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

• Analysis of RNA localization to nuclear speckles and fitting of splicing kinetic parameters

  Open MIND · 2026-02-10

  other

  This packge contains analysis codes for calculating RNA partition coefficient in nuclear speckles, and fitting time-course RNA abundance data to calculate rates related to RNA splicing and degradation. This package is used in the manuscript "RNA localization to nuclear speckles follows splicing logic".

  DOI

• RNA localization to nuclear speckles follows splicing logic

  Nucleic Acids Research · 2026-02-18

  articleOpen accessSenior author

  Nuclear speckles are membraneless organelles implicated in multiple RNA processing steps. In this work, we systematically characterize the sequence logic determining RNA localization to nuclear speckles. We find extensive similarities between the speckle localization code and the RNA splicing code, even for transcripts that do not undergo splicing. Specifically, speckle localization is enhanced by the presence of unspliced exon-like or intron-like sequence features. We demonstrate that interactions required for early spliceosomal complex assembly contribute to speckle localization. We also show that speckle localization of isolated endogenous exons is reduced by disease-associated single nucleotide variants. Finally, we find that speckle localization strongly correlates with splicing kinetics of splicing-competent constructs and is linked to the decision between exon inclusion and skipping. Together, these results suggest a model in which RNA speckle localization is associated with the formation of the early spliceosomal complex and enhances the efficiency of splicing reactions.

  PublisherDOI

• Analysis of RNA localization to nuclear speckles and fitting of splicing kinetic parameters

  Zenodo (CERN European Organization for Nuclear Research) · 2026-02-10

  otherOpen access

  This packge contains analysis codes for calculating RNA partition coefficient in nuclear speckles, and fitting time-course RNA abundance data to calculate rates related to RNA splicing and degradation. This package is used in the manuscript "RNA localization to nuclear speckles follows splicing logic".

  PublisherDOI

• Simultaneous Application of FISH and IF in FFPE Disease Tissue

  Knowledge@UChicago (University of Chicago) · 2026-01-01

  otherOpen accessSenior author

  Simultaneous Application of FISH and IF in FFPE Disease Tissue. Membraneless organelles spatially coordinate RNA and protein interactions, therefore playing an essential role in cellular organization. Dysregulation of these membraneless organelles is implicated in a range of diseases, including cancers and neurodegenerative diseases. For this reason, detecting and characterizing changes in these structures is clinically relevant with regards to diagnosis and creating specific therapeutic approaches. Formalin-fixed paraffin embedded (FFPE) tissue is the most readily available source of well-annotated tumor samples, including those from patients in clinical trials. Formalin fixation and paraffin embedding preserves cellular architecture; however, it increases the likelihood of nucleic acid degradation, prohibiting analysis with other molecular techniques. Typically, fluorescence in situ hybridization (FISH) is used to study expression levels and localization of specific RNA, but its use of proteases to expose the cellular RNA to fluorescent probes precludes simultaneous detection of proteins by immunofluorescence (IF). Our lab developed a protocol that addresses this gap by allowing for simultaneous application of IF and FISH. The protocol we designed preserves both nucleic acid hybridization efficiency and protein epitope integrity within the same tissue sample. This method combines controlled antigen retrieval, graded proteolysis, post-hybridization fixation, and optimized staining order to circumvent the natural incompatibility of FISH and IF in FFPE samples. By allowing for simultaneous detection of RNA and protein within the same FFPE tissue, the analytical utility of clinical samples is expanded. This method provides a useful tool for advancing spatial biology research and clinical pathology studies as it supports current translational research and disease-associated alterations in cellular spatial organization.

  PublisherOA PDFDOI

• Super-resolved spatial organization of the nucleolar transcriptome

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-05-21

  articleSenior authorCorresponding

  Membraneless organelles (MLOs) often exhibit internal architecture, yet whether the local transcriptome differentially partitions across MLO subdomains remains largely uncharacterized. Here we combine super-resolution imaging with in situ reverse transcription-based sequencing to profile transcriptomes within MLO subdomains. Using the human tripartite nucleolus as a model system, we identify distinct RNA populations in the fibrillar center (FC), dense fibrillar component (DFC), and granular component (GC). Pre-rRNA processing intermediates demonstrate a layered progression across nucleolar subdomains, reflecting the temporal order of the processing steps. Processing steps involved in large-small subunit separation show increased retention in the DFC in highly differentiated cells. Mature small nucleolar RNAs (snoRNAs) are preferentially enriched in the DFC and spatially segregated from their precursor transcripts. Many non-snoRNA-related transcripts, often derived from nucleolus-proximal genes, show modest enrichment in the GC. These results illustrate functional RNA organization across nucleolar subdomains and provide a framework for nanoscale transcriptome mapping of biomolecular condensates.

