Crawford Lab

Greg Crawford's Research Group

My primary research interest is understanding how the genome is regulated.  The human genome contains approximately 25,000 genes, which are encoded in ~2% of the genome. The overarching goal of my research program is to identify and characterize how these genes are turned on and off in different cell types, tissues, development states, environmental responses, diseases, and individuals. By understanding where all gene regulatory elements are located, how they work to regulate gene expression, and how non-coding variants within these regions affect function, my research program can address a number of important basic and clinical questions.

For over 35 years, the identification of DNaseI hypersensitive (DHS) sites has provided essential information to how genes are regulated. As a postdoctoral fellow at the NIH in 2004, I developed novel technologies to map DHS sites across the genome first using tiled microarrays (DNase-chip) and then using high-throughput sequencing (DNase-seq). Because each DNase-seq experiment (also ATAC-seq) identifies most gene regulatory elements in a single experiment, my laboratory has used these methods to explore how the genome functions across many biological contexts.

Research themes: I have been actively engaged in a number of diverse projects that are each based on highly collaborative research.

  • Diverse human cell types. We have developed methods to identify and characterize over a million regulatory elements that were detected across 100s of diverse cell and tissue types.  We have participated in ENCODE 1, ENCODE 2, ENCODE 4, and psychENCODE to map regulatory elements, and make these regions available to the public.  Our ongoing ENCODE 4 project with Tim Reddy, Maria Ciofani, and Charlie Gersbach is aimed at understanding, characterizing, and validating regulatory elements that are important for T-cell lineage specification.

  • Natural variation: By comparing DNase-seq data from human, chimpanzee, orangutan, gorilla, and macaque, we have collaborated with Greg Wray (evolutionary biologist) and Andrew Allen (Biostatistics) to identify species-specific regulatory elements (using cultured fibroblasts), and show that DNA variants in these regions are associated with species-specific transcription factor binding and enhancer activity.  We also collaborate with Allison Ashley-Koch (genetic epidemiologist) and Patrick Sullivan (psychiatric geneticist, UNC) to identify non-coding variants that contribute to altered chromatin accessibility (chromatin QTLs) and changes in gene expression. 

  • Environmental exposure:  An infinite number of environmental conditions may contribute to changes in gene expression, possibly through alterations in chromatin structure.  We have characterized how chromatin and expression changes occur in response to hormone (Tim Reddy), microbiome colonization (John Rawls), HDAC inhibitor treatment, butadiene (Ivan Rusyn, Terry Furey) and doxorubicin treatment.  We also collaborate with David Aylor (genetics, NC State) to use genetically diverse collaborative cross mouse strains to understand how endocrine disrupting chemicals like dioxin impact chromatin structure and gene expression.  These gene by environment studies are important to understand why some individuals are impacted more severely by toxic environmental exposures.

  • Development and cell cycle. We have participated in chromatin studies focused on different aspects of development, including cerebellum brain development (Ann West), X-chromosome inactivation (Terry Magnuson, UNC), sex determination (Blanche Capel), erythroid maturation, neuronal differentiation, muscle differentiation (Raluca Gordan), and T cell lineage specification.  We also have explored how chromatin accessibility changes during the cell cycle (Alex Hartemink and Dave MacAlpine) and during condensation of metaphase chromosomes.

  • Functional validation of gene regulatory elements.  While we and other groups have identified over a million gene regulatory elements, relatively little is known about what each of these elements are doing, what gene(s) they are regulating, and how strongly they contribute to gene expression levels. In collaboration with Charlie Gersbach (biomedical engineer) and Tim Reddy (computational and functional genomics), we have developed CRISPR-based methods to efficiently modulate chromatin structure of any region of the genome. While these initial studies perturbed one regulatory element at a time, we have recently scaled up this technology to characterize over 100,000 regulatory elements in a single experiment.  These tools will be essential in validating regulatory element activity, activating/repressing these regions in different contexts, and understanding the key chromatin-based changes that control gene expression levels.

  • Disease. Genome wide assiociation studies (GWA) for many complex disorders are largely pointing to noncoding regions of the genome.  However, due to linkage disequilibrium, it is challenging to narrow down causal variants that contribute to disease risk. In collaboration with Charlie Gersbach and Patrick Sullivan, we are using high-throughput CRISPR based methods to narrow the search space for functional noncoding variants that contribute to schizophrenia.  In addition to more common disorders, I collaborate with Priya Kishani (Pediatrics), Vandana Shashi (Pediatrics), and other clinicians to identify and characterize noncoding variants that contribute to rare and ultra-rare disorders.