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ENCODE Uncovers Value in “Junk” DNA

Linda Seaton
| Apr 17, 2013

EncodeUp until recently, scientists understood the biological function of just 1% of the genome, mainly the regions coding proteins. The non-coding regions were thought to be “junk”, evolutionary debris with no critical function.

In 2011, we spoke with John Mattick, Ph.D., then a Professor at the Institute of Molecular Bioscience at the University of Queensland in Australia. Dr. Mattick believed there might be some other element facilitating biological functions beyond genes and proteins. An enthusiast of scientific history, he pointed out that as far back as the 1950s, scientists were questioning the established philosophy of the gene as primarily a protein-coding entity. The advent of high-throughput sequencing enabled him to shed light on non-coding DNA regions and provide insight into the functional significance of their transcripts. 

Now the Executive Director of the Garvin Institute of Medical Research, Dr. Mattick’s theories about “junk” DNA have been proven true in papers recently published by the Encyclopedia of DNA Elements Consortium (ENCODE). ENCODE researchers analyzed the impact mutations have on several different cell types. Focused on mapping functional elements in the genome via sequencing data, they identified 70,000 promoters and 20,000 protein coding regions that control where transcription starts, 400,000 enhancers that determine whether a gene is switched on and by how much, and even some new genes. The data provides direct experimental evidence for function in > 12% of the genome and suggest that even more may be functionally relevant. 

Gary Schroth, Ph.D., Illumina Distinguished Scientist, noted that even in this handful of cell lines, all sorts of dynamic changes are occurring, from DNA methylation to which genes are being transcribed. “We’ve always known that, but this data gives us the clearest genome-wide detail we’ve ever seen,” Dr. Schroth said.

The data also supports the value of whole-genome sequencing (WGS). According to David Bentley, Ph.D., Illumina Vice President and Chief Scientist, most scientists haven’t felt it was necessary to perform WGS, because we didn’t understand 99% of the genome. “There’s now a definite payoff,” said Dr. Bentley. “ENCODE has given us a catalog of regions that are linked with common disease. Exome sequencing costs less, but you also get less. Exactly how much less was demonstrated by ENCODE.”