Using ChIP-Exo Team Maps Protein Binding Locations in Yeast

Researchers have mapped the precise binding locations of over 400 different kinds of proteins on the yeast genome. The study reveals two distinct gene regulatory architectures, expanding the traditional model of gene regulation.

The Penn State team used ChIP-exo, a high-resolution version of ChIP-seq, to precisely and reproducibly map the binding locations of the proteins that interact with the yeast genome, some at a few locations and others at thousands of locations.

"In traditional ChIP-seq, the pieces of DNA attached to the proteins are still rather large and variable in length—ranging anywhere from 100 to 500 base pairs beyond the actual protein binding site," said William K.M. Lai, an author of the paper published in Nature today. "In ChIP-exo, we add an additional step of trimming the DNA with an enzyme called an exonuclease. This removes any excess DNA that is not protected by the cross-linked protein, allowing us to get a much more precise location for the binding event and to better visualize interactions among the proteins."

The team performed over 1,200 individual ChIP-exo experiments producing billions of individual points of data. Analysis of the massive data required the development of several novel bioinformatic tools including a multifaceted computational workflow designed to identify patterns and reveal the organization of regulatory proteins in the yeast genome. The analysis revealed a surprisingly small number of unique protein assemblages that are used repeatedly across the yeast genome. "The resolution and completeness of the data allowed us to identify 21 protein assemblages and also to identify the absence of specific regulatory control signals at housekeeping genes," said Shaun Mahony, an author of the paper.

The traditional model of gene regulation involves transcription factors, however the researchers found that the majority of genes in yeast do not adhere to this model. "We were surprised to find that housekeeping genes lacked a protein-DNA architecture that would allow specific transcription factors to bind, which is the hallmark of inducible genes," said senior author B. Franklin Pugh. "These genes just seem to need a general set of proteins that allow access to the DNA and its transcription without much need for regulation. Whether or not this pattern holds up in multicellular organisms like humans is yet to be seen. It's a vastly more complex proposition, but like the sequencing of the yeast genome preceded the sequencing of the human genome, I'm sure we will eventually be able to see the regulatory architecture of the human genome at high resolution."