Chun-Kan Chen, PhD

Assistant Professor of Cell Biology & Physiology

Research Interests

The Chen lab is interested in non-canonical RNA-mediated gene regulation. Our research focus on investigating the biogenesis, regulation, and function of a peculiar class of non-canonical RNA, circular RNAs (circRNAs), and uncovering how dysregulation of these processes contributes to disease. The human genome encodes tens of thousands of circRNAs, some of which have been shown to contribute to disease pathogenesis when dysregulated. Despite their abundance and disease relevance, the function and regulation of circRNAs and their roles in disease pathogenesis remain largely unknown. Revealing the mechanisms behind the circRNA-mediated disease can provide valuable clinical insights for therapeutic interventions. To elucidate the mechanisms, We aim to develop novel multi-omic and high-throughput screening approaches to uncover the RNA elements, genomic features, and protein components regulating the functions of circRNAs. Our long-term goal is to harness the unique features of circRNAs to develop a new platform for RNA-based technologies and therapeutic interventions, providing valuable tools for both basic science research and clinical applications. Our research on the biogenesis, regulation, and function of circRNA will provide key insights into the roles circRNAs play in diverse biological processes and the molecular mechanisms behind circRNA-mediated disease, with implications for both basic science and translational research.

Professional Education

Postdoc, Department of Genetics, Stanford University School of Medicine

Ph.D., Division of Biology and Biological Engineering, California Institute of Technology

M.S., Biochemistry & Molecular Biology, University of Southern California

B.S., Life Science Department, National Taiwan University, Taiwan

Chen Lab

McDonnell Sciences Building

Circular RNA (circRNA) | RNA Binding Protein (RBP) | RNA Structures | Hypoxia | Single-Cell RNA Sequencing (scRNA-seq) | RNA Therapy

The Chen lab utilizes multi-omic and high-throughput screening approaches to investigate the regulation and function of circRNA and uncover the molecular mechanisms of circRNA mediated disease. We aim to uncover (i) the RNA elements, genomic features, and protein components regulating the functions of circRNAs, (ii) the molecular mechanism of how circRNAs regulate cell physiology, and (iii) how circRNA dysregulation can lead to disease pathogenesis. Our long-term goal is to harness the unique properties of circRNAs to develop new tools for RNA-based technologies and therapeutic interventions.


Chen, R., Wang, S.K., Belk, J.A., Amaya, L., Li, Z., Cardenas, A., Abe, B.T., Chen, C.-K., Wender, P.A. and Chang, H.Y. “Engineering circular RNA for enhanced protein production.” Nature Biotechnology (2022), pp.1-11.

Ali, M.K., Schimmel, K., Zhao, L., Chen, C.-K., Dua, K., Nicolls, M.R. and Spiekerkoetter, E., “The role of circular RNAs in pulmonary hypertension.” European Respiratory Journal (2022). (Review)

Cable J, Heard E, Hirose T, Prasanth KV, Chen LL, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, Chen, C-K, Wilusz JE, Lempradl A, McGeary SE, Wahba L, Pyle AM, Hargrove AE, Simon MD, Marcia M, Przanowska RK, Chang HY, Jaffrey SR, Contreras LM, Chen Q, Shi J, Mendell JT, He L, Song E, Rinn JL, Lalwani MK, Kalem MC, Chuong EB, Maquat LE, Liu X. “Noncoding RNAs: biology and applications-a Keystone Symposia report.” Ann N Y Acad Sci. (2021) 1506(1):118-141. (Review)

Chen, C.-K., Cheng, R., Demeter, J., Chen, J., Weingarten-Gabbay, S., Jiang, L., Snyder, M.P., Weissman, J.S., Segal, E., Jackson, P.K., Chang, H.Y. “Structured elements drive extensive circular RNA translation.” Molecular Cell (2021). 81(20), pp.4300-4318.

Pandya-Jones, A., Markaki, Y., Serizay, J., Chitiashvili, T., Leon, W.R.M., Damianov, A., Chronis, C., Papp, B., Chen, C.-K., McKee, R. and Wang, X.J., Chau, A., Sabri, S., Leonhardt, H., Zheng, S., Guttman, M., Black, D. L., Plath, K. “A protein assembly mediates Xist localization and gene silencing.” Nature 587.7832 (2020): 145-151.

Patil, D.P., Chen, C.-K., Pickering, B.F., Chow, A., Jackson, C., Guttman, M., and Jaffrey, S.R. (2016). “m6A RNA methylation promotes XIST-mediated transcriptional repression.” Nature. 537.7620 (2016): 369-373

Geng, J., Wang, L., Lee, J.Y., Chen, C.-K., and Chang, K.T. (2016). “Phosphorylation of Synaptojanin Differentially Regulates Endocytosis of Functionally Distinct Synaptic Vesicle Pools.” The Journal of Neuroscience 36.34: 8882-8894.

Chen, C.-K., Blanco, M., Jackson, C., Aznauryan, E., Ollikainen, N., Surka, C., Chow, A., McDonel, P., Cerase, A., and Guttman, M. “Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing.” Science. 354.6311 (2016): 468-472.

*McHugh, C.A., *Chen, C.-K., Chow, A., Surka, C.F., Tran, C., McDonel, P., Pandya-Jones, A., Blanco, M., Burghard, C., and Moradian, A. *Co-first author. “The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3.” Nature 521.7551 (2015): 232-236.

Yang, B., Treweek, J.B., Kulkarni, R.P., Deverman, B.E., Chen, C.-K., Lubeck, E., Shah, S., Cai, L., and Gradinaru, V. “Single-cell phenotyping within transparent intact tissue through whole-body clearing.” Cell 158.4 (2014): 945-958.

Chen, C.-K., Bregere, C., Paluch, J., Lu, J.F., Dickman, D.K., and Chang, K.T. “Activity-dependent facilitation of Synaptojanin and synaptic vesicle recycling by the Minibrain kinase.” Nature Communications. 5.1 (2014): 1-14.