New ChIP-Nexus Technique Precisely Maps Individual Transcription Factor Binding Sites in the Genome, Vastly Outperforming Existing Techniques

All the cells in an organism carry the same instruction manual, the DNA, but different cells read and express different portions of it in order fulfill specific functions in the body. For example, nerve cells express genes that help them send messages to other nerve cells, whereas immune cells express genes that help them make antibodies. In large part, this highly regulated process of gene expression is what makes us fully functioning, complex beings, rather than simply assemblies of like-minded cells. Despite its importance, researchers still do not completely understand how cells access the appropriate information in the DNA. They know this process is controlled by proteins called transcription factors, which bind to specific sites around a gene and - in the right combination - allowing the gene's sequence to be read. However, functional transcription factor binding sites in the DNA are notoriously difficult to locate. The large number of transcription factors and cell types allow endless possible combinations, making it incredibly hard to determine where, when, and how each binding event occurs. Moreover, results from genome-wide mapping efforts have only added to the confusion by suggesting that transcription factors bind very promiscuously all over the place, even to sites where they do not turn genes on or off. Now, researchers at the Stowers Institute for Medical Research in Kansas City, Missouri, have developed a high-resolution method that can precisely and reliably map individual transcription factor binding sites in the genome, vastly outperforming standard techniques.
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