Like many other websites looking to boost their traffic, we couldn’t resist calling attention to a few hot bodies. Back in the day, Golgi Bodies were a hot research focus, and for good reason–these mini protein boot camps put the final touches on our critical cellular proteins before sending them on to their job assignments. With miRNAs grabbing worldwide attention in recent years, P-bodies, our cellular RNA recycling centers, took the title in the 2007-2008 research season. Midway through 2009, it looks like gene bodies are taking a commanding lead in the race for the crown.
It wasn’t that long ago that the untranslated regions (UTRs) of our genes were THE regulatory hotbed, while coding sequences were limited to some splicing/editing. Now there’s heaps of evidence suggesting that there’s plenty of regulatory action in our previously under appreciated gene bodies. We couldn’t help but notice several recent publications where researchers studying DNA methylation expanded their studies well outside the 5’ UTR, into the gene body, and turned up some very interesting data in the process.
- A couple months back in Nature Biotechnology (April 2009), Ball et al., interrogated CpG Methylation at single base resolution, both at the genome-wide level with methyl-sensitive cut counting (MSCC) and in a targeted setting with bisulfite padlock probes (BSPP). In what was more of a proof of principle paper for these methods, the team still managed to call attention to the significant amount of functionally elusive gene body methylation in the regions studied and further supported recent evidence highlighting the increased differential methylation in intermediate CpG density promoters vs. low/high CpG density promoters.
- Then, in The EMBO Journal (April 2009), we saw featured work from Miura and colleagues highlighting novel gene-body methylation in Arabidopsis. Utilizing whole-genome bisulfite profiling, they analyzed differential methylation targeting in a mutant background lacking functional IBM1, an H3K9me demethylase. They found drastic gene-body hypermethylation upon loss of IBM1, with differential effects on transcription; highlight the emerging, complex story behind gene-body methylation and epigenetic regulation.
- Just last month in Lande’s Epigenetics (May 2009), a team led by Liselotte Bäckdahl showed how gene body methylation could be used to discriminate undifferentiated from differentiated ES cells. They utilized MeDIP-Chip screen to find differentially methylated regions, or DMRs. Their data uncovered NS-specific hypermethylation in the gene-body of Ddah2, a key enzyme in the nitric oxide pathway. They go on to show a significant increase in Ddah2 mRNA levels in the hypermethylated NS cells – yet one more piece of evidence implicating gene-body methylation in regulation.
Several groups have provided evidence linking gene body methylation and transcription, but there are still more questions than answers, so we’re looking forward to following this hot body (in a completely non-creepy way of course) into the foreseeable future. If you’re looking for a quick way to firm and tone your gene body knowledge, check these pubs out: