The word “island” conjures up images of a tropical paradise with a sandy beach and a sunny sky—a nice place to hang out. In a similar way, CpG islands turn out to be nice places for Pol II to hang out without worrying about pesky nucleosomes getting in the way, according to researchers in France and Spain. They say that GC content and CpG islands correlate with open chromatin and paused transcription at mammalian promoters.
The researchers knew that nucleosome depletion at promoters was linked with CpG islands, but no one had ever shown a direct correlation between the two. And no one knew which came first—the nucleosome depletion or transcription. So, the team decided to investigate. Here’s what they learned:
- They observed three different classes of promoters. For each class, GC content was correlated with so-called apparent nucleosome-depleted regions (aNDRs).
- The length of the CpG islands tcorrelated with aNDR width. Also, the location of the major nucleosome of each promoter moved as GC content increased.
- The CpG island and aNDR correlation held up, regardless of whether Pol II was present at the promoter.
“Our work adds several lines of evidence that CpG islands directly correlate with the level of nucleosome depletion at promoters and that GC content is the prominent, if not the most essential mark for maintenance of opened chromatin structures,” they say.
The team also concludes that Pol II doesn’t form aNDRs, but it can make aNDRs a little bigger and possibly push some of the bordering nucleosomes out of the way.
Read all the data at Genome Research, October, 2012.