MeCP2 is expressed in all the body’s cells, but some of its highest concentration of activities is in the CNS. The hypothalamus, at least in laboratory animals, is particularly robust. The MeCP2 binds to DNA that has been previously methylated. Indeed, MeCP2 literally means “methyl CpG binding protein 2.” This binding functions as a gene-silencing mechanism and, until recently, MeCP2 was considered to be a canonical repressor protein. As we shall see, this job description turned out to be overly simplistic.
Animal studies and the 40,000-foot view
As mentioned, a number of animal models have been used to investigate the molecular biology of MeCP2. Animals were genetically engineered to not express MeCP2 (“knock-out animals”) or to overexpress it. By examining gene expression profiles in specific tissues, it is possible to evaluate the “40,000-foot” view of the regulatory effects of MeCP2. The researchers did so by examining tissues in the hypothalamus.
The studies showed that MeCP2 did not just affect the expression of 1 or 2 genes but rather thousands. In some cases, the overexpression of MeCP2 turned off gene sequences in the hypothalamus. This is something you might predict, given MeCP2’s more traditional role as a repressor. However, in other cases, the overexpression actually turned on certain genes, which was not expected.
How can an overexpressed repressor actually turn on a gene? The explanation turned out to be more conceptual than biological. MeCP2 was not always acting as a repressor. Sometimes it was an activator. Indeed, it was shown to be an activator 85% of the time!
The same expected/unexpected results were observed in the MeCP2-deficient animals (knock-outs). The absence of MeCP2 clearly caused some genes to overexpress (something you might predict if their “repressor” was missing). But in some cases, certain genes were actually turned off in backgrounds without MeCP2. This would only make sense if MeCP2 activated these genes.
The 40,000-foot view gives us a lot of information about general expression patterns, but it does not identify individual sequences. Researchers next sought to narrow down the choices by asking which genes are being turned on, which ones are being turned off, and what, if anything, does this have to do with cognition?
The researchers used 2 overall thrusts to answer these questions. The first thrust had to do with trying to discern any common patterns of activation and repression in the thousands of genes MeCP2 appeared to be regulating. The second involved naming the specific proteins to which MeCP2 might be binding. The researchers hit pay dirt on both accounts.
MeCP2 appeared to activate any gene whose promoters were greatly enriched in CpG islands. MeCP2 also seemed to repress genes whose promoters were not greatly enriched in CpG islands. A counterintuitive finding was also made regarding the number of methyl groups in the activating promoters. Close examination of these promoters revealed that the CpG islands were not heavily methylated. The odd combination (lots of chances to methylate but few actual methyl groups) seemed to “trick” the MeCP2 into activating the gene.