Editorial: 鈥Don鈥檛 junk the 鈥榡unk DNA鈥 just yet鈥
鈥淗EART disorder: 99 per cent probability, early fatal potential. Life expectancy: 30.2 years.鈥
At birth, the time and cause of Vincent鈥檚 death were already known. His inferior genes meant that the best job he could hope to get was as a cleaner, rather than realising his ambition of becoming an astronaut.
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Thus begins the film Gattaca, set in a future when a person鈥檚 potential is thought to be determined by their genes. Gattaca was released in 1997 during the middle of the Human Genome Project, and its plot reflected what many believed at the time: we鈥檇 soon be able to predict all kinds of things about people based on their genes. 鈥淭here was this belief that we could answer huge amounts of things just by studying genes and gene variants,鈥 says geneticist Tim Spector of Kings College London, who was involved in the project.
Yet today, this prospect seems more distant than ever. After the genome was sequenced, another major project was launched to try to understand which bits of the genome do what. The results, released this week, reveal that our genome is far more complex and mysterious than biologists imagined just a decade ago.
Back in the 1960s, a beautifully simple picture emerged. Our DNA consisted of recipes for proteins. The double helix could be unzipped to allow RNA copies of these recipes to be made and sent to the protein-making factories in cells. But by the 1970s, it had become clear that only a tiny proportion of our DNA codes for proteins 鈥 just 1.2 per cent, we now know. What about all the rest? Some assumed it must do something, others suggested it was mostly junk. 鈥淎t least 90 of our genomic DNA is 鈥榡unk鈥 or 鈥榞arbage鈥 of various sorts,鈥 the geneticist .
Ohno knew, though, that some of the DNA that didn鈥檛 code for proteins still played a vital role. For instance, the process of making RNA copies of genes 鈥 transcription 鈥 involves clusters of proteins binding to specific sequences near the genes. These proteins 鈥 called transcription factors 鈥 control the activity of genes by either boosting or blocking transcription, so the sequences to which they bind are known as regulatory DNA or switches.
So how much DNA acts a switch, or has some other function? To provide an overall picture of which parts of the genome do what, the project was set up in 2003. It involves many teams around the world using a variety of techniques. The results of a pilot study looking at just 1 per cent of the genome were released in 2007. This week, the results of its study of the entire genome were released, with the publication of more than 30 papers in Nature and other journals.
Among other things, ENCODE looked for switches that control gene activity. The researchers did this by taking known transcription factors and seeing which bits of DNA these proteins bound to. So far, , covering 8.5 per cent of the genome 鈥 far more than anyone expected.
Even this is likely to be a gross underestimate of the true number, because ENCODE hasn鈥檛 yet looked at every cell type, or every known transcription factor. 鈥淲hen we extrapolate up, it鈥檚 more like 18 or 19 per cent,鈥 says of the European Bioinformatics Institute in Cambridge, UK, who is coordinating the data analysis for ENCODE. 鈥淲e see way more switches than we were expecting, and nearly every part of the genome is close to a switch.鈥
鈥淲e see way more switches than we were expecting. Nearly every part of the genome is near a switch鈥
But 鈥 and it is a big but 鈥 these findings do not show whether these switches actually do anything useful. Many of them may have played a role in the past, for instance, but are now 鈥渄isconnected鈥.
The other big surprise is that these regulatory regions are widely dispersed throughout the genome, with many lying in the middle of long stretches between genes that were thought to be barren wastelands. More than 95 per cent of the genome may lie within 10,000 base pairs of a switch. 鈥淚t means that nearly all of the genome is in play for doing something, or if you change it maybe it would have an effect on something somewhere,鈥 Birney says.
The way in which these switches work is also turning out to be vastly more complicated than thought. found that individual switches interact with many genes. What鈥檚 more, most genes are being influenced by numerous switches at the same time. 鈥淎lmost every gene we look at is physically touching other pieces of DNA, and it鈥檚 never just one, it tends to be five, eight, 10 sites, and each site in turn has RNAs on it, proteins on it, histones on it,鈥 says team member Job Dekker of the University of Massachusetts Medical School in Worcester.
