Honors & Awards

  • Helen Hay Whitney-AGBT Postdoctoral Fellowship, Helen Hay Whitney Foundation & AGBT (2023-2026)
  • Walter V. and Idun Berry Postdoctoral Fellowship, Stanford School of Medicine (2022-2023)
  • Dean's Postdoctoral Fellowship, Stanford School of Medicine (2021-2022)
  • Graduate Research Fellowship, National Science Foundation (2017-2020)

Professional Education

  • Doctor of Philosophy, Princeton University (2021)
  • Master of Arts, Princeton University (2017)
  • Bachelor of Science, California Institute of Technology (Caltech), Bioengineering (2015)

Stanford Advisors

Lab Affiliations

All Publications

  • ERK signaling dissolves ERF repression condensates in living embryos PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Weaver, C. J., Patel, A. L., Shvartsman, S. Y., Levine, M. S., Treen, N. 2022; 119 (9)


    Phase separation underlies the organization of the nucleus, including the biogenesis of nucleoli and the packaging of heterochromatin. Here we explore the regulation of transcription factor condensates involved in gene repression by ERK signaling in gastrulating embryos of a simple proto-vertebrate (Ciona). ERK signaling induces nuclear export of the transcriptional repressor Ets-2 repressive factor (ERF), which has been linked to various human developmental disorders. Using high-resolution imaging, we show that ERF is localized within discrete nuclear condensates that dissolve upon ERK activation. Interestingly, we observe dynamic pulses of assembly and dissociation during interphase, providing visualization of a nuclear phase separation process regulated by cell signaling. We discuss the implications of these observations for producing sharp on/off switches in gene activity and suppressing noise in cell-cell signaling events.

    View details for DOI 10.1073/pnas.2119187119

    View details for Web of Science ID 000766706200002

    View details for PubMedID 35217620

    View details for PubMedCentralID PMC8892517

  • Capicua is a fast-acting transcriptional brake CURRENT BIOLOGY Patel, A. L., Zhang, L., Keenan, S. E., Rushlow, C. A., Fradin, C., Shvartsman, S. Y. 2021; 31 (16): 3639-+


    Even though transcriptional repressors are studied with ever-increasing molecular resolution, the temporal aspects of gene repression remain poorly understood. Here, we address the dynamics of transcriptional repression by Capicua (Cic), which is essential for normal development and is commonly mutated in human cancers and neurodegenerative diseases.1,2 We report the speed limit for Cic-dependent gene repression based on live imaging and optogenetic perturbations in the early Drosophila embryo, where Cic was originally discovered.3 Our measurements of Cic concentration and intranuclear mobility, along with real-time monitoring of the activity of Cic target genes, reveal remarkably fast transcriptional repression within minutes of removing an optogenetic de-repressive signal. In parallel, quantitative analyses of transcriptional bursting of Cic target genes support a repression mechanism providing a fast-acting brake on burst generation. This work sets quantitative constraints on potential mechanisms for gene regulation by Cic.

    View details for DOI 10.1016/j.cub.2021.05.061

    View details for Web of Science ID 000688368900012

    View details for PubMedID 34166605

    View details for PubMedCentralID PMC8612007

  • From complex datasets to predictive models of embryonic development NATURE COMPUTATIONAL SCIENCE Dutta, S., Patel, A. L., Keenan, S. E., Shvartsman, S. Y. 2021; 1: 516-520


    Modern studies of embryogenesis are increasingly quantitative, powered by rapid advances in imaging, sequencing and genome manipulation technologies. Deriving mechanistic insights from the complex datasets generated by these new tools requires systematic approaches for data-driven analysis of the underlying developmental processes. Here, we use data from our work on signal-dependent gene repression in the Drosophila embryo to illustrate how computational models can compactly summarize quantitative results of live imaging, chromatin immunoprecipitation and optogenetic perturbation experiments. The presented computational approach is ideally suited for integrating rapidly accumulating quantitative data and for guiding future studies of embryogenesis.

    View details for DOI 10.1038/s43588-021-00110-2

  • Optimizing photoswitchable MEK PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Patel, A. L., Yeung, E., McGuire, S. E., Wu, A. Y., Toettcher, J. E., Burdine, R. D., Shvartsman, S. Y. 2019; 116 (51): 25756-25763


    Optogenetic approaches are transforming quantitative studies of cell-signaling systems. A recently developed photoswitchable mitogen-activated protein kinase kinase 1 (MEK1) enzyme (psMEK) short-circuits the highly conserved Extracellular Signal-Regulated Kinase (ERK)-signaling cascade at the most proximal step of effector kinase activation. However, since this optogenetic tool relies on phosphorylation-mimicking substitutions in the activation loop of MEK, its catalytic activity is predicted to be substantially lower than that of wild-type MEK that has been phosphorylated at these residues. Here, we present evidence that psMEK indeed has suboptimal functionality in vivo and propose a strategy to circumvent this limitation by harnessing gain-of-function, destabilizing mutations in MEK. Specifically, we demonstrate that combining phosphomimetic mutations with additional mutations in MEK, chosen for their activating potential, restores maximal kinase activity in vitro. We establish that this modification can be tuned by the choice of the destabilizing mutation and does not interfere with reversible activation of psMEK in vivo in both Drosophila and zebrafish. To illustrate the types of perturbations enabled by optimized psMEK, we use it to deliver pulses of ERK activation during zebrafish embryogenesis, revealing rheostat-like responses of an ERK-dependent morphogenetic event.

    View details for DOI 10.1073/pnas.1912320116

    View details for Web of Science ID 000503281500059

    View details for PubMedID 31796593

    View details for PubMedCentralID PMC6926043

  • Outstanding questions in developmental ERK signaling DEVELOPMENT Patel, A. L., Shvartsman, S. Y. 2018; 145 (14)


    The extracellular signal-regulated kinase (ERK) pathway leads to activation of the effector molecule ERK, which controls downstream responses by phosphorylating a variety of substrates, including transcription factors. Crucial insights into the regulation and function of this pathway came from studying embryos in which specific phenotypes arise from aberrant ERK activation. Despite decades of research, several important questions remain to be addressed for deeper understanding of this highly conserved signaling system and its function. Answering these questions will require quantifying the first steps of pathway activation, elucidating the mechanisms of transcriptional interpretation and measuring the quantitative limits of ERK signaling within which the system must operate to avoid developmental defects.

    View details for DOI 10.1242/dev.143818

    View details for Web of Science ID 000440421300001

    View details for PubMedID 30049820

    View details for PubMedCentralID PMC6078328