3D Chromatin Structure
In addition to the roughly 30,000 known human genes, the human genome harbors tens of thousands of enhancers, small genomic elements that can regulate the expression of genes that are several hundred of kilobases away. This regulation is often carried out via DNA looping events that bring enhancers into close three-dimensional proximity with their target genes. Enhancer-mediated gene regulation is a widespread phenomenon that is known to modulate a variety of biological processes including human development, cancer progression, and response to invasive pathogens. However, while our ability to predict enhancers is fairly mature, we know little about the mechanisms governing loop-mediated gene regulation and identifying enhancer-promoter loops remains an enormous challenge. We use a novel genomic technique, in situ Hi-C, to map changes in 3D chromatin structures as human cells undergo a variety of biological processes including cellar differentiation.
While genomic characterization of chromatin dynamics is a critical first step, a mechanistic understanding of how DNA looping alters gene transcription requires tools to precisely modify chromatin structures. To that end we are developing new CRISPR-based methods to rapidly and efficiently generate clonal genome-edited cell populations from monocyte cell lines. We are also interested methods for high-throughput CRISPR-based screening of edits to regulatory regions and DNA loop anchors.
The incredible ability of a single multipotent cell to give rise to a diverse spectrum of tissues and differentiated cell types is a hallmark of human development and requires a carefully coordinated and highly complex system of events. Misregulation of these events can lead to a variety of human pathologies ranging from limb malformation to cancer. Each differentiation process involves the transmittance of extra-cellular signals to the nucleus via protein phosphorylation, the restructuring of two- and three-dimensional chromatin architecture, and ultimately an altered transcriptional program. However, these phenomena have only been examined in a handful of the cell types for which in vitro differentiation protocols exist. We are characterizing the molecular underpinnings of multiple cellular differentiation process using an integrative multi-omics approach.
With the great increase in complexity of currently available -omic technologies comes an even greater need for tools to help investigate and interpret the data. We are working on tools focused on the interpretation of large data sets and data sets integrating multiple different data types. Our aims are to reduce data dimensionality into simple visualizable representations that improve our ability to interpret and communicate findings from these powerful techniques. We are working on software to improve data analysis of many data types including ChIA-PET, Hi-C, and mass-spectrometry-based proteomics.