Epigenomics Core Facility
The goal of the Epigenomics Core Center of the University of Kansas Medical Center (KUMC) is to facilitate researchers’ efforts to understand mechanisms through which transcriptional and epigenetic regulation occur during normal differentiation and disease progression, and to use this information to develop specific and potent therapeutic strategies.
What We Do
- Provide a unique opportunity for researchers to explore the mechanisms by which transcriptional regulation and epigenetic modifications are disrupted in human diseases, such as cancer, diabetes, cardiovascular disease and neurologic disorders.
- Offers a unique opportunity for researchers to explore how, when and where epigenetic marks become disrupted and lead to common human diseases.
- Provide an array of epigenomics and bioinformatics research resources and services that include DNA methylation profiling (Methylation Specific PCR, Bisulfite Sequencing, Bisulfite Pyrosequencing, Genome Wide Methylation Analysis as well as MeDIP-seq and MBD-seq), Protein-nucleic acid association (ChIP-seq and MeDIP-seq/MBD-seq), Gene expression profiling (RNA-seq), Bioinformatics analysis and Ingenuity Pathway Analysis (IPA), which includes experimental design and technical services.
- Will make sure the stability of the DNA methylation assays as well as the ChIP and ChIP-seq analysis among the at least three repeating samples.
- Help the clinician to identify the changes of epigenetic marks in patient samples and develop specific and effective therapeutic strategies for disease management based on the novel mechanisms identified with epigenomics techniques. Drugs targeting aberrant epigenetic changes exist and many more are in development. These agents provide novel ways to target tumor cells and restore normal epigenetic states. Use of such drugs can be further tailored to the patient's specific epigenetic and genetic landscapes (individualized medicine). In addition, detection of aberrant DNA methylation in bodily fluids holds promise as a noninvasive early detection biomarker. This would allow high-risk patients to be identified and treated in the early stages of disease.
- Provide educational outreach on epigenetics in human diseases and epigenetic techniques that can be applied to biomedical research.
What is Epigenetics?
Epigenetics refers to heritable changes in gene expression and/or phenotype without mutations in DNA sequences. Epigenetics mechanisms includes DNA and histone modifications, which are marked by methylation and hydroxymethylation on DNA as well as methylation, acetylation and phosphorylation on histones. These epigenetic marks are critical to regulate gene expression. Changes in histone modifications have been observed in different human diseases. However, it is largely unexplored on how epigenetic alterations contribute to the development of human diseases.
The Epigenomics Core Facility of KUMC will help researchers to analyze epigenetic changes during development and human disease progression using mouse models, human patient samples, and epigenomic methods such as DNA methylation assays and ChIP-sequencing (ChIP-seq) analysis. DNA methylation assays include Methylation Specific PCR, Bisulfite Sequencing, Bisulfite Pyrosequencing, and Genome Wide Methylation Analysis as well as MeDIP-seq and MBD-seq. ChIP-seq and MeDIP-seq/MBD-seq are state of art techniques to analyze histone modifications and DNA methylation, respectively, on a genome-wide scale. While these approaches may be considered standard practice for highly focused epigenomic laboratories, they are not for most laboratories and institutions at KUMC.
The Epigenomics Core has established a set of common protocols and procedures for acquisition of reliable and comparable epigenomic and transcriptomic data, has designated scientists to provide expertise supporting each project at KUMC, and could provide tertiary bioinformatics support to analyze the epigenome and transcriptome to gain insight into the impact of epigenetic changes on different human diseases. The Epigenomics Core will support the needs of each project at KUMC, help obtain reliable datasets, facilitate the successful completion of each project and reduce cost.
Key note: In general, the Epigenomics Core Facility of KUMC is the first and key step for all of the biomedical researchers who wish to perform transcriptional regulation and epigenomics study in their research. By consultation with the Core Director and staff, the core will help all biomedical researchers to design the experiments to avoid the missing of controls, to perform the key experiments to make sure the stability of the ChIP and ChIP-seq analysis among the at least three repeating samples, to do the trouble shooting if the researchers encounter any difficulties in performing the experiments and in data analysis. The Epigenomics Core can perform all of the experiments before sequencing, in which the sequencing will be performed at the genomics core at KUMC. Our services are provided to internal and external researchers and clinicians. All the core users should acknowledge the Epigenomics Core in their publications by stating that “DNA methylation analysis (or ChIP-seq, RNA-seq etc.) presented in this manuscript were performed by the Epigenomics Core facility at University of Kansas Medical Center.”