Our cells can pack nearly ~2 meters of DNA into a ~10μm nucleus, while still being able to accurately read, replicate, and segregate this tightly condensed genome. Each of us has enough DNA to reach from here to the sun and back, more than 300 times.
How is that entire genomic DNA organized in a tiny nucleus? How does the nucleus maintain this vast amount of information throughout life and how is it connected to human aging and diseases?
We aim to decipher the molecular mechanisms that allow cells to organize and maintain their genome throughout life. We pursue to deepen our understanding by using approaches that integrate single-molecule biophysics, cell imaging and computational analysis, nano/micro engineering, and molecular biology.
Nuclear Structure & Genome Organizers
Figure 1. Our genomic DNA molecule is gradually folded and packaged in the cell.
What is nuclear structure? Our genome is spatially organized in the cell nucleus and temporally regulated during the cell cycle. Scientists have made the effort to understand the three-dimensional (3D) nuclear architecture and dynamic modifications. Notably, the genomic DNA molecules gradually folded into the thicker chromosomes during mitosis while the interphase genome comprises unique chromatin domains and compartments.
Why do we study genome organization? How the DNA is organized in cells has something to do with the function of genomes such as transcription and DNA repair. For example, the formation of a DNA loop between a specific gene locus and its regulatory element turn on the gene activity. Notably, failure in maintaining a healthy genome structure has a great correlation with cancer predisposition and the aging process.
Who organizes our genome in the nucleus?
For example, the cohesin complex mediates the formation of chromosome loops and domains in cells. This epigenetically regulates gene expression and other DNA-based cellular processes. In addition, histone codes, chromatin remodelers, and self-assembling proteins contribute to the dynamic adaptation of the nuclear organization.
Figure 2. The mechanism of DNA loop formation and its regulation by the key proteins (genome organizers) in human cells.
Single-Molecule Technique for DNA-Protein Behavior
Movie 1. DNA curtains stained with YOYO-1 (green) and protein loaded onto the individual DNA molecules (magenta).
Why Single-Molecule Approach?
A single-molecule technique (SM) enables real-time imaging of individual biomolecules such as DNA, RNA, or protein of interest. By using SM approach, we can characterize their dynamic behavior that is hard to observe in traditional ensemble assays such as gel electrophoresis. Examples are shown below:
Figure 3. A schematic example of a DNA-binding protein scanning the genomic DNA wrapped around nucleosomes.
'DNA Motors' are Moving Proteins!
Our genomic DNA is a huge molecule that contains a vast amount of genetic information (3.2Gb). However, each functional protein should find a tiny segment quickly. For example, DNA damage occurs at a rate of 1:10G nucleotides. Transcription factors also have to target their promoters and enhancers.
SM imaging revealed that the one-dimensional (1D) movement of proteins provides a fast target search mechanism on the genome. Once a protein bind DNA, it can slide along the helical track of DNA (1D sliding), or it can jump with microscopic dissociation and re-association from DNA (hopping). The proteins can be trapped within the nucleosomes or can bypass the barriers.
Figure 4. Single-molecule imaging of human cohesin complex moving for DNA looping.
Epigenetic Response to Cellular Stress
Genes are protected from DNA damage by having compact heterochromatin at the nuclear periphery. Furthermore, peripheral chromatin is associated with the lamin network at the nuclear membrane, and this arrangement enables chromatin remodeling in response to mechanical stimuli. We will investigate how chromatin domains are regulated by cellular responses to stress such as DNA damage and cell motility.
Development of Biophysical Methods for the Nuclear Alteration
Nuclear architecture is highly dynamic during cell cycle to accommodate chromatin-based processes. Perturbance of such transitions in chromatin structure and nuclear proteins can lead to loss of cellular fitness. We plan to design and develop new methods that allow us to detect minute changes in chromatin movement by employing nano-/micro engineering and advanced microscopy.
Functional Diversity in Microorganisms
The diversity of structure and functions in bacteria provides numerous interesting characteristics of biology. For example, bacterial endospores formed by detrimental environments allow them to survive during adversity. We study the mechanism by which the cells naturally harbor such extreme resistance to the external environments.