For the first time we’ve acted out our paper in a 2 minute play that serves as a video abstract to explain our work. You can watch it here or you can read this blog, or the paper here or you can explore all three!
We’re hugely grateful to Natalie Choi who was great to work with and made the video for us.
Our lab works on how genes are turned on and off. It’s complicated and it’s simple. To regulate a gene something has to find the gene, bind to it, and either facilitate or block the reading of the gene.
As it happens specially shaped DNA-binding proteins (called transcription factors) can feel their way to the right gene, using Braille essentially, and then in eukaryotes (i.e. all lifeforms except bacteria) these proteins either loosen DNA packaging proteins (called histones), or tighten them to shut down the gene. (If you’re an undergraduate student in a course taught by me you’ll have heard this essential message too many times!).
So what does our new paper say?
We make, what in retrospect is an obvious point that we don’t think has been highlighted before – DNA-binding proteins that turn genes off (repressors) can work in a different way from those that turn genes on (activators).
The asymmetry arises from the fact that in eukaryotes the resting state of our DNA involves it being safely packaged up in proteins called histones. To turn a gene on, you have to do something. You have to move the histones away, or at least loosen them. If you stop loosening them, the DNA will soon be repackaged. So to keep a gene on, an ‘activator’ has to be there all the time, working against the histones.
On the other hand, ‘repressors’ can be different. They will ignore most genes because they are already packaged up. But if they see a gene that is on, and it’s time to turn it off, they just have to nudge the ‘activator’ out of the way or find some other mechanism to let the packaging resume. Unlike ‘activators’, they don’t have to stay there. They can just come in, shift the balance, and then leave those packaging histones to keep the gene off. In other words, ‘repressors’, but not ‘activators’, may work by ‘hit and run’ mechanisms, because the ground state in eukaryotes relies on histone-mediated repression, and only the on-state requires transcriptional ‘activator’ presence.
What this means is that when one looks at the gene landscape (using techniques like ‘ChIPSeq) one will see ‘activators’ resident at genes that are turned on, but one may not see any ‘repressors’ at genes that have been turned off and packaged up. The ‘repressors’ may have worked by ‘hit and run’ repression mechanisms. Looked at another way it is really the histones (and related proteins, collectively termed chromatin) that do the repression, so once the repression has been triggered the ‘repressors’ can leave. Some ‘repressors’ might stay and we are not saying that all ‘repressors’ work via ‘hit and run’, merely that some do.
There you have it. But it’s a bit dry isn’t it? So we acted it out in a video.
Kate was the narrator but she was also a ‘repressor’. Manan and I were ‘activators’. We had two genes, represented by boxes. The genes had bricks on their lids that represented the histones and kept the genes turned off.
At the beginning Manan and I pop up and lift the bricks and open the boxes, we are ‘activators’ that turn on the genes. You can tell that by the labels round our necks. Then Kate comes in, as the ‘repressor’. She nudges Manan out of the way, closes the box, and locks it shut with the brick. Then she leaves too.
When one looks at the genes – I’m still there struggling to hold up the brick and the lid, and keep my gene on. I’m an ‘activator’ so I’m always there when my gene is on. But importantly Kate, who was a ‘repressor’, and who repressed her gene, the one ‘activated by Manan, is now gone. In other words when researchers look for ‘repressors’ at their genes of interest they may not see them, because ‘repressors’ may work via ‘hit and run’ mechanisms.
Not many labs work on ‘repressors’ and it may be in part because they are hard to catch in the act. Appreciating the fact that they may work by ‘hit and run’ mechanisms can help explain failures to observe ‘repressors’ where we expect to see them, i.e. at genes that they repress. In our own work we tried for many years to see ‘repressors’ at the globin genes and while others gave up we persisted and ultimately used time course methods to catch them in the act. We published the work in an earlier paper and blog post. Our most recent review provides more detailed descriptions of the evidence that many ‘repressors’ work via ‘hit and run’ mechanisms, and suggestions for how to catch them in the act.