  PublisherDOI

• Abstract 1069 Context-dependent RNA localization to nuclear speckles

  Journal of Biological Chemistry · 2025-05-01

  articleOpen access1st authorCorresponding

  Bacteria defend themselves from viral infection using diverse immune systems, many of which sense and target foreign nucleic acids.Defense-associated reverse transcriptase (DRT) systems provide an intriguing counterpoint to this immune strategy by instead leveraging DNA synthesis, but the identities and functions of their DNA products have remained largely unknown.Here we show that DRT2 systems execute an unprecedented immunity mechanism that involves de novo gene synthesis via rolling circle reverse transcription of a non-coding RNA (ncRNA).Unbiased profiling of RT-associated RNA and DNA ligands in DRT2-expressing cells revealed that reverse transcription generates concatenated cDNA repeats through programmed template jumping on the ncRNA.The presence of phage then triggers second-strand cDNA synthesis, leading to the production of long double-stranded DNA.Remarkably, this DNA product is efficiently transcribed, generating messenger RNAs that encode a stop codon-less, never-ending ORF (neo) whose translation causes potent growth arrest.Phylogenetic analyses and screening of diverse DRT2 homologs further revealed broad conservation of rolling circle reverse transcription and Neo protein function.Our work highlights an elegant expansion of genome coding potential through RNA-templated gene creation, and challenges conventional paradigms of genetic information encoded along the one-dimensional axis of genomic DNA.

  PublisherOA PDFDOI

• Transcriptome-wide mRNP condensation precedes stress granule formation and excludes new mRNAs

  Molecular Cell · 2025-11-24 · 15 citations

  articleOpen access

  Stress-induced messenger ribonucleoprotein (mRNP) condensation is conserved across eukaryotes, resulting in stress granule formation under intense stresses, yet the mRNA composition and function of these condensates remain unclear. Exposure of ribosome-free mRNA following stress is thought to cause condensation and stress granule formation through mRNA-sequence-dependent interactions, leading to disproportionate condensation of long mRNAs. Here, we show that, by contrast, virtually all mRNAs condense in response to multiple stresses in budding yeast with minor length dependence and often without stress granule formation. New transcripts escape mRNP condensation, enabling their selective translation. Inhibiting translation initiation causes formation of mRNP condensates distinct from stress granules and processing bodies (P bodies), and these translation-initiation-inhibited condensates (TIICs) are omnipresent, even in unstressed cells. Stress-induced mRNAs are excluded from TIICs due to the timing of their expression, indicating determinants of escape that are independent of sequence. Together, our results reveal a previously undetected level of translation-linked molecular organization and stress-responsive regulation.

  PublisherDOI

• RNA localization to nuclear speckles follows splicing logic

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-28

  preprintOpen accessSenior authorCorresponding

  Nuclear speckles are membraneless organelles implicated in multiple RNA processing steps. In this work, we systematically characterize the sequence logic determining RNA localization to nuclear speckles. We find extensive similarities between the speckle localization code and the RNA splicing code, even for transcripts that do not undergo splicing. Specifically, speckle localization is enhanced by the presence of unspliced exon-like or intron-like sequence features. We demonstrate that interactions required for early splicesomal complex assembly contribute to speckle localization. We also show that speckle localization of isolated endogenous exons is reduced by disease-associated single nucleotide variants. Finally, we find that speckle localization strongly correlates with splicing kinetics of splicing-competent constructs and is tightly linked to the decision between exon inclusion and skipping. Together, these results suggest a model in which RNA speckle localization is associated with the formation of the early spliceosomal complex and enhances the efficiency of splicing reactions. Highlights: Sequences containing hallmarks of pre-mRNA dictate speckle localizationRNA speckle localization is coupled to early spliceosome assemblyDisease-associated single nucleotide variants reduce localization of isolated exonsRNA speckle localization strongly correlates with splicing kinetics.

  PublisherOA PDFDOI

• Structural dependence of ProQ-mRNA interactions in live bacterial cells

  Communications Biology · 2025-12-13

  articleOpen accessSenior authorCorresponding

  ProQ is a post-transcriptional gene regulator in bacteria known to globally interact with both messenger RNAs (mRNAs) and small regulatory RNAs (sRNAs). Here, we investigate ProQ-mRNA interactions in live bacteria using single-molecule tracking and reveal their dependence on the structural elements of ProQ. We illustrate that during exponential growth phase, stationary phase, and osmotic stress, ProQ mainly binds to mRNAs. All structural domains of ProQ, including N-terminal domain, linker region, and C-terminal domain, contribute to mRNA binding. While residue Y70 is generally required for global mRNA binding, other tested residues in the N-terminal domain have minor to moderate effects on mRNA binding, indicating that different mRNAs likely depend on different ProQ residues for binding. Finally, our data reveal that the expressed sRNA substrates have limited impacts on the fraction of mRNA-associated ProQ, likely due to the high abundance of mRNA-free ProQ inside the cell.

  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 stably enriched transcripts contain inefficiently excised introns and that disruption of nuclear speckles specifically affects splicing of speckle-enriched transcripts. We further reveal RNA sequence features contributing to transcript speckle localization, indicating a tight interplay between transcript speckle enrichment, genome organization, and splicing efficiency. Collectively, our data highlight a role of nuclear speckles in both co- and posttranscriptional splicing regulation. Last, we show that genes with stably enriched transcripts are over-represented among genes with heat shock-up-regulated intron retention, hinting at a connection between speckle localization and cellular stress response.

  PublisherDOI

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