Research

The folding of genomes has been postulated to modulate gene expression. And while data coming from a multifold of studies supports this perception, critical data contrasting this view exists.

Much of this knowledge gap is because most of these studies are performed at the ensemble level. Since these may reflect millions of structures, it precludes our ability to relate structure to function directly. In contrast, we propose to carry out our studies at the single-cell level, thus simultaneously detecting expression and structure. Working with single-cell resolution is critical for determining how structure relates to function.

Our lab is committed to study how genome organization can influence gene expression and how both of these influence cell fate decisions and disease. To that end, our lab is using a variety of tools, including multiplexed and correlative DNA and RNA imaging technologies, so that we can directly relate a given structure to its transcriptional output.

Here are some of the projects we are pursuing now in the lab:

Structural reorganization and transcriptional switches at compartmental interfaces.

Is the breakage of active and inactive chromatin predictive of changes in gene expression?

Here, we are investigating structural and functional changes that occur during several disease processes, such as aging and cancer. For instance, at the transition from proliferation to senescence, where we know of global changes in genome organization and gene expression, and a change in cell fate accompanies these. However, we do not know how these functional and structural changes are connected to each other, and whether they are intertwined? To answer that, we are focusing on chromosomal regions that switch their transcriptional state when the cell transforms from a proliferating to a senescent state.

Does the folding of regulatory elements within TADs dictate gene expression, and if so, how?

Loop domains are a genomic organizational unit, discovered by Hi-C studies, and confirmed by microscopy images. Loci within these domains interact with each other more frequently than with loci of other domains, whereas domain boundaries, enriched with CTCF motifs in mammals, have been shown to regulate gene expression by restricting the interaction of cell-type-specific enhancers with their target genes. However, recent studies have questioned the role of domains in regulating gene expression. For instance, our collaborators in the Mundlos laboratory have shown that domain fusion driven by CTCF boundary deletion, doesn’t necessarily affect gene expression. However, an inversion, which includes a boundary region, not only leads to domain fusion but also a considerable change in gene expression. Therefore, we still don’t really understand how structural variations may regulate gene expression. And, it’s very likely that averaging over millions of structures is precluding us from connecting a given structure to its resulting function. Utilizing correlative RNA/DNA imaging, we are hoping to determine the relationship between structural deformations and gene expression in developing mice.

Multiplexed (each color is a different genomic locus) super-resolution imaging of mouse embryonic stem cells colony.

Super resolution imaging of human chromosome 3:150,000,000-158,000,000 (hg19) at 500 kb-resolution. Each pseudo-color is a single 500 kb step. All together, there are 16 sequential steps.

Technology Development

In addition to solving biophysical enigmas, we also continue to develop new technologies to explore the genome in higher genomic, spatial and temporal resolutions.

Finally, and most importantly, we are open to new ideas. If you want to share your ideas and/or join our team, please email niguy@utmb.edu