If a picture is worth a thousand words then surely a video must be worth more? So far, our knowledge about DNA methylation has been limited to a comic strip of static images at different stages. That may all be about to change with a new tool reported by the lab of Rudolf Jaenisch, which may enable DNA methylation’s first steps to be caught on film.
Their system relies on one major principle: the methylation status of CpG regions can affect that of adjacent CpG sites. So, if a reporter gene is coupled to a methylation-sensitive promoter and this construct is in turn introduced next to a CpG region of choice, in theory, the activity of the reporter gene would provide a direct readout of the methylation status of this region. Neat.
Only one problem remained: finding the right methylation-sensitive promoter. The methylation status of many methylation-sensitive promoters depends on context; i.e., if a pluripotency gene is inserted into a somatic cell, its promoter will become methylated. However, the methylation of imprinted genes, which are expressed in a parent-of-origin specific manner, is controlled in cis by adjacent sequences and is not affected by tissue context. Bingo.
In their methylation reporter system, Jaenisch’s team coupled the minimal promoter from the imprinted Snrpn gene next to a fluorescent reporter gene. They then used CRISP/Cas9-mediated gene editing in mouse embryonic stem cells (ESCs) to insert the construct into the key pluripotency genes Sox2 and miR290, which are methylated and silenced during differentiation.
As expected, the fluorescent ESCs began to lose reporter gene expression during differentiation. The team used bisulfite sequencing to confirm that this event correlated with the methylation of target loci and the Snrpn promoter. Using a similar approach, they also studied the dynamics of demethylation at the same loci during cellular reprogramming.
This technique, reported in Cell, September 2015, will enable researchers to image the dynamics of DNA methylation at single cell resolution and in real time. Let’s just hope that some genes don’t prove to be camera shy.