Dr. David Gilbert discusses the ins and outs of 3-D chromosome folding, DNA replication and the highly dynamic cell nucleus.
3-D Chromatin and DNA Replication
There’s no question. The thing that I’m most excited about is the uncanny alignment between three dimensional chromatin confirmation maps and replication timing. The alignment is the greatest alignment that I know of in genomics. And what this means is that the three dimensional folding of chromosomes into segments is somehow highly related to the replication program. And we know that there are regions of chromosomes that will interact with each other, and interact with other parts of chromosome, but will not interact with their next-door neighbors. And those next-door neighbors are replicating at very different times.
And another interesting part about that, exciting part about that, is that there’s DNA a in between those domains. And that DNA a in between the domains has an intermediate ability to interact with either domain. But we know those regions as the regions of temporal difference in replication, so the regions where an early replicating part of a chromosome has completed replication. And replication forks are traversing towards a region that’s going to be replicated later.
…we know that there are regions of chromosomes that will interact with each other, and interact with other parts of chromosome, but will not interact with their next-door neighbors. And those next-door neighbors are replicating at very different times.
So those regions of what we call temporal transition regions in replication are the regions that are spatially linking parts of chromosomes that do not touch each other. So what prevents two spatially adjacent regions of chromosomes from touching each other when they’re right next to each other is incredibly fascinating. And why do those replicate as separate, individual units is the other thing we’re really excited about.
The Chromatin Conundrum
So the chicken or the egg question always comes up in chromatin, doesn’t it? And it’s almost always impossible to address. But as of now, we really don’t know what the biological significance of a replication timing program is. There’s no a priori reason why you would have to believe that replication have to proceed in a particular temporal sequence in order to accomplish the simple job of duplicating the genome.
So any model for the significance of replication to chromatin has to stack up against the null hypothesis, which is just that you organize chromatin for other functions. And replication is the read out. When you organize chromosomes for other functions, they become, by default, organized for replication. That’s still a viable model.
However, we do know that different types of chromatin are assembled at different times during S phase. And we do know that chromatin is assembled at the replication fork. So it’s very attractive to think that there is a causal relationship between the two. But we’re going to have to understand a lot more about replication before we’re going to be able to link them causally.
The Dynamic View of a Dynamic Nucleus
In terms of what’s changed in the perception of nuclear dynamics, in my view it’s that people are paying attention. I think molecular biologists and biochemists really didn’t look at cell biology as a serious science. And now that’s happening.
We know that the nucleus is a dynamic place, that proteins are moving all over the place, that things are done combinatorially by clusters of different types of proteins. Another thing that we’ve learned, and another problem for the future is going to be tackling heterogeneity. We now know, when we can measure it, that there’s a lot of cell-to-cell heterogeneity in what’s going on. Different cells are transcribing different genes. And in terms of chromosome folding, what we were talking about earlier, there’s a lot of open question.
So we know that chromosomes don’t fold like proteins. If the chromosome doesn’t fold correctly, the cell doesn’t just degrade the chromosome. It has to deal with different folding conformations on a cell-to-cell basis.
So I think we need to understand how cells deal with that kind of heterogeneity. And cell biology is really informing those questions. Because we look at single cells in cell biology.
And in biochemistry and molecular biology, we use ensemble techniques to look at cell populations. So you lose a lot of information there. And there’s a lot of questions in heterogeneity that need to be tackled.