Epigenetics Assays in the KUGR Facility

Epigenetic changes affect chromatin or DNA without making permanent changes or mutations in the DNA sequence. The most common types of epigenetic changes are DNA methylation or histone modifications, e.g. histone acetylation or ubiquitination. There are several types of assays that can be performed to detect epigenetic changes. The KUGR facility focuses primarily on whole genome assays such as chromatin immunoprecipitation, which can detect changes in DNA methylation, histone modifications or specific binding sites of transcription factors in the genome.

Currently, epigenetics and chromatin immunoprecipitation assays can be performed using Affymetrix promoter tiling arrays. The procedure involves several steps:

• Prepare appropriate DNA or cross-linked chromatin samples.
  
• Use specific antibodies to immunoprecipitate the methylated DNA or modified chromatin.
  
• Amplify the immunoprecipitated DNA to prepare hybridization probes.
  
• Label the probes and hybridize to the Affymetrix promoter tiling arrays.
  

The Ness laboratory and the KUGR Facility have optimized several of these steps. However, individual laboratories performing these assays must perform the initial immunoprecipitations and must identify positive and negative control genes for use in validating the amplification steps.

The KUGR facility is planning to offer epigenetics assays based on next-gen sequencing in summer, 2009. Check back later for more updated information or contact the KUGR Facility Director, Scott A. Ness, Ph.D., for more information.