Functional Genomics Core (FGC)

Functional Genomics is the field of molecular biology that examines gene (and protein) regulation, function, and interactions on a genome-wide scale. Leveraging the rapidly expanding new capabilities of functional genomic approaches for mechanistic understanding of rheumatic diseases requires new functional genomic data from cells and tissues derived from patients with inflammatory conditions specific to rheumatic diseases and animal models with disease-relevant pathology.

In the FGC, we aim to reduce the time, financial resources, and technical expertise necessary to incorporate state-of-the-art functional genomic analysis into the labs of investigators in the research community.

The mission of the Functional Genomics Core is to provide resources, services, and infrastructure to enable our research community to advance their statistical, associative studies beyond epidemiologic findings and towards definitive molecular mechanisms.

We provide technical expertise and starter reagents to investigators to perform functional genomic experiments and support genotype-specific functional genomic studies.

Selected experiments facilitated by the Functional Genomics Core:

• DNA-sequencing to obtain genotypes to use in genotype-dependent analyses and polygenic risk scores to understand individual-level genetic burden of genetic risk variants for specific diseases and phenotypes
• RNA-sequencing, including the sequencing of RNA from primary cells for which specialized library preparation is needed
• HiChIP experiments using immunoprecipitation of chromatin loops bound by the H3K27ac histone mark for connecting putative enhancers to the promoters of the genes they regulate
• ATAC-seq for robustly measuring accessible chromatin available for driving transcriptional or enhancer activity
• Immunoprecipitation with deep sequencing (ChIP-seq, CUT&RUN, CUT&TAG) experiments for identifying DNA sequences that are associated with histone modifications or bound by specific transcriptional regulators
• Electrophoretic mobility shift assays (EMSA) and DNA affinity precipitation assays (DAPA) for experimentally confirming genotype-dependent binding of specific regulatory proteins to a specific DNA sequence
• Reporter constructs transiently transfecting luciferase or stably transformed GFP plasmids to assess the ability of a section of DNA to promote gene transcription
• Massively Parallel Reporter Assays (MPRA) for screening 1000s of genetic variants for allele-specific DNA regulatory activity in numerous cell and inflammatory contexts
• Pathology expertise to prepare tissue samples, and develop strategies for single cell RNA-seq and spatial transcriptomic studies performed in the Single Cell Phenotyping Core

Contact Us

Contact Leah Kottyan, PhD, for more information or to use our services.