About Emily
I am always curious about how cells maintain their internal order and fitness across generations. My research focuses on how the cytoskeletal organization orchestrates cargo transport, organelle inheritance and quality control during asymmetric cell division to maintain age asymmetry. As a postdoctoral researcher in Dr. Liza Pon’s lab at Columbia University, I discovered an uncharacterized actin structure, the Actin Cable Organizing Center (ACOC), which captures actin cable and promotes disassembly at site to organize them. This finding sheds light on how budding yeast cells regulate actin cable dynamics to enhance the efficiency of cargo transport and ensure organelle quality, processes that are crucial to maintain cellular fitness and longevity. By combining quantitative imaging, biosensors, and molecular genetics, I aim to investigate the fundamental principles linking cytoskeletal regulation to aging. My long-term objective is to build a research program that bridges cell biology, biophysics, and aging biology to understand how cells preserve their functional asymmetry through cytoskeletal organization and ensure organelle quality across divisions.
Organellar differentiation in chloroplast development
My research interest in organelle biology began when I was a graduate student. I reported a nuclear-encoded protein, named NUCLEAR CONTROL OF PEP ACTIVITY (NCP), which is essential for chloroplast development in plants. What is intriguing is that this protein acts as a dual agent--it localizes to both the nucleus and the chloroplasts, communicating between the two compartments. In the nucleus, NCP activates light-induced development by triggering the degradation of master transcriptional repressors; in the chloroplast, it participates in photosynthetic gene expression through mediating the plastid-encoded RNA polymerase complex formation. This dual role revealed how light signaling and chloroplast transcription are tightly coordinated to drive photosynthesis. Through phylogenetic analysis, I found that NCP belongs to an ancient family of dual-targeted proteins conserved across land plants, suggesting that this chloroplast–nuclear crosstalk mechanism arose early in evolution to coordinate gene expression across cellular compartments.
Yang, E.J., Yoo, C.Y., Liu, J., Wang, H., Cao, J., Li, F.-W., Pryer, K.M., Sun, T., Weigel, D., Zhou, P., et al. (2019). NCP activates chloroplast transcription by controlling phytochrome-dependent dual nuclear and plastidial switches. Nat Commun 10, 2630. https://doi.org/10.1038/s41467-019-10517-1.
Mitochondrial inheritance and quality control in asymmetric cell division
My postdoctoral work has centered on understanding how mitochondrial positioning and quality control influence cellular lifespan. I was inspired by early findings from the Pon lab showing that not all mitochondria within a cell are equal—those with higher functioning are selectively delivered to where they are needed most, such as the neuronal synapse or the yeast bud tip, which is a process essential for maintaining cell health. Focusing on the mitochondrial F-box protein Mfb1, I found that it anchors a small population of high-functioning mitochondria at the mother cell tip in yeast, guided by cell polarity cues. This work uncovered a novel mechanism by which the polarity machinery regulates lifespan through spatial control of mitochondrial quality. To dissect these processes, I developed quantitative imaging tools, open-source analysis pipelines, and cellular aging assays using the MiniStat and HYAA microfluidic systems. Together, these approaches have provided new insights into how cells spatially organize their organelles to sustain function and longevity.
Yang, E.J., Pernice, W.M., and Pon, L.A. (2022). A Role for Cell Polarity in Lifespan and Mitochondrial Quality Control in the Budding Yeast Saccharomyces cerevisiae. ISCIENCE, 103957. https://doi.org/10.1016/j.isci.2022.103957.
Liao, P.-C., Yang, E.J., and Pon, L.A. (2020). Live-Cell Imaging of Mitochondrial Redox State in Yeast Cells. STAR protocols 1, 100160.
Yang, E.J., and Pon, L.A. (2022). Enrichment of aging yeast cells and budding polarity assay in Saccharomyces cerevisiae. STAR Protocols 3, 101599. https://doi.org/10.1016/j.xpro.2022.101599.
Yang, E.J., Boldogh, I.R., Ji, H., Pon, L.A., and Swayne, T.C. (2023). Imaging of mtHyPer7, a Ratiometric Biosensor for Mitochondrial Peroxide, in Living Yeast Cells. Journal of visualized experiments : JoVE. https://doi.org/10.3791/65428.
