregation mechanisms that lead to increase oncogene copy number and heterogeneity. I am also interested in how enhancer function drives oncogene amplifications on ecDNA or chromosomes, as well as how its genetic and epigenetic architecture deregulates oncogene expression in cancer.

Headshot of Yoon Jung Kim, Ph.D.
Yoon Jung Kim, Ph.D., earned her bachelor’s degree in environmental engineering from Ewha Woman’s University in Seoul and stayed to complete her master’s in environmental microbiology….
Headshot of Yoon Jung Kim, Ph.D.

Yoon Jung Kim, Ph.D.

Yoon Jung Kim, Ph.D., earned her bachelor's degree in environmental engineering from Ewha Woman’s University in Seoul and stayed to complete her master's in environmental microbiology. From there, she pursued a Ph.D. in chemical and biomolecular engineering from the Korean Advanced Institute of Science and Technology in Daejeon. Then she completed a postdoctoral fellowship in genetics at Yale University School of Medicine, where she studied transcriptional mechanisms modulated by enhancer and chromosome structure in cell development and disease. As a research scientist, she continued to work on gene regulation, establishing multiple genomic techniques.

Dr. Kim joined the Xu lab at Children’s Medical Center Research Institute (CRI) at UT Southwestern in 2019 as a research scientist focused on genomics and gene regulation by phase-separate condensate formation and cell-specific enhancers. In 2023, she was promoted to Assistant Professor of Research in CRI.

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Xie, Y., Lim, J.Y.S., Liu, W., Gilbreath, C., Sun, X., Qiao, K., Kim, Y.J.#, and S. Wu#. (2026). Cis and trans regulatory mechanisms of extrachromosomal DNA segregation. Nature Cell Biology. (online ahead of print)

Kim, H.B., Nandu, T., Kim, Y.J., Camacho, C.V., and W.L. Kraus. (2026). Dose-dependent hormone actions at estrogen receptor enhancers specify distinct molecular and biological outcomes. Science Advances 12 :eaec2424. (PubMed)

Lee, Jr., M., Zhang, Y., Lim, J.Y.S., Dai, T., Ye, J., Cervantes, M., Sondhi, V., Zheng, S., Kim, Y.J., Chen, B., DeBerardinis, R.J.*, and J. Xu *. (2026). LINE-1 locus transcription nucleates oncogenic chromatin architecture. Cancer Discovery 16: 800-21. (PubMed)

Wang, K., Wang, J., Feng, R., Dudnyk, K., Kim, Y.J., Lim, J.Y.S., Lee, M., Zhang, Y., Gao, X., Cheng, Y., Orkin, S., Zhou, J., Weiss, M., Yue, F., and J. Xu. (2026). Silencing of BCL11A by Disrupting Enhancer-Dependent Epigenetic Insulation. Blood 147: 1470-84. (PubMed)

Stokes, M.S., Kim, Y.J., Kim, Y., Koul, S.,  Chiu, S.P., Dasovich, M., Zuniga, J., Nandu, T., Huang, D., Mathews, T.P., Solmonson, A., Camacho, C.V., and W.L. Kraus. (2026). NAD+ sensing by PARP7 Regulates the C/EBPb-Dependent Transcription Program during adipogenesis. Cell Report 45: 116929. (PubMed)

Chowdhury, B.,* Zhu, K.,* Chaohui, L.,* Alsing, J., Luebeck, J., Stefanova, M.E., Owen S. Chapman, Katerina Kraft, Shu Zhang, Jun Yi Stanley Lim, Xie, Y., Kim, Y.J., Wu, S., Chavez, L., Nir, G., Henssen, A.G., Mischel, P.S., Chang, H.Y., and V. Bafna. (2025). Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3D. Nature Communication 17: 894. (PubMed)

Pal Choudhuri, S., Girard, L., Lim, J.Y.S., Wise, J.F., Freitas, B., Yang, D., Wong, E., Hamilton, S., Chien, V.D., Kim, Y.J., Gilbreath, C., Zhong, J., Phat, S., Myers, D.T., Christensen, C.L., Mazloom-Farsibaf, H., Stanzione, M., Wong, K.K., Hung, Y.P., Farago, A.F., Meador, C.B., Dyson, N.J., Lawrence, M.S., Wu S.,* and B.J. Drapkin.* (2024). Acquired Cross-resistance in Small Cell Lung Cancer due to Extrachromosomal DNA Amplification of MYC paralogs. Cancer Discovery 14: 804–27. (PubMed)

Kim, Y.J.,* Lee, M. Jr.,* Lee, Y.T.,* Jing, J.,* Sanders, J.T., Botten, G., He, L., Lyu, J., Zhang, Y., Mettlen, M., Ly, P., Zhou, Y., and J. Xu. (2023). Light-activated macromolecular phase separation modulates transcription by reconfiguring chromatin interactions. Science Advances 9, eadg1123. (PubMed)

Botten, G., Zhang, Y., Dudnyk, K., Kim, Y.J., Liu, X., Sanders, J.T., Imanci, A., Droin, N., Cao, H., Kaphle, P., Dickerson, K.E., Kumar, K.R., Chen, M., Chen, W., Solary, E., Ly, P., Zhou, J., and J. Xu. (2023). Structural variation cooperates with permissive chromatin to control enhancer hijacking-mediated oncogenic transcription. Blood. 142, 336-351. (PubMed)

