Roche NimbleGen and Sigma-Aldrich started a collaboration to further chromatin immunoprecipitation-on-microarray (ChIP-chip) research by aligning their two complementary technologies, Roche NimbleGen’s ChIP-chip high-density microarrays and GenomePlex by Sigma-Aldrich. Together, the platforms enable researchers to effectively study the entire genome for epigenetic interactions between DNA and DNA-binding proteins to determine regions of the genome that are transcriptionally active or repressed, as well as the mechanisms that regulate these processes. Understanding the fundamental epigenomic and genomic regulatory pathways underlying normal cell growth and tissue differentiation, as well as changes in regulatory control associated with disease, is crucial for the development of drugs that target these pathways.
To facilitate the ChIP-chip workflow, Roche NimbleGen and Sigma-Aldrich will publish protocols for ChIP-chip research and provide technical support to researchers integrating the two technologies, as well as co-market their complementary products.
ChIP-chip is a powerful tool that combines chromatin immunoprecipitation (ChIP) with microarrays to understand DNA-protein interactions. The ChIP step deploys a specific antibody against a regulatory protein of interest, which results in the enrichment of DNA fragments bound to the target protein. Usually these enriched DNA fractions are at very low concentrations and need to be further amplified for detection. The technologies from Sigma-Aldrich and Roche NimbleGen facilitate effective ChIP-chip research by addressing two critical bottlenecks in the workflow: efficient amplification of targeted sections of DNA and high-resolution microarray detection. For researchers, GenomePlex is the preferred method to amplify targeted small (less than 200bp) DNA fragments in an efficient and unbiased manner. The amplified genome can then be analyzed on Roche NimbleGen’s high density (up to 2.1 million probes per array), long oligonucleotide, ChIP-chip arrays, the most sensitive on the market, to examine the interactions between DNA and proteins such as transcription factors, histones and polymerases.
‘The Sigma-Aldrich whole genome amplification technology is our method of choice for preparing ChIP samples for microarray analysis. The high reproducibility and effectiveness of GenomePlex for amplifying ChIP samples from a small number of cells, in combination with the outstanding sensitivity of the Roche NimbleGen high density microarrays, allows us to study chromatin patterns in small amounts of normal and cancer tissues,’ said Dr. Peggy Farnham, Professor of Pharmacology and Associate Director of Genomics at the University of California Davis.
Whole genome amplification provides advantages over other techniques researchers have relied on in the past. For example, ligation-mediated PCR, a commonly used technique for preparing DNA for ChIP analysis, often causes investigators to miss important binding sites. With the whole genome effectively amplified by GenomePlex, analysis on Roche NimbleGen high-density arrays can reveal rare protein-DNA interactions with a high signal to noise ratio and sensitivity.
Release Date: April 21, 2009
Filed Under: Drug Discovery