Enhanced yeast helps identify complex interactions in genes

Series of papers describe important new tool for regulatory network mapping

By Jim Fessenden

UMass Medical School Communications

October 31, 2011
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Marian Walhout, PhD 

A major challenge in the field of systems biology involves understanding the complex and interconnected ways that gene regulatory networks drive development, physiology and pathology. A series of papers in the latest edition of Nature Methods describe innovative techniques for identifying the complex interactions among genes, proteins and transcription factors that comprise gene regulatory networks in worms, plants, humans and flies.

 

Three of the forthcoming papers, which will give scientists new tools for answering important questions about how genes are controlled, originated in the lab of A. J. Marian Walhout, PhD, co-director of the Program in Systems Biology and professor of molecular medicine. The fourth paper is from a former post-doc in Dr. Walhout’s lab, Bart Deplancke, PhD, who is now running his own lab at Ecole Polytechnique Fédérale de Lausanne in Switzerland.

In the paper, Walhout and colleagues present a new technique that improves “throughput and coverage” over previous methods. One method that researchers often employ to study gene regulatory networks uses a particular type of yeast, called yeast one-hybrid (Y1H) to identify and characterize the various transcription factors that can bind to a specified piece of DNA in a cell. This technique requires sequencing of large pieces of DNA fragments that can be time consuming to produce and analyze. In the paper, Dr. Walhout and colleagues present a new type of “enhanced” yeast one-hybrid (eYIH) that uses a robotic platform and automated readout techniques to improve both throughput and coverage over previous experimental methods in a shorter amount of time.

“eYIH assays will be an important tool for gene regulator network mapping in C elegans and other model organisms, as well as humans,” wrote Walhout and colleagues in the paper abstract.

 

Related Link on UMassMedNow:

Marian Walhout featured in Cell