In the 1970s, when biologists first glimpsed the landscape of human genes, they saw that the small pieces of DNA that coded for proteins (known as exons) seemed to float like bits of wood in a sea of genetic gibberish. What on earth were those billions of other letters of DNA there for? No less a molecular luminary than Francis Crick, co-discoverer of DNA’s double-helical structure, suspected it was “little better than junk.”
The phrase “junk DNA” has haunted human genetics ever since. In 2000, when scientists of the Human Genome Project presented the first rough draft of the sequence of bases, or code letters, in human DNA, the initial results appeared to confirm that the vast majority of the sequence—perhaps 97 percent of its 3.2 billion bases—had no apparent function. The “Book of Life,” in other words, looked like a heavily padded text.
Now, in a series of papers published in September in Nature (Scientific American is part of Nature Publishing Group) and elsewhere, the ENCODE group has produced a stunning inventory of previously hidden switches, signals and sign posts embedded like runes throughout the entire length of human DNA. In the process, the ENCODE project is reinventing the vocabulary with which biologists study, discuss and understand human inheritance and disease.
Ewan Birney, 39, of the European Bioinformatics Institute in Cambridge, England, led the analysis by the more than 400 ENCODE scientists who annotated the genome. He recently spoke with Scientific American about the major findings. Excerpts follow.
Scientific American: The ENCODE project has revealed a landscape that is absolutely teeming with important genetic elements—a landscape that used to be dismissed as “junk DNA.” Were our old views of how the genome is organized too simplistic?
BIRNEY: People always knew there was more there than protein-coding genes. It was always clear that there was regulation. What we didn’t know was just quite how extensive this was.
Just to give you a sense here, about 1.2 percent of the bases are in protein-coding exons. And people speculated that “maybe there’s the same amount again involved in regulation or maybe a little bit more.” But even if we take quite a conservative view from our ENCODE data, we end up with something like 8 to 9 percent of the bases of the genome involved in doing something like regulation.
Thus, much more of the genome is devoted to regulating genes than to the protein-coding genes themselves?
And that 9 percent can’t be the whole story. The most aggressive view of the amount we’ve sampled is 50 percent. So certainly it’s going to go above 9 percent, and one could easily argue for something like 20 percent. That’s not an unfeasible number.
Should we be retiring the phrase “junk DNA” now?
Yes, I really think this phrase does need to be totally expunged from the lexicon. It was a slightly throwaway phrase to describe very interesting phenomena that were discovered in the 1970s. I am now convinced that it’s just not a very useful way of describing what’s going on.
What is one surprise you have had from the “junk”?
There has been a lot of debate, inside of ENCODE and outside of the project, about whether or not the results from our experiments describe something that is really going on in nature. And then there was a rather more philosophical question, which is whether it matters. In other words, these things may biochemically occur, but evolution, as it were, or our body doesn’t actually care.
That debate has been running since 2003. And then work by ourselves, but also work outside of the consortium, has made it much clearer that the evolutionary rules for regulatory elements are different from those for protein-coding elements. Basically the regulatory elements turn over a lot faster. So whereas if you find a particular protein-coding gene in a human, you’re going to find nearly the same gene in a mouse most of the time, and that rule just doesn’t work for regulatory elements.
New Map Of Human Genome proves ‘Junk DNA’ Has A Purpose
Prior to new research that was published in late 2012, junk DNA was the term used to describe 97 percent of our DNA. The genetic drivers seat of the human body that is responsible for regulating the activity of over 20,000 genes has been revealed for the first time by scientists. Before it was believed that our junk DNA had no biological function. It turns out that what we mistook as junk DNA does indeed have a biological function. Keep in mind that junk DNA could have an enormous amount of biological and non biological functions that we have not yet discovered. The project looked at the bulk of genetic material that does not fall under the category of protein-coding genes- the building blocks necessary for life that comprise only two per cent of the human genome.
Researchers from 32 institutions around the world collaborated to determine the hidden messages within the 97 percent of human DNA that was said to have no function. They found that roughly 80 percent of the human genome has at least one biochemical activity associated with it. I always believed that junk DNA wasn’t really junk DNA, it’s there for a reason. I also believe that DNA is multidimensional and connected to non-physical phenomenon and other aspects of ourselves which might make it more difficult to understand and measure in a quantitative way.
The studies found a number of hidden switches and signals embedded throughout the entire length of human DNA. All cells within the human body have the same genes, but different cells switch on different kinds of genes. Scientists have always wondered how genes are controlled, and what turns certain ones on and off. Researches collected DNA maps from 349 tissue samples that cover all major organ systems in all stages of human development and contrasted them with genetic studies of more than 300 common diseases.
They found that most diseases that are associated with genetic changes occur within switches that regulate the genes that are said to be located far away from the genes that they control. Basically, the study determined that genetic switches occur within our junk DNA that could be responsible for a range of illnesses. These findings only provide a new view to look through with regards to the role of genetics and genome function in disease. The majority of switches that occur on the DNA molecule are far away from the genes that they control, which makes in very hard to identify them.
Information in our DNA is stored as codes using four different chemical bases, keep in mind that human DNA consists of approximately 3 billion bases. The sequence of these bases determines what information is available as building blocks for maintaining and organism. Just because scientists have identified switches, does not mean they have identified how genes are controlled. We are still a long way from determining that, and this is a very small portion of it. Emotions, feelings, intuition and perception of the environment all play a part. DNA is programmable, certain genes are turned off, and others are turned on. We don’t even know every gene and the function of it. We know very little about anything when it comes to our DNA.
With 2013 here, and looking ahead, I am sure that we will all be experiencing gene activation triggered by a multitude of different switches, but I do not think that gene activation, in this case will lead to disease. I believe new gene activation is a result of the evolution of our consciousness.
We are beginning to open up to different aspects of reality and ourselves. Even the brain allows itself to change its structure and its function. It’s a response to sensing and perceiving the world, even to thinking and imagining. Human thoughts and learning actually turn on certain genes in our nerve cells which allow those cells to make new connections between them. If our thoughts and perception have the ability to do this, who knows what it can do for our DNA that has yet to be activated. Maybe the ‘switches’ have a switch, and maybe the switch is us.
Scientists have also discovered that DNA can be re-programmed by words and frequencies, see article below.