Department of Biological Science

Biological Science Faculty Member

Miao Lab Website

Research and Professional Interests:

Most animal life begins with the union of a sperm and an egg. The newly formed zygote develops under precise regulation, undergoing in vivo reprogramming to gain the potential to become any cell type and eventually a whole organism. While we have gained some understanding of this process, many of the underlying mechanisms remain unknown. For example, what are the factors and regulatory networks that orchestrate reprogramming and differentiation? And what happens when these regulators malfunction?

Answering these questions not only helps us decode how life begins but also provides critical insights into disease, including cancer. To address them, our lab uses zebrafish as a model organism and integrates advanced genetics, genomics, and imaging approaches. We focus on both Development and Disease aspects. Please see our lab website for more details and our updated publications.

Interested in joining us?

Publications:

(Newest First; # denotes co-corresponding authors; * denotes equal contributions)

• Youlten, S.E.*, Miao, L.*, Hoppe, C., Boswell, C.W., Musaev, D., Abdelmessih, M., Olowookere, D., Weiss, L.A., Krishnaswamy, S., and Giraldez, A.J., and Tornini, V.A. (2025). In vivo differentiation of embryonic cells devoid of key reprogramming factors. Cell Reports, accepted
• Boswell, C.W., Hoppe, C., Sherrard, A., Miao, L., Kojima, M.L., Martino, P., Zhao, N., Stasevich, T.J., Nicoli, S., and Giraldez, A.J. (2025). Genetically encoded affinity reagents are a toolkit for visualizing and manipulating endogenous protein function in vivo. Nat Commun 16, 5503.
• Youlten, S.E.*, Miao, L.*, Hoppe, C., Boswell, C.W., Musaev, D., Abdelmessih, M., Krishnaswamy, S., Tornini, V.A., and Giraldez, A.J. (2024). Novel cell states arise in embryonic cells devoid of key reprogramming factors. bioRxiv, 2024.2005.2013.593729.
• Pownall, M.E.#, Miao, L.#, Vejnar, C.E., M'Saad, O., Sherrard, A., Frederick, M.A., Benitez, M.D.J., Boswell, C.W., Zaret, K.S., Bewersdorf, J., and Giraldez, A.J.# (2023). Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin. Science 381, 92-100.
• Tornini, V.A., Miao, L.*, Lee, H.J.*, Gerson, T., Dube, S.E., Schmidt, V., Kroll, F., Tang, Y., Du, K., Kuchroo, M., et al. (2023). linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells. Elife 12.
• Boswell, C.W., Hoppe, C., Sherrard, A., Miao, L., Kojima, M.L., Krishna, S., Musaev, D., Zhao, N., Stasevich, T.J., and Giraldez, A.J. (2023). Genetically encoded affinity reagents (GEARs): A toolkit for visualizing and manipulating endogenous protein function in vivo. bioRxiv, 2023.2011.2015.567075.
• Tornini, V.A., Lee, H.-J., Miao, L., Tang, Y., Dube, S.E., Gerson, T., Schmidt, V.J., Du, K., Kuchroo, M., Kroll, F., et al. (2022). linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells. bioRxiv, 2022.2007.2021.501032.
• Miao, L.*#, Tang, Y*., Bonneau, A.R., Chan, S.H., Kojima, M.L., Pownall, M.E., Vejnar, C.E., Gao, F., Krishnaswamy, S., Hendry, C.E., and Giraldez, A.J. # (2022). The landscape of pioneer factor activity reveals the mechanisms of chromatin reprogramming and genome activation. Mol Cell 82, 986-1002 e1009.
• Miao, L.*, Tang, Y.*, Bonneau, A.R., Chan, S.H., Kojima, M.L., Pownall, M.E., Vejnar, C.E., and Giraldez, A.J. (2020). Synergistic activity of Nanog, Pou5f3, and Sox19b establishes chromatin accessibility and developmental competence in a context-dependent manner. bioRxiv, 2020.2009.2001.278796.
• Sun, Y., Zhang, B., Luo, L., Shi, D.L., Wang, H., Cui, Z., Huang, H., Cao, Y., Shu, X., Zhang, W., et al. (2019). Systematic genome editing of the genes on zebrafish Chromosome 1 by CRISPR/Cas9. Genome Res 30, 118-126.
• Chan, S. H., Tang, Y., Miao, L., Darwich-Codore, H., Vejnar, C. E., Beaudoin, J. D., Musaev, D., Fernandez, J. P., Benitez, M., Bazzini, A. A., Moreno-Mateos, M. A., & Giraldez, A. J. (2019). Brd4 and P300 Confer Transcriptional Competency during Zygotic Genome Activation. Developmental Cell, 49(6), 867–881.e8.
• Chan, S.H., Tang, Y., Miao, L., Darwich-Codore, H., Vejnar, C.E., Beaudoin, J.-D., Musaev, D., Fernandez, J.P., Moreno-Mateos, M.A., and Giraldez, A.J. (2018). Brd4 and P300 regulate zygotic genome activation through histone acetylation. bioRxiv, 369231.
• Fernandez, J.P., Moreno-Mateos, M.A., Gohr, A., Miao, L., Chan, S.H., Irimia, M., and Giraldez, A.J. (2018). RES complex is associated with intron definition and required for zebrafish early embryogenesis. PLoS genetics 14, e1007473.
• Zhu, D., Gong, X., Miao, L., Fang, J., & Zhang, J. (2017). Efficient Induction of Syncytiotrophoblast Layer II Cells from Trophoblast Stem Cells by Canonical Wnt Signaling Activation. Stem Cell Reports 9(6), 2034–2049.
• Miao, L., Yuan, Y., Cheng, F., Fang, J., Zhou, F., Ma, W., Jiang, Y., Huang, X., Wang, Y., Shan, L., Chen, D., Zhang, J. (2017). Translation repression by maternal RNA binding protein Zar1 is essential for early oogenesis in zebrafish. Development (Cambridge, England) 144, 128-138.
• Cheng, F., Miao, L., Wu, Q., Gong, X., Xiong, J., and Zhang, J. (2016). Vinculin b deficiency causes epicardial hyperplasia and coronary vessel disorganization in zebrafish. Development (Cambridge, England) 143, 3522-3531.
• Fang, J., Wang, H., Miao, L., Kuang, X., Ma, W., Wang, C., Zhang, J., and Xia, G. (2016). Involvement of Protein Acyltransferase ZDHHC3 in Maintaining Oocyte Meiotic Arrest in Xenopus laevis. Biology of Reproduction.
• Wang, H, Fang, J, Kuang, X., Miao, L., Wang, C., Xia, G., King, M.L., and Zhang, J. (2012). Activity of long-chain acyl-CoA synthetase is required for maintaining meiotic arrest in Xenopus laevis. Biology of Reproduction.