What is Suppressing The Suppressors?: Modified CTCFs linked to silenced tumor suppressors

Looking for exotic enzymes to silence tumor suppressor genes? You might be searching in vain. Maybe try looking for heterochromatin instead.

Salk Institute postdoc Michael Witcher was baffled by what made p16INK4a not tick in breast cancer cells. He fed the genetic sequence into some prediction software, but it wasn’t much help. So he did what any technophobe might do – he eyeballed it, upstream and down. “I looked at the sequence – the forward strand and the reverse strand.” He found long repeat elements and AT-rich regions, which are classically associated with nuclear matrix and condensed chromatin structure, along with a curious CCCTC motif, about 2 kb upstream of the proximal promoter.

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CTCF – the zinc-finger protein also known as CCCTC-binding factor – is associated with chromatin boundaries. Though there’s no difference in the CTCF target sequence itself, it turns out that CTCF was only binding there in cells that make the p16 tumor suppressor, and not in those that don’t. And the same thing was found with other tumor suppressor genes and in other types of cancers, too. Maybe, thought Witcher and boss Beverly Emerson, the loss of CTCF binding allowed heterochromatin to encroach upon and silence the gene.

He found a clear boundary at about 2 kb upstream of the proximal promoter, with heterochromatin upstream and euchromatin closer to the promoter. That boundary is missing in the silenced p16 gene. Previously, heterochromatin-like structure wasn’t known to be between actively transcribed areas, but only in places like centromeres, Witcher says. Now we know “it’s already there, it’s just being constrained.”

It turns out that in cells with a silenced p16, there’s an aberrant post-translational modification of the CTCF protein. To learn more about what it all means, check out the article in Molecular Cell, May 2009