Emma Farley - Sea squirts and switches

Emma Farley's work focuses on understanding exactly what the switches in our genome look like, and how they switch on genes.
14 November 2016

Interview with 

Emma Farley, UCSD


Gene regulation in seasquirts


Kat - One of the most exciting talks of the conference came from Emma Farley, assistant professor at the University of California San Diego, whose work focuses on understanding exactly what the switches in our genome look like, and how they switch on genes - known as gene expression. And her studies have led her towards a rather unusual - not to mention squirty - organism.

Emma - So I'm trying to figure out how the instructions for development and cellular integrity are encoded in our DNA sequence. We have a set of genes in our genome. We kind of understand these genes, but we don't understand how these genes are turned on in different cell types. And this is the key for building all of the different cells of our body and for maintaining their health during adult life. So that's a huge question in biology at the moment.

Kat - I know that we have 20,000 genes but of course, we have lots of different types of cells. You can't have all genes on in all cells or we'd just be a blob, wouldn't we?

Emma - Exactly, yeah. We need like heart-specific cells in our hearts and so we need to turn these genes on with specific switches. We need cells that have expression of particular proteins leading to neural functions so that they're neurons and these genes need to be switched on by particular enhancers or switches in the genome.

Kat - This is interesting - the switches - because the actual genes is only 1 or 2 per cent of all the DNA that we have in all our cells. What is the rest of it? How much of our genome is these switches that turn the genes on and off?

Emma - So, we really have no idea. We have methods to detect these switches in the genome. So, we can detect them by the proteins that bind to them and particular marks on the DNA. Using those methods, we estimate that there are somewhere on the order of a million enhancers in the genome. And so, this really provide the instructions for when and where all the genes are deployed in the human body.

Kat - A million switches to 20,000 genes. That starts to make more sense now because I remember people saying, "What do you mean? We've only got 20,000 genes." But a million switches!

Emma - Yeah. Each cell needs to turn on different genes at different times and this gives them a key identity and allows them to become say, heart or nervous system. It's really the diversity in these switches and deploying these genes that allows us to have all these different cell types.

Kat - Let's zoom in a little bit more. So what is a switch? What does it look like? Is it a stretch of DNA? What do we know about them right down on that DNA level?

Emma - So, switches are pieces of DNA in our genome. They're on the order of a hundred to a thousand base pairs, so a hundred to a thousand letters of DNA sequence. They contain within them sequences to which transcription factors, these proteins, bind and the binding of these proteins to the switch is like somebody with a finger turning a switch on and turning a light bulb on, and that leads to expression of particular genes.

Kat - So, what are you doing to try and unpack these switches and work out exactly what they look like and how they work.

Emma - I'm trying to understand how the sequence of DNA that makes up a switch encodes the information for a particular expression pattern. So during development, we have genes expressed in the nervous system or in the heart or in our skin cells. So, I want to understand how the information to turn them on in those locations is encoded in our DNA sequence within these enhancers. And so, we know that there are proteins in our cells known as transcription factors that bind to these switches. But that is not the whole story because the same transcription factors bind to different switches and turn on different patterns. So for example, there's one called ETS and one called GATA - these two transcription factors - they turn on expression in the heart, they turn on expression of genes in the gut, and they turn on expression of genes in the nervous system. But the switches are slightly different. There are different sequence identities of the particular binding sites that allow different expression and I'm trying to understand the regulatory principles that can translate enhancer sequence into expression patterns and find principles that can help us much like the relationship between coding DNA leading to protein sequence - what is the relationship between enhancer sequence and expression pattern.

Kat - So it's not as simple as say, AAGTC, that transcription factor always sticks to that sequence and always turns on a gene. So, it's more subtle than that?

Emma - Yes. So, if you look in the genome for a particular transcription factor binding site, there's probably 10 million locations where that binds and not all of those are functional. The question is, where in the genome do proteins bind and mediate function. A key component of this is combinatorial control. By this, I mean when you have two different transcription factors and the combination of the two leads to an expression of something. This added complexity allows this small set of genes to turn on expression in many different cell types.

Kat - So it's got to be the right kind of looking set of letters. You've got to have the right factors, right time, right place, and then you get the right genes turned on to make the right stuff.

Emma - Exactly. It sounds simple but we're still trying to work out exactly why certain sequences turn on in certain locations and not in others. And then the question beyond that is, what happens when people have mutations in their switches, and how do mutations in switches change gene expression and cause disease?

Kat - You're using quite an unusual organism to study this kind of question. Tell me a bit more about that because I guess people think, "Human genes, let's use humans." I guess you can't do these experiments in people.

Emma - Exactly, so I used an organism called Ciona intestinalis. The common name for it is the sea squirt because when you pick them up, they squirt water out. So they live in the ocean. They're sessile so they're attached to rocks and the bottom of boats. They're a long see-through sort of object and they have water that pumps in and out of them through two siphons. But they have a heart and when they're embryos, they look very similar to us, developing chordates. They have a notochord which is really important for development of the nervous system and they have a dorsal nerve chord which is the key definition of a chordate embryo. And they're actually the sister group to vertebrates. So they're basically our closest invertebrate relative.

Kat - So, our little sea squirty sisters. How are you studying these switches in these organisms?

Emma - So, these switches as I said are pieces of DNA sequence in our genome that can be somewhere on the order of a hundred to a thousand base pairs. We want to understand within that region, how does that region code for a precise expression pattern. It's really challenging to understand and look at this question. We've taken an approach where we want to change the sequence of this switch and see how changes in sequence of the switch impact gene expression, and then work out how you code for precise expression. If you think about a small sequence of DNA, you've got your A, C, T, and G letters. So, if you want to change each position to any four other positions, even on a small piece of DNA about 70 base pairs long, you're talking over 10 to the 30 possible sequence variants.

Kat - Wow! That's a lot.

Emma - Exactly. So, if we want to understand how a switch encodes tissue-specific expression, we need to be testing hundreds of thousands, millions, maybe even one day, billions of sequence variants. If we want to understand how variation in the sequence impacts where the expression is, we need to be doing this in intact developing embryos. And so, Ciona intestinalis offers a system where we can obtain millions of fertilised eggs and then we can introduce millions of variants of a particular switch and then see where these switches are turning on. And from that, we can start to find principles about how switches turn on in precise locations and what sorts of violations in these regulatory principles lead to disease.

Kat - What seems to be the indications so far? What do we know about what makes a good switch?

Emma - So, we had some really surprising results. If you think of a switch to turn on in the nervous system, you might think this switch is built to be really great at turning on in the nervous system. But what we found was actually, you want to make sure you don't turn on anywhere else. So you want to be bad at turning on in all other tissues and to do that, you have to be quite poor at turning on in the nervous system. So we found that you don't use optimal features in the enhancer. You're actually using these suboptimal features and this ensures that you don't turn on in the wrong place.

Kat - This is putting me in mind of the light switch in my hallway where you just have to really smack at it to get it to work. but in the end, it will go on when you want it to.

Emma - Exactly. You want something to turn on only in the right place because turning genes on in the wrong place is known to cause disease. So we think that those mechanisms within the genome that have allowed these switches to be turned on only if you press them in exactly the right way.

Kat - Emma Farley from the University of California San Diego. And now it's time to find out about the latest news in the world of genetics.


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