Lyu, J., Liu, Y., Gong, L., Chen, M., Madanat, Y.F., Zhang, Y., Cai, F., Gu, Z., Cao, H., Kaphle, P., Kim, Y.J., Kalkan, F.N., Stephen, H., Dickerson, K.E., Ni, M., Chen, W., Patel, P., Mims, A.S., Borate, U., Burd, A., Cai, S.F., Yin, C.C., You, M.J., Chung, S.S., Colins, R.H., DeBerardinis, R.J., Liu, X., and J. Xu. (2023). Disabling uncompetitive inhibition of oncogenic IDH mutations drives acquired resistance. Cancer Discovery 13, 170-193. (PubMed)

Shen, Y., Verboon, J.M., Zhang, Y., Liu, N., Kim, Y.J., Margolous, S., Nandakumar, S.K., Voit, R.A., Fiorini, C., Ejaz, A., Basak, A., Orkin, S.H., Xu, J., and V.G. Sankaran. (2021). A unified model of human hemoglobin switching through single-cell genome editing. Nature Communications 12, 4991. (PubMed)

Hao, Q., Zong, X., Sun, Q., Lin, Y.C., Song, Y.J., Hashemikhabir, S., Hsu, R.Y.C., Kamran, M., Chaudhary, R., Tripathi, V., Singh, D.K., Chakraborty, A., Li, X.L., Kim, Y.J., Orjalo, A.V., Polycarpou-Schwarz, M., Moriarity, B.S., Jenkins, L.M., Johansson, H.E., Zhu, Y.J., Diederichs, S., Bagchi, A., Kim, T.H., Janga, S.C., Lal, A., Prasanth, S.G., and K.V. Prasanth. (2020). The S-phase-induced lncRNA SUNO1 promotes cell proliferation by controlling YAP1/Hippo signaling pathway. eLife 9:e55102. (PubMed)

Kim, Y.J., Xie, P., Cao, L., Zhang, M.Q., and T.H. Kim. (2018). Global transcriptional activity dynamics reveal functional enhancer RNAs. Genome Res. 28, 1799-1811. (PubMed)

Zhao, Y.T., Kwon, D.Y., Johnson, B.S., Fasolino, M., Lamonica, J.M., Kim, Y.J., Zhao, B.S., He, C., Vahedi, G., Kim, T.H., and Z. Zhou. (2018). Long genes linked to autism spectrum disorders harbor broad enhancer-like chromatin domains. Genome Research 28, 933-942. (PubMed)

Johnson, B.S., Zhao, Y., Fasolino, M.D., Lamonica, J.M., Kim, Y.J., Wood, K.H., Bu, D., Cui, Y., Goffin, D., Kim, T.H., and Z. Zhou. (2017). Biotin tagging of MeCP2 reveals contextual insights into the Rett syndrome transcriptome. Nature Medicine 23, 1203-1214. (PubMed)

Kim, Y.J., and T.H. Kim. (2017). Chromosome conformation capture for research on innate antiviral immunity. Methods in Molecular Biology 1656, 195-208. (PubMed)

Tan, J.L., Fogley, R.D., Flynn, R.A., Ablain, J., Yang, S., Saint-André, V., Fan, Z.P., Do, B.T., Laga, A.C., Fujinaga, K., Santoriello, C., Greer, C.B., Kim, Y.J., Clohessy, J.G., Bothmer, A., Pandell, N., Avagyan, S., Brogie, J.E., van Rooijen, E., Hagedorn, E.J., Shyh-Chang, N., White, R.M., Price, D.H., Pandolfi, P.P., Peterlin, B.M., Zhou, Y., Kim, T.H., Asara, J.M., Chang, H.Y., Young, R.A., and L.I. Zon. (2016). Stress from nucleotide depletion activates the transcriptional regulator HEXIM1 to suppress melanoma. Molecular Cell 62, 34-46. (PubMed)

Banerjee, A.R.,* Kim, Y.J.,* and T.H. Kim. (2014). A novel virus-inducible enhancer of the interferon-β gene with tightly linked promoter and enhancer activities. Nucleic Acids Research 42, 12537-54. (PubMed)

Kim, Y.J., Greer, C.B., Cecchini, K., Harris, L.N., Tuck, D.P., and T.H. Kim. (2013). HDAC inhibitors induce transcriptional repression of high copy number genes in breast cancer through elongation blockade. Oncogene 32, 2828-2835. (PubMed)

Kim, Y.J., Cecchini, K.R., and T.H. Kim. (2011). Conserved, developmentally regulated mechanism couples chromosomal looping and heterochromatin barrier activity at the homeobox gene A locus. PNAS 108, 7391-7396. (PubMed).

Zorca, C.E.,* Kim, L.K.,* Kim, Y.J., Krause, M.R., Zenklusen, D., Spilianakis, D.G., and R.A. Flavell. (2015). Myosin VI regulates gene pairing and transcriptional pause release in T cells. PNAS 112, 1587-93.(PubMed)

Greer, C.B.,* Tanaka, Y.,* Kim, Y.J., Xie, P., Zhang, M.Q., Park, I.H., and T.H. Kim. (2015). Histone deacetylases positively regulate transcription through the elongation machinery. Cell Reports 13, 1444-1455. (PubMed)

*Contributed equally
#Co-corresponding author

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