By using a modified microarray technique, HMS geneticists have identified a surprising feature of how one of the two copies of the X chromosome in females is silenced. The researchers looked at patterns of DNA methylation, a mechanism associated with silencing, and found that it is more concentrated on the activated X chromosome. The discovery, reported in the Feb. 23 Science, overturns the dogma that methylation occurs mainly on the inactivated X.
Proper dosage of gene products requires turning off one of the two Xs that females inherit. Choosing to silence the maternal or the paternal X chromosome is a random event, occurring on a cell-by-cell basis. Once that choice is made early in development, it is maintained through subsequent cell divisions.
DNA methylation has become recognized as central for maintaining the silenced state of genes. In humans, methyl groups bind to CpG DNA sequences, where a cytosine nucleotide links with a guanine nucleotide.
Research fellow Asaf Hellman and HMS professor of medicine Andrew Chess, both at Massachusetts General Hospital’s Center for Human Genetic Research, compared methylation on activated and inactivated X chromosomes. They incubated human immune cells with an enzyme that cuts DNA wherever it is unmethylated. Then they loaded the sample onto a gene chip that can probe thousands of sites on the X chromosome. The NIH-funded study showed that methylation was two times greater on the activated X than on the inactivated X and that the X active–specific methylations concentrate at the transcribed regions of genes.
The team’s approach of looking at many sites at once contrasts with previous work, which has been limited to studying a select few CpG sites and has led to the belief that methylation is more abundant on inactivated sites. “You used to have to pick out a candidate; now you can look across the entire genome,” Chess said.
Understanding patterns of DNA methylation may be a new key in deciphering and treating inheritable diseases, including cardiovascular disease, diabetes, and schizophrenia.