Identification of the Actin Cable Organizing Center (ACOC)
Organellar inheritance can also be seen as a form of cargo transport, which is solely relied on actin cytoskeleton in budding yeast. I start being intrigued by how cells organize their cytoskeletons to control polarity and inheritance. While the microtubule organizing center (MTOC) is well known for anchoring and organizing microtubules, I discovered that the actin cytoskeleton has its own functional counterpart, the Actin Cable Organizing Center (ACOC), in budding yeast. The ACOC localizes to the mother cell tip, a polarity site remained less understood. I found that it performs four key functions: (1) capture of the pointed ends of actin cables emanating from the bud to align them along the mother–bud axis; (2) control of the length of cables through conserved disassembly machinery; (3) remodeling low-functioning cables through capture-induced breakage; and (4) anchorage of Mfb1and high-functioning mitochondria at the mother cell tip to preserve healthspan and lifespan.
To investigate the function of ACOC, I developed open-source FIJI macros for quantitative analysis of cytoskeletal architecture and polarity. I also optimized live-cell imaging approaches—using Lifeact to visualize actin structures, collaborating with Dr. Jason Vevea to enhance actin visualization by using Halo, SNAP, and CLIP tagging for multicolor imaging, and partnering with Dr. Dirk Trauner to test a light-switchable version of Latrunculin in yeast that enables rapid, reversible disruption of actin cables. Together, these tools allowed me to study actin organization with unprecedented spatial and temporal precision.
Yang, E.J.-N., Filpo, K., Boldogh, I., Swayne, T.C., and Pon, L.A. Tying up loose ends: an actin cable organizing center contributes to actin cable polarity, function and quality control in budding yeast.
Sing, C.N., Yang, E.J., Swayne, T.C., Higuchi-Sanabria, R., Tsang, C.A., Boldogh, I.R., and Pon, L.A. (2022). Imaging the Actin Cytoskeleton in Live Budding Yeast Cells. In Methods in molecular biology (Clifton, N.J.), pp. 53–80.
Sing, C.N., Yang, E.J., Higuchi-Sanabria, R., Pon, L.A., Boldogh, I.R., and Swayne, T.C. (2022). Imaging the Actin Cytoskeleton in Fixed Budding Yeast Cells. In Methods in molecular biology (Clifton, N.J.), pp. 81–100.
Sing, C.N., Garcia, E.J., Lipkin, T.G., Huckaba, T.M., Tsang, C.A., Coughlin, A.C., Yang, E.J., Boldogh, I.R., Higuchi-Sanabria, R., and Pon, L.A. (2022). Identification of a modulator of the actin cytoskeleton, mitochondria, nutrient metabolism and lifespan in yeast. Nat Commun 13, 2706. https://doi.org/10.1038/s41467-022-30045-9.
VepÅ™ek, N.A., Cooper, M.H., Laprell, L., Yang, E.J.-N., Folkerts, S., Bao, R., Boczkowska, M., Palmer, N.J., Dominguez, R., Oertner, T.G., et al. (2024). Optical Control of G-Actin with a Photoswitchable Latrunculin. J. Am. Chem. Soc. 146, 8895–8903. https://doi.org/10.1021/jacs.3c10776.
Other research contributions
In addition to my research achievements, I have authored two themed reviews on how the cytoskeleton interacts with lipid droplets and how organelle quality control is regulated in budding yeast, Saccharomyces cerevisiae. Beyond writing, I enjoy making scientific concepts visually attractive and accessible by creating clear and compelling scientific illustrations. You can check out my portfolio to see how I combine accuracy and creativity to convey complex ideas effortlessly.
Yang, E.J., Liao, P., and Pon, L. (2024). Mitochondrial protein and organelle quality control—Lessons from budding yeast. IUBMB Life 76, 72–87. https://doi.org/10.1002/iub.2783. (Featured in Cover Art)
Liao, P.-C., Yang, E.J., Borgman, T., Boldogh, I.R., Sing, C.N., Swayne, T.C., and Pon, L.A. (2022). Touch and Go: Membrane Contact Sites Between Lipid Droplets and Other Organelles. Frontiers in Cell and Developmental Biology 10.