Dr. Gerd Blobel discusses chromatin organization and the recent technology developments that have deepened our understanding of regulatory domains in the nucleus.
Investigating Long Distance Chromatin Interactions
So there have been phenomenal developments in our field which address the mechanism of chromatin organization. And I would argue that it’s like in the early days of medicine, we started off with anatomy. We described what we saw. And we used colors and dyes.
And now, people have better tools in hand where they can look much more deeply. And over the last 10 years or so, people have developed biochemical techniques that are C type technologies– or 3 C, 4 C, 5 C, high C type methods– that are basically tools to measure the relative distances among chromosome fragments. And that has allowed us to give a better view of how the genome is organized in three dimensions.
And with the advent of high throughput computing and powerful deep sequencing technologies, we’ve been able to get much finer resolutions. And this is given a very exciting insight into how the nucleus is organized, how the chromatin fiber is organized in the nucleus. And it has revealed domain structures– that the nucleus is non-randomly organized– there are very large genomic distances that can communicate with each other.
And some of those larger domains are also called topologically associating domains. Those are remarkably conserved between cell types, and even between organisms. And there is, within those domains, smaller domains and interactions that are maybe 100 kilo base or so– even less– that are more tissue or gene specific where enhancer elements interact specifically as promoter elements. And they account for the more tissue specific gene expression patterns.
So to me, this kind of recognition of regulatory interactions, I think, are very, very important. And they have really transformed our view of the organization of the genome.
Towards a Functional Analysis of Chromatin
However, I should also say that these interactions are, by nature, descriptive. We look at large populations of cells, so there a lot of challenges lying ahead of us in trying to see what happens at the individual cell. What happens to these structures throughout the cell cycle? What happens in mitosis or phase? Are these structures maintained or are they dissolved?
And then how are these structures set up? And once you understand that, we can also ask functional questions.And this is what our lab has gotten into and made a contribution to– is can we manipulate those interactions andreally test their functions?
“So to me, this kind of recognition of regulatory interactions, I think, are very, very important. And they have really transformed our view of the organization of the genome.”
In other words, can we generate long range interactions in the nucleus and ask, can we turn the gene on that way? Can we silence a gene in this manner? Can we localize a gene to a different nuclear compartment and ask,what are the effects of relocalization?
And people have done this, mostly with artificial loci But it’s been done much less so with native, endogenous gene loci and this is what we have tried, too. We’ve had a collaboration with Sangamo Biosciences, and they helped us design zinc finger proteins, which allowed us to target a specific site in the genome.
In this case, we targeted regulatory elements in the beta globin locus and asked, can we fuse the zinc fingers to domains that will allow the interaction with distal enhanced elements and form a chromatin loop? And to that,we’ve been lucky in this has worked. After many years of trying, we’ve being able to generate a chromatin loop at an endogenous, native gene locus, and been able to turn a gene on that way.
So that suggested that chromatin looping actually causally underlies transcriptional regulation,which had been an open question in the field at the time.