Dr. Gerd Blobel discusses emerging techniques for visualizing the interactions of RNAs and chromatin.
The Future of Chromatin Contact Analysis
So there are other approaches that people are taking, which is: you use FISH, for example, Fluorescent In Situ Hybridization. And this is a method that can be used to validate interactions that have been detected by 3C. And these FISH-based methods are also getting much, much better. There’s now a single molecule FISH, where people can detect individual RNA molecules, for example, and we can use this is a way where we can really pinpoint the site of transcription in the nucleus.
…I think the holy grail, and a number of labs are working on this, is trying to image genes in living cells.
So those methods have the disadvantage that you’re only looking at one allele at a time. So I think ultimately those two separate areas have to be bridged. But I do think that FISH is an important and improving method. Microscopy-based methods are getting better and they will be useful in monitoring these interactions more closely in a cell-to-cell basis. And you can also relate this into different phases of the cell cycle very easily.
And I think the holy grail, and a number of labs are working on this, is trying to image genes in living cells. And there has been a flurry of developments recently where you can tag genes. And you could imagine putting fluorophores on these and then watch cells, perhaps in living cells if you have multilayer confocal microscopy, and observe these interactions dynamically, for example, in response to a stimulus or in a cell that undergoes a division cycle.