RNAs and RNA-binding proteins regulate gene expression in every living system. We seek the fundamental principles that govern how they interact, where they go inside the cell, and how that shapes their function. We combine single-molecule and super-resolution imaging with localized transcriptomics, working across scales from purified molecules to live cells, and from single genes to the whole transcriptome.
Eukaryotic cells are highly compartmentalized. Beyond membrane-bound organelles, they contain many membraneless organelles (MLOs), such as nuclear speckles, nucleoli, paraspeckles and PML bodies. These condensates assemble through multivalent RNA–protein interactions. RNAs are selectively localized to and organized within these bodies, and that localization is dynamic, regulated and important for RNA processing and gene expression.
We focus on nuclear speckles, which are built on the scaffold proteins SON and SRRM2 and enriched in spliceosomal components, splicing factors, polyadenylated RNAs and certain lncRNAs. We have mapped the speckle transcriptome and found that speckle localization is tightly linked to splicing efficiency. We have also shown that speckles have a layered internal organization that positions RNA substrates at their surface. We are now working out the sequence rules that send an RNA to speckles, and the functional consequences of getting there.
MLOs are also increasingly linked to human disease. Nuclear speckles have been implicated in neurodegenerative diseases, infectious diseases and cancers. RNAs carrying disease-associated repeat expansions, such as CAG repeats in Huntington's disease and CGG repeats in fragile X-associated tremor/ataxia syndrome, accumulate at speckles, as do influenza A viral RNAs. Many diseases also stem from mis-splicing. Yet direct evidence for how speckles contribute to RNA metabolism and to disease is still lacking. Filling in these mechanistic gaps is a central goal of our work, and may reveal new ways to modulate RNA localization and splicing.
What are the rules and mechanisms of RNA localization? How do MLOs and localized RNAs drive function or dysfunction in cells?
Which transcripts go to speckles, and why. Gene position relative to speckles, GC content, intron length and splicing features all help predict speckle enrichment.
How speckle localization boosts intron removal, regulates intron retention and favors exon inclusion, and how this changes under stress.
How RNA–protein interactions arrange RNAs and proteins into layers inside speckles, and whether different sub-domains carry out different functions.
In situ reverse transcription-based sequencing methods to map which transcripts reside in nuclear speckles and other organelles, and how that changes with cell state.
Visualizing individual RNAs and proteins in and around organelles at nanometer resolution to resolve their internal organization and dynamics.
Diverse regulatory RNAs help bacteria respond to changing signals, and they support survival during infection, biofilm formation and antibiotic stress. This makes essential bacterial RNAs attractive potential drug targets, but targeting them depends on a precise understanding of how they work.
We study the kinetic mechanisms of both cis-acting regulatory RNAs, focusing on riboswitches in the 5′ UTRs of mRNAs, and trans-acting small RNAs (sRNAs) and their chaperones Hfq and ProQ. In vitro, we use single-molecule FRET to follow how a riboswitch recognizes its ligand. In live cells, we combine quantitative imaging with modeling to measure how RNAs compete for shared proteins and targets. Together, this work shows how regulatory RNAs read cellular physiology to control gene expression.
How do regulatory RNAs sense the state of the cell, and how do binding kinetics and competition inside a crowded cell decide which genes are regulated, and when?
How T-box riboswitches decode the tRNA anticodon and sense its aminoacylation state, with kinetics tuned to transcriptional or translational control.
How sRNAs and mRNAs compete for Hfq and ProQ in live cells, and how stress redirects these chaperones toward sRNA-dependent regulation.
How binding rates set regulatory priority among an sRNA's targets, including co-transcriptional regulation by sRNAs long thought to act only after transcription.
Real-time conformational dynamics and binding kinetics of riboswitch–ligand interactions.
Super-resolution imaging and single-particle tracking of RNAs and chaperones in bacterial cells.
Mathematical models that turn imaging data into rate constants for regulation in vivo.
We welcome students and postdocs from biology, chemistry, physics and mathematics.