This might help to explain one of biology鈥檚 biggest puzzles: the mystery of the 鈥渕issing heritability鈥. We know there鈥檚 a big genetic component to traits and diseases such as height and diabetes, but the genetic variants found so far typically account for only a tiny percentage of this heritability.
The missing inheritance
The assumption has been that genetic variants work in isolation, so their effects are additive: if you鈥檝e got one variant that increases the risk of, say, heart disease 5 per cent and another that increases it 10 per cent, your overall risk is 15 per cent. But Dekker鈥檚 discovery suggests that the effects of some variants can multiply: these variants may have a small effect on their own, but a much bigger effect if a person has certain other variants too.
鈥淚 firmly believe that much of the missing heritability is due to complex interactions between multiple genes, multiple non-coding variants and multiple environmental factors,鈥 says of the Geisel School of Medicine at Dartmouth in Hanover, New Hampshire. 鈥淭he reason we鈥檝e missed a lot of the heritability for complex diseases could be because we鈥檝e ignored the complexity of the interactions that we know exist in biology.鈥
So up to 20 per cent of the genome may consist of regulatory switches, working or otherwise. What about the rest? ENCODE tried to address this by mapping what proportion of the genome is involved in some kind of biochemical event, which might suggest how much of it is in daily use. The results suggest that up to 80 per cent of the genome is active, with much of it being transcribed into RNAs.
This RNA is not carrying the codes for making proteins, so what is it for? We know that there are lots of different kinds of functional RNAs, many of which are involved in regulating gene activity, such as microRNAs. What鈥檚 more, some non-coding RNA is turning out to perform other unexpected jobs.
鈥淭hey can work like taxi drivers to deliver proteins around the genome, but they can also tether one part of the genome to another and act as a bridge,鈥 says of the Scripps Research Institute in La Jolla, California. Yet others act as decoys, reducing protein output by soaking up coding RNAs.
But so far all the RNAs with known functions do not begin to add up to 80 per cent of the genome. One explanation is that most RNA transcripts are useless, being mere 鈥渘oise鈥 generated by overzealous enzymes that don鈥檛 know when to stop transcribing DNA into RNA. It鈥檚 like getting a cat to kill mice in your house, and not being able to stop it killing birds in the neighbourhood too.
鈥淭ranscription of non-coding DNA does not automatically indicate function,鈥 says Ryan Gregory of the University of Guelph in Ontario, Canada, who studies genome evolution. 鈥淚 don鈥檛 think ENCODE will show that the majority of the 98 per cent of non-coding DNA in the human genome is functional for regulation. It would be astonishing if it took so much to regulate a mere 20,000 genes.鈥
Only a handful of biologists, the most vocal being John Mattick of the University of Queensland in Brisbane, Australia, think most non-coding RNAs will turn out to have an important role. 鈥淚t鈥檚 now up to the proponents of the noise theory to explain why there鈥檚 so much of the genome that鈥檚 showing functional signatures,鈥 says Mattick.
But doing something is not the same as doing something useful, and there are good reasons to think that most of our DNA does not play a vital role. For starters, at conception we all have dozens of new mutations. Most of us have one to five mutations that adversely affect gene function in our protein-coding DNA alone, says of the Institute for Systems Biology in Seattle, Washington.
If most of our DNA were vital, populations would acquire harmful mutations faster than they lose them through the death of embryos and children with lots of nasty mutations. 鈥淚f the fraction of the genome that鈥檚 functional increases, the question is: how do we tolerate that? Why aren鈥檛 we dead many times over?鈥 asks Nadeau.
鈥淚f most of our genome is functional, how do we tolerate the high number of mutations? Why aren鈥檛 we dead?鈥
One way to get a sense of the importance of a given bit of DNA is to look at whether it can accumulate mutations without consequence or whether it remains unchanged in a population because natural selection eliminates any individuals with mutations. 鈥淪omething like seven out of ten nucleotide changes in [protein] coding sequences get kicked out because they鈥檙e deleterious, but nine out of ten changes in non-coding sequence don鈥檛 get kicked out,鈥 says of the University of Oxford. 鈥淭hat鈥檚 telling us something about the importance of coding changes versus non-coding changes.鈥
Birney agrees, although he says ENCODE has looked at the transcribed RNA that鈥檚 specific to primates and found that some of it seems to be under selective pressure in humans.
