Organization of the Cell Nucleus

Each cell in our body contains a copy of our genetic information encoded in DNA polymers that are densely packed inside the cell nucleus. Myriads of proteins constantly read out information from the DNA to repair damaged sites, replicate chromosomes for cell division, and synthesize coding and non-coding RNA transcripts.

We use genome editing and quantitative fluorescence microscopy to elucidate the physical mechanisms that govern the organization of DNA, RNA, and proteins in the cell nucleus. Ultimately, we aim to understand at the molecular level how biological function arises from physical properties. To tackle this problem we bring together expertise from physics, biology, chemistry, engineering, and beyond.

Biomolecular Condensates

The notion that biomolecules can self-organize in phase-separated condensates has received a lot of attention in recent years. But quantitative descriptions of this process in the non-equilibrium environment of the living cell nucleus are lacking. We use single molecule imaging techniques to develop mechanistic models of condensate organization and function.

Collective behavior like self-organization into condensates arises from molecular properties. Small changes to these properties can have dramatic effects at the cellular level and lead to misregulation and disease states. Our work provides a framework to predict complex behavior arising in multi-component condensates.

Support for this work come from the Gordon and Betty Moore Foundation and the Research Corporation for Science Advancement through two Scialog: Chemical Machinery of the Cell awards.

Collaborators: Masha Kamenetska (BU), Lu Wang (Rutgers), Stephen Yi (UT Austin).

Super-resolved clusters of epigenetic marks in the cell nucleus. Scale bar 2um (inset: 250nm).

Scaffolded condensates in the cell nucleus

Condensation is a phase transition that occurs in super-saturated systems. Nucleation seeds grow into mature, stable condensates. To make use of condensation in biological processes such as gene transcription it is desirable for the cell to form condensates in specific locations. A more accurate model of condensate formation has to take into account nuclear structures that provide a scaffold for condensate formation such as chromatin topology. We use multimodal, multiplexed super-resolution and electron microscopy to determine the interplay between scaffold structures and condensates.

Support for these projects comes in part from the NIH (NIAID R21AI159626 with Dr. Kenter).

Collaborators: Amy Kenter (UIC Immunology), Jie Liang (UIC Biomedical Engineering), Primal deLanerolle (UIC Physiology), Alex Ruthenburg (UChicago).


Quantitative imaging

Fluorescence microscopy provides a great tool box for measuring physical properties directly in live cells. Our microscopes deliver more than just images. We use them as quantitative instruments and constantly develop new imaging assays and analysis methods. Understanding how an image is formed is crucial for extracting precise information from it. We use a combination of commercial and custom-built fluorescence microscopes with single molecule sensitivity for our studies.

Genome engineering

We use CRISPR/Cas9 technology to modify genome and function of cells. We tag endogenous proteins with fluorescent labels, visualize RNA transcripts, and highlight DNA loci to see all these factors at work in the cell nucleus. Genome editing also allows us to systematically replace endogenous factors with synthetically engineered counterparts.

Thank you to the sponsors making our work possible!