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Jingyi Fei

Assistant Professor
jingyifei@uchicago.edu
Research Summary
The main focus of my research is to understand the mechanisms by which RNAs mediate gene expression and regulation in both bacterial and eukaryotic systems. We are currently studying regulatory RNAs and RNA modifications using various single-molecule fluorescence microscopy and super-resolution imaging tools. my group is also interested in the development of new labeling, imaging and data analysis methods.
Keywords
Gene regulation, RNA, Single-molecule microscopy, Super-resolution imaging,
Biosciences Graduate Program Association
Publications

  1. Deep learning modeling m6A deposition reveals the importance of downstream cis-element sequences. Nat Commun. 2022 05 17; 13(1):2720. View in: PubMed

  2. Binding of the RNA Chaperone Hfq on Target mRNAs Promotes the Small RNA RyhB-Induced Degradation in Escherichia coli. Noncoding RNA. 2021 Sep 28; 7(4). View in: PubMed

  3. Kinetic modeling reveals additional regulation at co-transcriptional level by post-transcriptional sRNA regulators. Cell Rep. 2021 09 28; 36(13):109764. View in: PubMed

  4. K29-linked ubiquitin signaling regulates proteotoxic stress response and cell cycle. Nat Chem Biol. 2021 08; 17(8):896-905. View in: PubMed

  5. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. Elife. 2021 03 29; 10. View in: PubMed

  6. Dynamic interactions between the RNA chaperone Hfq, small regulatory RNAs, and mRNAs in live bacterial cells. Elife. 2021 02 22; 10. View in: PubMed

  7. Effects of individual base-pairs on in vivo target search and destruction kinetics of bacterial small RNA. Nat Commun. 2021 02 08; 12(1):874. View in: PubMed

  8. Mechanical expansion microscopy. Methods Cell Biol. 2021; 161:125-146. View in: PubMed

  9. Deoxyribozyme-based method for absolute quantification of N6-methyladenosine fractions at specific sites of RNA. J Biol Chem. 2020 05 15; 295(20):6992-7000. View in: PubMed

  10. Continuous active development of super-resolution fluorescence microscopy. Phys Biol. 2020 04 07; 17(3):030401. View in: PubMed

  11. An Improved Method for Bacterial Immunofluorescence Staining To Eliminate Antibody Exclusion from the Fixed Nucleoid. Biochemistry. 2019 11 12; 58(45):4457-4465. View in: PubMed

  12. Conducting Multiple Imaging Modes with One Fluorescence Microscope. J Vis Exp. 2018 10 28; (140). View in: PubMed

  13. Specific structural elements of the T-box riboswitch drive the two-step binding of the tRNA ligand. Elife. 2018 09 25; 7. View in: PubMed

  14. RNA Localization in Bacteria. Microbiol Spectr. 2018 09; 6(5). View in: PubMed

  15. Mechanisms of improved specificity of engineered Cas9s revealed by single-molecule FRET analysis. Nat Struct Mol Biol. 2018 04; 25(4):347-354. View in: PubMed

  16. Quantitative Super-Resolution Imaging of Small RNAs in Bacterial Cells. Methods Mol Biol. 2018; 1737:199-212. View in: PubMed

  17. Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution. J Cell Sci. 2017 Dec 15; 130(24):4180-4192. View in: PubMed

  18. An Automated Image Analysis Method for Segmenting Fluorescent Bacteria in Three Dimensions. Biochemistry. 2018 01 16; 57(2):209-215. View in: PubMed

  19. Robust nonparametric quantification of clustering density of molecules in single-molecule localization microscopy. PLoS One. 2017; 12(6):e0179975. View in: PubMed

  20. The Small Protein SgrT Controls Transport Activity of the Glucose-Specific Phosphotransferase System. J Bacteriol. 2017 06 01; 199(11). View in: PubMed

  21. A Prophage-Encoded Small RNA Controls Metabolism and Cell Division in Escherichia coli. mSystems. 2016 Jan-Feb; 1(1). View in: PubMed

  22. Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9. Nat Commun. 2016 09 14; 7:12778. View in: PubMed

  23. Natural antisense RNA promotes 3' end processing and maturation of MALAT1 lncRNA. Nucleic Acids Res. 2016 Apr 07; 44(6):2898-908. View in: PubMed

  24. Effects of DNA replication on mRNA noise. Proc Natl Acad Sci U S A. 2015 Dec 29; 112(52):15886-91. View in: PubMed

  25. Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells. Sci Rep. 2015 Nov 27; 5:17295. View in: PubMed

  26. RNA biochemistry. Determination of in vivo target search kinetics of regulatory noncoding RNA. Science. 2015 Mar 20; 347(6228):1371-4. View in: PubMed

  27. RNA fluorescence in situ hybridization in cultured mammalian cells. Methods Mol Biol. 2015; 1206:123-36. View in: PubMed

  28. The ribosome uses cooperative conformational changes to maximize and regulate the efficiency of translation. Proc Natl Acad Sci U S A. 2014 Aug 19; 111(33):12073-8. View in: PubMed

  29. A frameshifting stimulatory stem loop destabilizes the hybrid state and impedes ribosomal translocation. Proc Natl Acad Sci U S A. 2014 Apr 15; 111(15):5538-43. View in: PubMed

  30. EttA regulates translation by binding the ribosomal E site and restricting ribosome-tRNA dynamics. Nat Struct Mol Biol. 2014 Feb; 21(2):152-9. View in: PubMed

  31. Understanding the photophysics of the spinach-DFHBI RNA aptamer-fluorogen complex to improve live-cell RNA imaging. J Am Chem Soc. 2013 Dec 18; 135(50):19033-8. View in: PubMed

  32. Watching DNA breath one molecule at a time. Proc Natl Acad Sci U S A. 2013 Oct 22; 110(43):17173-4. View in: PubMed

  33. Transfer RNA-mediated regulation of ribosome dynamics during protein synthesis. Nat Struct Mol Biol. 2011 Aug 21; 18(9):1043-51. View in: PubMed

  34. Graphical models for inferring single molecule dynamics. BMC Bioinformatics. 2010 Oct 26; 11 Suppl 8:S2. View in: PubMed

  35. A microfluidic approach for investigating the temperature dependence of biomolecular activity with single-molecule resolution. Lab Chip. 2011 Jan 21; 11(2):274-81. View in: PubMed

  36. A highly purified, fluorescently labeled in vitro translation system for single-molecule studies of protein synthesis. Methods Enzymol. 2010; 472:221-59. View in: PubMed

  37. Learning rates and states from biophysical time series: a Bayesian approach to model selection and single-molecule FRET data. Biophys J. 2009 Dec 16; 97(12):3196-205. View in: PubMed

  38. Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation. Proc Natl Acad Sci U S A. 2009 Sep 15; 106(37):15702-7. View in: PubMed

  39. Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling. Nat Struct Mol Biol. 2009 Aug; 16(8):861-8. View in: PubMed

  40. Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation. Mol Cell. 2008 May 09; 30(3):348-59. View in: PubMed
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