Jingyi Fei

About

Jingyi Fei is an Associate Professor of Biochemistry and Molecular Biology at the University of Chicago, with a focus on understanding the mechanisms by which RNAs mediate gene expression and regulation in both bacterial and eukaryotic systems. Her research involves studying regulatory RNAs and RNA modifications using various single-molecule fluorescence microscopy and super-resolution imaging tools. Her group is also interested in developing new labeling, imaging, and data analysis methods to advance the understanding of RNA dynamics. Her work includes investigating transcriptome-wide mRNP condensation that precedes stress granule formation and excludes new mRNAs, as well as exploring the organization of RNA molecules at nuclear speckles and their connection to splicing efficiency. She has contributed to the understanding of RNA localization, higher-order RNA structures, and RNA-RNA interactions through innovative sequencing and imaging techniques. Jingyi Fei has received numerous awards and honors, including the BIV Junior Faculty Award from the Biophysical Society, the Kavli Fellowship, and election to the National Academy of Sciences in 2024.

Research topics

• Computer Science
• Biology
• Cell biology
• Artificial Intelligence
• Data science
• Physics
• Biochemistry
• Genetics
• Computational biology
• Chemistry

Selected publications

• FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices

  eLife · 2021 · 305 citations

  Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining…

  DOI

• K29-linked ubiquitin signaling regulates proteotoxic stress response and cell cycle

  Nature Chemical Biology · 2021 · 83 citations

  DOI

• Fluorescence resonance energy transfer at the single-molecule level

  Nature Reviews Methods Primers · 2024-03-28 · 75 citations

  articleOpen access
  PublisherOA PDFDOI

• Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency

  Science Advances · 2024-10-16 · 57 citations

  articleOpen accessSenior author

  Nuclear speckles are nuclear membraneless organelles in higher eukaryotic cells playing a vital role in gene expression. Using an in situ reverse transcription-based sequencing method, we study nuclear speckle-associated human transcripts. Our data indicate the existence of three gene groups whose transcripts demonstrate different speckle localization properties: stably enriched in nuclear speckles, transiently enriched in speckles at the pre-messenger RNA stage, and not enriched. We find that s…

  PublisherDOI

• KARR-seq reveals cellular higher-order RNA structures and RNA–RNA interactions

  Nature Biotechnology · 2024-01-18 · 51 citations

  articleOpen access

  Abstract RNA fate and function are affected by their structures and interactomes. However, how RNA and RNA-binding proteins (RBPs) assemble into higher-order structures and how RNA molecules may interact with each other to facilitate functions remain largely unknown. Here we present KARR-seq, which uses N 3 -kethoxal labeling and multifunctional chemical crosslinkers to covalently trap and determine RNA–RNA interactions and higher-order RNA structures inside cells, independent of local protein b…

  PublisherOA PDFDOI

Recent grants

• Quantitative imaging of epitranscriptomic regulation mediated by RNA modification

  NIH · $2.4M · 2017–2022

Frequent coauthors

• Taekjip Ha

  Howard Hughes Medical Institute

  46 shared

• Ruben L. Gonzalez

  Columbia University

  30 shared

• Seong-Jin Park

  17 shared

• Digvijay Singh

  15 shared

• Samuel H. Sternberg

  Columbia University

  11 shared

• Isaac T. S. Li

  University of British Columbia

  11 shared

• Jiacheng Zhang

  La Sierra University

  11 shared

• Carin K. Vanderpool

  University of Illinois Urbana-Champaign

  10 shared

Labs

• Fei LabPI

  Department of Biochemistry and Molecular Biology

Awards & honors

• BIV Junior Faculty Award The Biophysical Society 2025
• Kavli Fellow National Academy of Sciences 2024
• Scialog Fellow Research Corporation for Science Advancement…
• NIH Director’s New Innovator Award NIH 2017
• Searle Scholar Searle Scholars Program 2017

Similar researchers at University of Chicago

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• Eduardo Perozoh-64
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