The Faculty


RNA biophysics, cell biology


University of Science and Technology China, B.A., 2005

Columbia University, Ph.D., 2010

Columbia University, Postdoctoral Fellow, 2011

University of Illinois, Urbana-Champaign, Postdoctoral Fellow, 2015

University of Chicago, Assistant Professor, 2016-

Research Interests

RNA molecules play highly diverse functions in living cells, including carrying genetic information (mRNA), performing catalytic functions (e.g. ribozyme and ribosome) and regulating gene expression (e.g. various types of noncoding RNAs). Our research is centered on RNA biophysics and cell biology with cutting-edge single-molecule and cell imaging techniques.

Bacterial small RNA Small regulatory noncoding RNAs (here broadly defined as sRNAs) play critical roles in regulating genes involved in almost all cellular processes. Due to their specificity and versatility, sRNAs have inspired broad applications including new therapies for human diseases and genome engineering, among other applications. That said, a precise quantitative description of the fundamental mechanism of sRNA-mediated regulation and interference can largely benefit the further improvement of the efficiency and robustness of these applications by providing critical models and parameters. Our research aims at providing a quantitative description at the molecular, cellular, and the systems levels. Using bacteria as model systems, our missions are to understand the molecular mechanisms by which sRNAs modulate gene expression, as well as physiological response caused by sRNA-mediated regulation in the context of pathogenic bacteria-host interactions.

RNA/protein granule In eukaryotic cells, RNAs and proteins can self-assemble into various types of non-membranous structures or domains under natural or stressed conditions, including P body and stress granule, etc. in cytoplasm, and nucleolus, nuclear speckle, paraspeckle, and Cajal body, etc. in nucleus.  As one of the most conspicuous domains in the nucleus, nuclear speckles are highly heterogeneous in composition, enriched with poly A+ RNAs and numerous proteins involved in mRNA processing.  Many cellular functions have been implicated to be associated with nuclear speckles, including the storage and/or assembly sites of pre-mRNA processing factors, as well as the structural domains that control the efficiency and integration of distinct steps in gene expression, ranging from transcription to mRNA export. We aim at mapping the distribution of components within the speckle using cell imaging techniques, and determining the involvement of such organization in the speckle-ascribed functions. Furthermore, with such imaging-based quantitative analysis, we are interested in understanding the biophysical properties of RNA/protein granules in general.

Selected publications

E Lerner†*, A Barth†*, J Hendrix†*, B Ambrose , V Birkedal , SC Blanchard , R Borner, HS Chung , T Cordes , TD Craggs, AA Deniz, J Diao, J Fei , RL Gonzalez, IV Gopich, T Ha, C A Hanke, G Haran, NS Hatzakis, S Hohng, S-C Hong, T Hugel, A Ingargiola, C Joo, AN Kapanidis, HD Kim, T Laurence, NK Lee, T-H Lee, EA Lemke, E Margeat, J Michaelis, X Michalet, S Myong, D Nettels, T-O Peulen, E Ploetz, Y Razvag, NC Robb, B Schuler, H Soleimaninejad, C Tang, R Vafabakhsh, DC Lamb*, CAM Seidel*, S Weiss*, (2021) FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices, eLife, 10:e60416.

S Park#, K Prevost#, EM Heideman^, M-C Carrier^, MS Azam, MA Reyer, W Liu, E Masse*, J Fei*, (2021) Dynamic interactions between the RNA chaperone Hfq, small regulatory RNAs and mRNAs in live bacterial cells, eLife, 10:e64207. (*Co-correspondence; #,^ Co-authorship)

A Poddar, MS Azam, T Kayikcioglu, M Bobrovskyy, J Zhang, X Ma, P Labhsetwar, J Fei, D Singh, Z Luthey-Schulten, CK Vanderpool, T Ha, (2021) Nature Communications, 12:874.

MA Reyer, S Chennakesavalu#, EM Heideman#, X Ma, M Bujnowska, L Hong, AR Dinner, CK Vanderpool, J Fei, (2020) Kinetic model of small RNA-mediated regulation suggests that a small RNA can regulate co-transcriptionally, bioRxiv. (#Co-authorship)

M Bujnowska, J Zhang, Q Dai, EM Heideman, J Fei, (2020) Deoxyribozyme-based method for absolute quantification of N6-methyladenosine fraction at specific sites of RNA,  Journal of Biological Chemistry, 295:6992 [PDF][SI].

Y Fan, Y Lim, LS Wyss, S Park, C Xu, H Fu, J Fei, Y Hong, B Wang, (2020) Mechanical expansion microscopy,  Methods in Cell Biology [PDF]

Y Wang*, J Fei*, (2020) Continuous active development of super-resolution fluorescence microscopy,  Physical Biology, 17:030401 [PDF]

S Park, MA Reyer, EL McLean, W Liu, J Fei, (2019) An improved method for bacterial immunofluorescence staining to eliminate antibody exclusion from the fixed nucleoid, Biochemistry 58: 4457 [PDF][SI].

S Park, J Zhang, MA Reyer, J Zareba, AA Troy, J Fei. (2018) Conducting Multiple Imaging Modes with One Fluorescence Microscope. JoVE (Journal of Visualized Experiments), e58320 [PDF].

J Zhang#, B Chetnani#, ED Cormack, W Liu, A Mondragón, J Fei. (2018) Specific structural elements of the T-box riboswitch drive the two-step binding of the tRNA ligand. eLife 7: e39518 [PDF][SI]. (#Co-authorship)

J Fei, CM Sharma. (2018) RNA localization in baceria. Microbiology Spectrum 6: no. 5 doi:10.1128/microbiolspec.RWR-0024-2018 [PDF].

D Singh, Y Wang, J Mallon, O Yang, J Fei, A Poddar, D Ceylan, S Bailey, T Ha. (2018) Mechanisms of improved specificity of engineered Cas9s revealed by single-molecule FRET analysis. Nat Struct Mol Biol 25: 347 [PDF].

 S Park, M Bujnowska, EL McLean, J Fei. (2018)  Quantitative Super-Resolution Imaging of Small RNAs in Bacterial Cells. Methods in Molecular Biology  Bacterial Regulatory RNA:199-212 [PDF].