Gene expression is regulated by functional elements in the genome such as enhancer elements. Tissue-specific gene expression through regulated use of specific enhancer sequences is a major mechanism of development in an organism. Genomics provides powerful tools to study the DNA sequences involved in these processes. We use unbiased proteomics approaches to study proteins and assembled protein machinery at regulatory genomics elements, using a well studied in vitro model of C2C12 muscle differentiation.

We apply DNA baits to pulldown proteins and complexes from nuclear lysates.  Using this approach, we identified nearly 20 novel regulators and validated these using shRNA.