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Junk DNA implicated in disease

By Wendy Barnaby
Papers published today in Nature and other scientific journals promise to throw more light on how genes cause disease. The papers, the culmination of ten years of research from the Encyclopedia of DNA Elements (ENCODE) Consortium, concern the 98 per cent of the human genome which used to be thought of as “junk DNA”. 
Commenting on the papers at the British Science Festival, Royal Society President Sir Paul Nurse said, “We used to think that diseases were caused by large mutations in single genes, for example, cystic fibrosis.  Now we realise that they’re more likely to result from small mutations in many genes.
“The scientists have been analysing the human sequence to try to identify biochemical activities throughout the genome,” he continued. “Fifteen years ago, it was thought that only 1-2 per cent of the genome encoded protein sequences which led to the functioning of the genome.  Since then, it has become clear that the other 98 per cent is doing much more than was previously thought, through the production of RNA. 
“RNA does not code for proteins but for a variety of different RNAs involved in regulating the whole genome. When you do sequence analysis, looking for mutational differences across the genome, now we know that lots of the ‘junk’ is also having biochemical activity working through these RNAs so potentially has function as well.
“Knowledge of what’s going on in what used to be called junk DNA will contribute to our understanding of the biochemical activities associated with the genome and therefore its function.”
The significance of the new findings is that they will lead to associations of mutations in the genome with disease predisposition.
“In the past,” said Nurse, “they can only have made sense of mutational changes in regions of the 1-2 per cent of the genome they thought had functional significance.  The rest they’d have seen as silent markers for disease, and not of functional causal significance.   Now, knowing that those regions actually do something means they will identify biochemical activities which means it may have functional significance for disease.
The Encyclopedia of DNA Elements(ENCODE) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). Its goal is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. Part of the work is done at the Wellcome Trust Sanger Institute.

The consortium’s mapping of regions of transcription, transcription factor association, chromatin structure and histone modification is published in six papers in Nature today, along with twenty-four associated papers in two other journals: Genome Research and Genome Biology.

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