Our Interests

We are a group of scientists interested in understanding gene regulation, with an especial focus on the role of genome structure and development of advanced microscopy techniques. We value diversity, equity and inclusion as cornerstones of what makes science work. We aim to build an environment that embraces self-expression and acknowledges our diverse cultures, opportunities, and experiences rather than one that is color blind and culture blind. We enjoy building things, from molecules, to gene circuits, to microscopes, to software, and aspire to help build a welcoming community in the process. 

We seek to understand the control of gene expression. Differences in gene expression underlie the tremendous variety of cell types in our bodies. These differences are encoded in the non-transcribed parts of our genome called cis regulatory elements, regions that bind proteins (in a sequence dependent manner), which regulate transcription of surrounding genes. Surprisingly, these regulatory elements can be very far away (in linear sequence) from the transcribed elements they control, frequently tens to hundreds of thousands of basepairs apart.  A major direction in the lab is to understand how such long-range interactions occur, how they achieve target specificity, and how they may be reprogrammed by alterations to the genome sequence.

We believe the answers to these questions require understanding the 3-D organization of the genome.  What this 3-D organization looks like, how it is established, how it changes over development, and what the consequences are for the control of gene expression are all poorly understood questions, which our lab is working to answer.

Our Tools

To answer these questions we need new tools.  Our lab is engaged in using developing and combining new technologies to enable this research, including:

  • super-resolution imaging
  • single molecule microscopy
  • genetic engineering
  • next generation sequencing approaches
  • mathematical and biophysical modeling

See our research projects below for some examples of this approach in action.

Developing tools for imaging transcriptional regulation

We are interested in developing microscopy tools for single cell genomics and transcriptomics and applying these to understand transcriptional regulation during development.

What role does 3D genome organization play in cell differentiation and embryonic patterning?

We are interested to learn to what extent changes in 3D genome folding facilitate changes in cell fate during development, using both fly and mouse development as a model system.  In Drosophila, distinct levels of 3 posterior Hox genes specify the anterior-posterior cell identities in the 10 most posterior segments of the animal. The three genes are positioned next to one another in the genome, amidst a large gene desert densely packed with regulatory sequences.  We have found that the genome is folded in a distinctive 3D structure in each of these 10 segments, altering the interaction frequencies among enhancers, promoters, and repressive elements to create 10 distinct expression states (see figure, below), (Mateo 2019).

Distinct 3D organization of the Hox genes and their regulatory DNA define distinct patterns of gene expression and distinct cell identities.

Deletion of enhancers in this locus results in misexpression of the Hox genes and corresponding homeotic transformations. The most famous of which, a triple deletion of enhancers that drive expression of the gene Ubx in the third-thoracic segment, converts the halteres into an extra set of wings, changing the fruit-fly to a dragon-fly appearance.  However, genetic alterations that do not map to enhancers, repressors, or genes also have dramatic pheontypes in this locus.

We have found the strongest of these non-enhancer/gene mutations perturb the cell-type specific 3D structure, resulting in changes in cell fate (Mateo 2019). For example, deletion of a short region 3’ of the gene abd-A, which lies at a structural boundary (TAD boundary) we found results in a dramatic change to 3D structure, increasing proximity between both regulatory regions of both flanking genes and resulting in their misexpression (see figure below). This deletion is embryonic lethal in homozygotes. 

We continue to use Hox loci to investigate roles of 3D genome structure in developmental patterning, taking advantage of their prominent roles in development, their complex regulatory landscapes, and their curious collinear organization in the genome. 

Deletion of genomic structural elements change 3D organization and alter gene expression in the posterior Hox gene complex in Drosophila. Shown left, in anterior abdomen cells (A2-A4), sequences downstream of the gene abd-A are statistically closer to Ubx, while upstream sequences are statistically closer to abd-A. This tissue expresses both genes in distinct patterns. Deletion of a short sequence located at this border decreases the average distance between upstream and downstream elements, resulting in ectopic contacts of enhancers and promoters and ectopic expression of both genes.

Computational modeling of feedback between epigenetic state and 3D chromatin structure

Prominent epigenetic chromatin states are associated with distinctive 3D organization.  We are interested in understanding how epigenetic state effects 3D structure and transcriptional state and v.v. We are currently tackling this through a combination of single-cell imaging and computational modeling.

Molecular Mechanisms of 3D organization

Combining genetic tools like induced protein degradation with single-cell imaging (described above) we aim to improve our understanding of the molecular mechanisms that shape genome function.

Patterning in mammalian embryos and synthetic embryos

Correct patterning and development of many mammalian tissues depends on the activity on cis-regulatory interactions at ultra-long range. We are interested to understand how such long range regulatory interactions are established, and how they derive specificity. Several examples we are studying in the lab include distal enhancers for Pitx1 expression in posterior limbs (300 kb), distal enhancers of Myc (700 kb) the limb enhancer of Shh (1 Mb), distal enhancers of the Hoxa and Hoxd clusters (1 Mb), and some of the cranial neural crest enhancers of Sox9 (1.4 Mb).


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