Dr. Steven Henikoff discusses interesting observations like chromosome puffs in polytene chromosomes back in the days before sequencing. This interview took place at the Keystone Symposia’s Epigenomics and Chromatin Dynamics joint meeting in January, 2012.
Epigenetics Before Sequencing
So when I was a graduate student you couldn’t do any of this stuff, right? It was even before sequencing, and before cloning. What we had were polytene chromosomes in drosophila and we had these puffs. And with heat shock you’d see these puffs go up, and this was discovered in the ‘60s, actually, and then in the ‘70s a lot of it was worked-out. I got into it as a gradate student together with Sue Lindquist. We looked at the proteins, we looked at the RNAs after heat shock, and within minutes you get these puffs that are sites of active transcription, and you could show that. But, one thing that got left behind, that we never figured out, was if you look at the puffs that were previously there – the developmental puffs on the polytene chromosomes, they went down. So there was regression of those puffs. What is that? What’s going on there?
“…when I was a graduate student you couldn’t do any of this stuff, right? It was even before sequencing, and before cloning.”
What we’ve done, at the Sheila Teves graduate student lab, what she’s done – and she’s also here as a post – is to actually to look at paused RNA polymerase, and turnover using Roger’s method, again, at high resolution – we can do this now – after heat shock. And after heat shock what she found was that – it’s quite striking – RNA polymerase, the paused polymerase actually disengages – comes off; turnover goes down over gene bodies. And the drop in turnover is the same as what happens if you inhibit RNA polymerase elongation – transcription elongation; you basically see the same thing, and over the same genes. Most of the genes go down, the ones that go up include genes that are involved in the heat shock transcription in the process, in gene regulation.”…when I was a graduate student you couldn’t do any of this stuff, right? It was even before sequencing, and before cloning.”
So what you realize is that this whole phenomenon that I never understood as a graduate student, turns out to be a reduction in the disruption of chromatin and the turnover of chromatin in gene bodies that’s occurring with heat shock. And it’s an evolved process, because the particular genes that avoid it include the ones that are involved in the process.
So, yeah, that was like a very straightforward thing to look at, but it’s quite general, and we’d like to use this tool to look at other perturbations, not just environmental perturbations, perturbations during oncogenesis is a major one that we’d like to look at.