Another way to assess the importance of a given bit of DNA is to delete it to see what happens. This obviously can鈥檛 be done in people, but in mice huge chunks of non-coding DNA that appeared to be functional have been deleted without any obvious effect. Then again, from organisms such as yeast without any obvious effect, too.
One explanation is that in cossetted lab conditions, organisms can manage without DNA that is essential for survival in more challenging environments. Another is that there is a lot of redundancy in the genome. Although you would expect mutations to eliminate redundancy, in which it can be maintained.
鈥淸Redundancy] could be what makes the system robust,鈥 says Dekker. 鈥淚f any given piece of DNA is only part of the context, deleting it may have very limited effects. I think it may explain why we can tolerate huge variation between individuals yet we鈥檙e all still walking down the street.鈥
A third reason to think most of our DNA isn鈥檛 vital is that although there is , there is very little correlation between the complexity of animals and their genome size. There is no obvious reason why the marbled lungfish needs around 40 times as much DNA as we do, and nearly 400 times as much as the green pufferfish, for instance.
Because they can
Gregory has found that some kinds of animals, such as metamorphosing amphibians whose cells need to divide rapidly at times, . This suggests that organisms tend to accumulate DNA until its size becomes detrimental, rather like the way people in a big house tend to fill the attic with junk whereas those in small houses have to keep throwing things out.
So we are left with something of a mystery. Although several lines of evidence suggest that most of our DNA is far from essential, ENCODE鈥檚 results suggest that most regions of our genome do do something. One answer could be that most of these regions do not do anything of any great consequence. 鈥淭hey may still have effects. They may change someone鈥檚 facial anatomy,鈥 says Ponting. 鈥淭hey may have very small effects which evolution isn鈥檛 acting upon.鈥
Birney thinks some of these regions do matter, though. 鈥淲e don鈥檛 yet have a definitive answer to how much of it is important, but we鈥檝e discovered a lot more things that could be important than anybody had ever suspected,鈥 he says. 鈥淧eople often say it鈥檚 the protein coding regions, plus a bit more. It鈥檚 not a bit more, it鈥檚 a lot more.鈥
When ENCODE鈥檚 work started, Birney himself was also highly sceptical about the role of non-protein-coding RNAs in genome function. He even bet Mattick a case of vintage champagne that less than 20 per cent of non-coding RNAs would turn out to be useful. 鈥淚 am definitely closer to losing this bet,鈥 he says.
It could be a long time before one of them gets the champagne, though. Working out which of the millions of regions ENCODE has identified as functional are actually important is an immense task that could take many decades. Ultimately, the only way to prove that a particular region is vital is to show that variants in this region have some effect on people, which is far from easy. In some cases, though, the evidence already exists: the positions of significant genetic variants identified by studies looking for associations between genetic variants and diseases often coincide with ENCODE regions. 鈥淢ost of the time we have something that鈥檚 either bang on top of those regions identified by [these] studies, or really close by,鈥 says Birney.
This is already giving us clues about the causes of diseases. For example, some variants associated with Crohn鈥檚 disease are in switches that ENCODE found are active in immune cells called T-helper cells.
It seems, though, that the more we learn about the genome, the less we know. 鈥淥ur genome knows how to make a human, but I think it is hubris to think that that recipe book would be simple and well laid out,鈥 says Birney. 鈥淲e are one of the most complicated things that we know about, and indeed it does look very complicated.鈥
鈥淲e are one of the most complicated things we know of. It is hubris to think the recipe book would be well laid out鈥
We鈥檙e certainly a long way from the complete understanding of the genome portrayed in Gattaca. In fact, we may never achieve it. 鈥淚t may well be too complex,鈥 says Moore.
Part of this complexity comes from the many ways in which our genome interacts with the environment. 鈥淚 think DNA will become more predictive, but the flip side of this research is understanding how much of complex traits are due to environmental effects, or free will 鈥 things that we can change,鈥 says Birney. 鈥淒NA is not destiny.鈥
To some extent, even the writers of Gattaca agreed. (Spoiler alert.) Despite Vincent鈥檚 genetic inadequacies, he refused to accept his genetic fate and ultimately achieved his goal of leaving Earth.
