Junk DNA: The ‘dark matter’ in your genome

Did you know that your some of your DNA appears to be useless? Geneticist Kat Arney explains the science and mysteries of the junk in your genome…

I’m sorry to be the one that breaks it to you, but your genome is full of crap. Or, to put it more politely, junk.

The term ‘junk DNA’ is widely believed to have been coined by Korean geneticist Susumu Ohno in a 1972 paper entitled ‘So much “junk” DNA in our genome’, although it was probably in common usage in scientific circles from the 1960s onwards.

Ohno pointed out that scientists had already figured out how much DNA was in a single bacterial cell (the molecular biologist’s favourite bug, E. coli) and knew that it contained a few thousand genes. They also knew how much DNA was in each one of our own human cells: 750 times more than the bacteria.

If the number of genes in a genome is directly proportional to the amount of DNA, then a simple back-of-the-envelope calculation says that we should have around three million genes. This seems unbelievable, given that lungfish and salamanders have up to 36 times more DNA than human cells – and what would a lungfish need with a hundred million genes, eh?

DNA sequence
DNA contains pairs of 4 chemical ‘letters’ called bases and the order they come in is known as a DNA sequence.

We now know that less than 2 per cent of the 3 billion ‘letters’ of the human genome contains proper genes – the instructions that our cells use to build proteins and other useful molecules. We have around 20,000 genes, putting us roughly on a par with tiny nematode worms and lagging way behind wheat plants, which have 100,000.

It’s not just the lack of genes that’s puzzling. Most of the human genome is dull and repetitive, packed full of millions of copies of long-dead virus-like elements called transposons and other repeated sequences.

It might be expected that evolution would kick this stuff out, through the process of natural selection. Indeed, if a stretch of DNA is useful, it sticks around and becomes a permanent part of the genome. And if not… well, it sticks around anyway, because evolution is a slow and imperfect process. As Ohno eloquently wrote in his paper, ‘The triumphs as well as failures of nature’s past experiments appear to be contained in our genome.’

So if it isn’t encoding genes, what’s all the rest of this DNA ‘dark matter’ doing?

However, according to the Encyclopedia of DNA Elements (ENCODE) – a major international project rifling through the junk in our genomes – up to 80 per cent of our DNA is functional in some way. Yet although it sounds impressive, this figure is hotly contested.

Much of the argument hangs on what we mean by ‘functional’. Is it enough to discover that a particular stretch of DNA has some kind of protein molecule stuck to it or is being ‘read’ to make a cellular messenger called RNA, as the ENCODE team found for a large percentage of the genome? Or does it have to be doing something genuinely useful in the cell?

It’s like walking into a busy office and seeing everyone staring intently at their computer screens. But while some of them might be actually working, others are just keeping the seat warm and checking social media until it’s time for lunch. If I was the boss, I know which ones I would class as ‘functional’ when it came to annual appraisal time. Furthermore, merely finding someone in an office doesn’t mean they actually work there. They could be a visitor, or just wandered in off the street.

It’s the same problem with DNA. The nucleus of the cell, where all the DNA hangs out, is a crowded place packed with all sorts of molecules involved in turning genes on and off. By sheer chance some of them are going to end up in the wrong place, however briefly, and can be detected using modern super-sensitive techniques like those used by the ENCODE team. It doesn’t mean they’re doing something biologically important or useful.

The latest estimates suggest that less than a tenth of the human genome is genuinely functional, and the ENCODE team have revised their initial figure downwards towards 50 per cent. For now, there’s not enough evidence to say for sure either way.

Then there are other ideas about what the function of all the junk might be. Some researchers think that our abundance of apparently useless DNA is the biological equivalent of bubble wrap, acting as protective packing around our genes and helping to dilute out the impact of cancer-causing agents such as X-rays and other carcinogens.

It’s a controversial idea, though, as many species have much more compact genomes than we do and aren’t riddled with cancer. For example, Fugu pufferfish – the infamously poisonous Japanese delicacy – essentially have all the same genes that we do but get by just fine with an eighth as much DNA.

It may be that some of the junk is structural, helping to space genes and their control switches out in the right way, although this is hard to prove. Using genetic-engineering techniques, researchers can ‘glue’ a gene right next to the switch that activates it and it still works, suggesting that the precise spacing isn’t all that important.

As researchers develop better techniques for probing the functions of stretches of DNA – including using the latest gene-editing technology such as CRISPR – we’ll have a better idea of how much junk we truly have in our biological trunk, and just what it’s doing there.

Kat Arney is the author of Herding Hemingway’s Cats: Understanding how our genes work, published by Bloomsbury Sigma. 

Herding Hemingway's Cats
Herding Hemingway’s Cats by Kat Arney
  • Pentti S. Varis

    In the old days many evolutionists believed that e.g. humans had nearly two hundred rudiments, non functional organs.
    Now we have only handful “rudiments”, they all being controversial. I wait some equivalent thing for “non functional” genes..

    • Aceofspades25

      Evolutionism is an outdated belief system that organisms inherently improve themselves through progressive inherited change over time. Today we know that this isn’t often the case, there are many organisms that lose functionality and become simpler as their environment places less burden upon them to maintain existing structures. For example: humans have lost many of their olfactory genes due to the ravages of random mutation over time. There has been little to no selective pressure to keep these genes functional and so hundreds of them now exist in our genome as junk DNA. They are relics of the past and point to a time when we had a much more finely tuned sense of smell.

      If you think evolutionism still exists then no wonder you think junk DNA couldn’t exist!

      Genes are functional by definition so a “non-functional gene” is an oxymoron.

      I’ve described one of the ways we know that junk DNA exists – pseudogenes or broken genes are for the most part non-functional and are historical relics in our genome but there are many more ways to know that junk DNA exists – if you’re going to have an opinion on this then it is at least worth informing yourself on what the experts know. Here is a paper which is very easy to read which sets out some of the many lines of evidence which point to junk DNA

      http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004351

  • Aceofspades25

    Kat Arny, I listen to and enjoy naked genetics so thank you for presenting an entertaining podcast.

    A few months back you said some things about junk DNA (or perhaps it was one of your guests) which I found a bit strange and out-of-step with what I read from other geneticists so I am pleased to see a well informed article here that presents the current case as I understand it fairly. The only thing I disagree with is the statement which reads “For now, there’s not enough evidence to say for sure either way.” I think the evidence leans fairly conclusively in favour of junk DNA.

    Some of that evidence is set out here: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004351