Analyzing Protein-DNA Interactions Across the Genome
Epigenetic marks are as important as DNA sequences in determining phenotypes and their study has heightened focus on protein-DNA interactions versus traditional gene-based heredity studies. Characterization of these epigenetic patterns and regulatory networks has progressed beyond standard chromatin immunoprecipitation (ChIP) based techniques to include ChIP-chip, genome-wide microarray analysis of ChIP isolated DNA.
This high content approach provides insights into how regulatory and structural proteins, such as transcription factors and histone subunits, bind and interact with the genome. Immunoprecipitation of these protein-DNA complexes through high quality antibodies selective against post-translational modifications, combined with promoter or genomic tiling microarrays, identify sequence-specific DNA binding sites with precise resolution.
ChIP-chip is a popular method for exploring chromatin structure and nuclear protein function. However, the combined techniques result in staggering challenges, both in protocol development and in reagent cost. As a result ChIP-chip is generally limited to a small number of expertly-trained and well-funded laboratories.
As the leading provider of ChIP (chromatin immunoprecipitation) solutions, Millipore offers innovative tools for epigenetic research. Our comprehensive portfolio of ChIP reagents, based on the expertise of Upstate, now includes our new Magna ChIP2 kits for performing ChIP-chip analysis. ChIP-chip is a powerful technique that helps bridge the gap between proteomics and genomics, and is capable of characterizing complex regulatory networks on a genome-wide scale.
References:
1. Genome-wide location and function of DNA binding proteins. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, Volkert TL, Wilson CJ, Bell SP, Young RA. Science. 2000 Dec 22;290(5500):2306-9.2. ChIP-chip for genome-wide analysis of protein binding in mammalian cells. Kim TH, Barrera LO, Ren B. Curr Protoc Mol Biol. 2007 Jul;Chapter 21:Unit 21.13.


