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The Wily Ways of a Transcription Factor

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Paul Brindle and his research colleagues at St. Jude Children’s Research Hospital have long worked on transcription factors, so it should come as little surprise that to test out some hypotheses they called in that old standby, the CREB protein. After all, it’s “one of the best understood transcription factors in terms of signaling in mammals,” Brindle says.

Here’s the twist: when the research team took what was known about CREB in vitro and made mouse models to study the protein in vivo, it became clear that the transcription factor was a lot more complex than anyone had realized. The key activator known for CREB, CBP/p300, turned out to be “important, but it wasn’t as universally important as we thought from our many in vitro studies,” Brindle says. In fact, his team saw that CREB was activated by different co-factors depending on which gene it was turning on. “Each CREB-responsive gene seemed to have a different requirement from each particular interaction.”

What made all the difference, says Brindle, was moving the CREB study to an in vivo platform. “Many of these things would not have been revealed without mouse genetics,” he adds, noting that all of the work was done in cells cultivated from mouse models. The team studied those cell systems using microarrays at first — those offered a big-picture view of what was going on, Brindle says — and then key genes were homed in on for deeper gene expression studies. To round out the project, the scientists also looked at protein-protein interactions with chromatin immunoprecipitation.

A key finding of the study, which was published this summer in The EMBO Journal, is that CREB likes to keep its co-activators close — whether or not it will need them. Brindle and his colleagues suspect that the protein’s co-factors are present “in most, if not all, of its target genes” regardless of whether they will be used. If that’s true, it means that understanding the transcription factor has an extra layer of complexity. “A lot of the other approaches being used [in other studies] are relying on looking at, is a protein present in a given gene,” Brindle says. “The implication is that protein will be important wherever you find it.” But this latest work indicates that that supposition needs some tweaking. In fact, sheer location “doesn’t necessarily mean it’s important,” Brindle adds. “There’s no way right now to know … unless you actually disrupt [the system] whether that protein [is] at that gene or not.”

Up next, the team plans to test out the CREB findings in additional organisms and other tissue types, especially in brain. “One prediction is that, for example, in other tissues where CREB is thought to be important, like in the brain, that this dependence on different co-activators by CREB may be different there. It may add another layer of regulation,” Brindle says. In the brain, CREB function is thought to help with memory, making it an appealing target for diseases such as Alzheimer’s. Meanwhile, in the liver, CREB may have a role in producing glucose during fasting conditions, Brindle says.

Naturally, any therapeutic developed for, say, the CREB role in Alzheimer’s would have the immediate hurdle of having to avoid hitting the entire CREB pathway (and affecting major organs like the liver). Brindle says that while it’s a long way off, this discovery of CREB’s multitude of co-factors is actually a step toward better-targeted therapeutics. In theory, a compound could be designed to target CREB only when it’s acting in conjunction with certain co-factors, drastically limiting the otherwise wide swath of biological hits that would come with a compound that broadly worked on CREB itself.

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