Biologists are developing ever more sophisticated means to characterize molecular interactions in living systems.
But a new study suggests that many of the interactions detected by a widely-used experimental method are functionally irrelevant.
ChIP-chip is a “hot technique” in biology, allowing scientists to visualize the binding between regulatory proteins and genes and thereby investigate the mechanisms and controls that operate as an organism develops from a fertilized egg to a complicated adult. However, a new study published in this week's PLoS Biology shows that there are many more of these binding events than expected and that most of them appear not to be involved in gene expression.
The fruit fly is an important model for the study of development, the process by which embryonic cells are able to multiply and form three-dimensional structures that eventually become tissues, organs and finally entire organisms. The blueprints for this transformation are encoded in the genes of every cell, and are “read out” by vast networks of regulatory proteins called transcription factors, which determine where and when genes are expressed.
It has been generally assumed that transcription factors are targeted to a limited set of genes and that they regulate expression wherever they are bound. However, a team of researchers from the Lawrence Berkeley National Lab and the University of California at Berkeley, led by Mark Biggin and Michael Eisen, found that there are thousands of regions reproducibly bound by each factor. “This is several orders of magnitude more genes than these factors are thought to regulate,” said Eisen, “raising the question of what the function of the binding is.”