When the German physiologist Albrecht Kossel first isolated histones in the late 1880s, the complexity of these nuclear proteins in contrast to the simpler nucleic acids suggested they might be an essential component of the elusive heritable material. But later, following the discovery of DNA and genes, histones were largely dismissed as a mere DNA scaffold.
Today, the recognition that histones actively participate in gene regulation has led to a surge of interest in the enzyme complexes that regulate them. In the Dec. 5 issue of Molecular Cell, HMS professor of pathology Yang Shi and his colleagues describe a novel histone-modifying complex that represses a subset of human genes, including at least one oncogene.
The discovery of this complex, which contains histone-modifying enzymes, a DNA-binding factor, and a linking protein called CDYL, sheds light on how histone-modifying enzymes are recruited to chromatin. The interaction is central to epigenetic control of gene expression.
Peter Mulligan, a former postdoctoral fellow in Shi’s lab, found this novel histone-modifying complex by going fishing. He applied a technique called tandem affinity purification, in which tagged CDYL served as bait to catch interacting proteins. As Mulligan had hoped, the interactors he reeled in immediately suggested a function for CDYL.
Together, the interacting proteins had all the hallmarks of a histone-modifying complex. In fact, the list of CDYL interactors was reminiscent of another histone-modifying complex, the CtBP complex, which the Shi lab had previously identified. Like CtBP, CDYL interacted with numerous histone-modifying enzymes, including methyltransferases like G9a. The complex also contained a DNA-binding factor known as REST.
REST is a transcriptional repressor capable of silencing a subset of genes, but it does not work alone. “When we saw that CDYL was interacting with REST and methyltransferases, we thought it might recruit these enzymes to REST,” said Mulligan. He and his colleagues confirmed that CDYL is a novel REST co-repressor that serves an essential function.
“CDYL is a biochemical bridge,” explained Shi. “Without CDYL, the histone-modifying enzyme G9a cannot bind REST and the target gene is not silenced.”
Although there are other REST co-repressors, such as CoREST, which also recruit histone-modifying enzymes, the researchers found that when CDYL is knocked down, some REST target genes are upregulated, suggesting that certain targets may be preferentially silenced by a CDYL-containing complex.
In 2005, Stephen Elledge, the Gregor Mendel professor of genetics and of medicine, and Thomas Westbrook, a former postdoc in his lab, both co-authors on this paper, identified REST as a tumor suppressor that when knocked down in cultured mammary epithelial cells facilitated oncogenic transformation. Mulligan and colleagues observed a similar effect when they knocked down CDYL, but not CoREST, indicating that it is the CDYL-containing complex that is responsible for the tumor-suppressor function of REST.
By a stroke of serendipity, Natalya Pavlova in the Elledge lab had recently determined that overexpression of a receptor tyrosine kinase called TrkC is oncogenic. Mulligan and colleagues went on to show that the receptor, a REST target gene, was de-repressed in the absence of CDYL, suggesting that it might mediate transformation in their model. Future studies will determine if the CDYL complex represses other oncogenes as well.
If CDYL does function as a tumor suppressor, one might expect that human tumors would display disruptions in the CDYL gene. Interestingly, several clinical studies have reported frequent loss of heterozygosity in a region of chromosome 6 that encompasses CDYL. A striking 43 to 70 percent of invasive cervical carcinoma tumors display loss of heterozygosity in this region, and these abnormalities correlate with a poor prognosis.
Students may contact Yang Shi at yang_shi@hms.harvard.edu for further information about this and other lab projects.
Conflicts of interest: Yang Shi is a cofounder of the biotech company Constellation Pharmaceuticals.
Funding Sources: The National Institutes of Health
