Protocols features high-throughput methods for analyzing gene activity (3/9/2008)

New high-throughput methods are revolutionizing our understanding of transcriptional regulation. This month's issue of Cold Spring Harbor Protocols (www.cshprotocols.org/TOCs/toc3_08.dtl) highlights two methods for analyzing the switches that turn genes on and off. Both methods are freely accessible on the Web site for Cold Spring Harbor Protocols (www.cshprotocols.org).

Our knowledge of epigenetics, the changes in gene regulation through modulation of chromatin not brought about by changes in the DNA sequence, has rapidly expanded in recent years. The first protocol describes a rapid, genome-wide method for identifying regions where methylation, an epigenetic control mechanism, is occurring. This method, "Methylated CpG Island Amplification and Microarray (MCAM) for High-Throughput Analysis of DNA Methylation," was developed by Marcos Estecio and Jean-Pierre Issa of the MD Anderson Cancer Center and Pearlly Yan and Tim Huang of the Ohio State University Comprehensive Cancer Center.

The protocol, freely accessible at http://www.cshprotocols.org/cgi/content/full/2008/4/pdb.prot4974, has proven successful for use in comparing normal tissues and tumors, helping researchers better understand the factors responsible for cancer.

The second protocol, available at http://www.cshprotocols.org/cgi/content/full/2008/4/pdb.prot4972, looks at the binding of regulatory proteins to DNA. These proteins play a role in turning activity of individual genes on and off. The method, "DNA Immunoprecipitation (DIP) for the Determination of DNA-binding Specificity," allows researchers to determine the specific DNA sequence that a regulatory protein binds. The technique allows for rapid screening of the entire genome for these binding sites, which gives insight into which genes these protein factors control.

Note: This story has been adapted from a news release issued by Cold Spring Harbor Laboratory

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