Promoters get all the glory when it comes to gene regulation. Sure, they’re important, but save a little love for enhancers—they may help cells decide what to be when they grow up! Historically, most methylation studies have focused on promoters, but instead of giving all the attention to these spotlight hogs, researchers at University Hospital Regensburg in Germany looked at DNA methylation across entire gene loci in conventional (Tconv; CD4+) and regulatory (Treg; CD4+CD25+) human T cells to find out what makes these cells different. It turns out that the methylation status of enhancer regions is cell-type specific, suggesting that enhancers might be big shots when it comes to cell fate.
The scientists identified differentially methylated regions (DMRs) in the genomes of Tconv and Treg cells by using their methyl-CpG-immunoprecipitation (MCIp) method. Basically, they fish out methylated sequences from a pool of genomic DNA fragments with MBD-Fc, a methyl-binding protein. By varying the NaCl concentrations of the buffers, researchers can fractionate the sequences and finally get a handle on those elusive lower methylated regions.
The upshot is that most of the >100 T-cell DMRs found in 69 gene loci weren’t in promoters. And the researchers have good reason to believe these “promoter-distal” DMRs are enhancers. Here’s why:
- The differential DNA methylation correlated with histone H3K4 methylation, a known mark of an enhancer.
- Many DMRs increased transcription in reporter assays, another piece of enhancer evidence.
Several DMRs contained transcription-factor binding motifs important for Tconv– or Treg-specific functions, so silencing enhancers may be a general way that a cell commits to a certain fate. Check out the paper at Genome Research, June 2009.