The blog Science Life (University of Chicago Medical Center) has an excellent follow-up piece to the story about the discovery of non-coding DNA that contributes to heart disease (SciTechStory: More ‘junk DNA’ that actually does something) The Science Life post mentions that work and details another study done by the University of Chicago and the National Institute of Health (NIH, USA), which also considered the vast stretches of ‘junk DNA’ and decided to look for DNA switches – pieces of DNA that do not code for proteins, but instead are used to switch on or off protein building in heart related cells.

To help with the enormous task of searching nearly 3 billion DNA pairs for these switches, the team developed computer routines that looked for sequences related to heart cell development. To their great surprise they didn’t find a few switches, or even many switches, but a whole network of 42,000 potential switches involved with heart cell regulation. That’s more than twice the number of genes in the human genome.

We can finally say that there is a well-defined genetic code hardwired in our genomes that can be used to specifically identify heart regulatory elements in the vast sequence that makes up the human genome,” said Ovcharenko, of the NIH’s National Center for Biotechnology Information. “With the advance of computational methods, we can use computers to break this code, learn its encryption, and understand the signals heart cells receive to regulate genes.”
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The model is not specific to the heart; a shorter experiment in the paper demonstrated that the program can also be used to detect switches important for certain types of brain cells, and the authors note that it can be applied to any organ or tissue. And characterizing the chorus of switches that orchestrate cell development is more than just mere code-breaking; knowledge about what needs to go right can turn up clues about what goes wrong in cases of heart disease or other illnesses. One such instance of a “junk DNA” sequence causing heart disease was described yesterday in Nature – deletion of a non-coding sequence in mice dramatically affected the expression of two genes and caused the mice to die earlier than normal.

“For some of these diseases, there’s nothing wrong with the protein sequence itself,” Nobrega said. “But there may be an alteration in how and when the protein is made, which can lead to disease as well. That’s the urgency and need for this kind of work to basically crack the other codes that are present in the genome.

[Source: A fishfinder for the junk dna seas]

Finding a ‘network of 42,000 potential switches’ is like opening a can of worms – or maybe 5,000 cans, give or take. It means there are more complications to the story of ‘junk DNA’ than scientists had bargained for (by misreading these huge tracts of DNA as junk). This and other studies indicate that at least some of these segments of DNA are vital for the proper differentiation and development of cells – or conversely, may be responsible for some of the diseases caused by malfunctioning cells.

There’s a lot of work to be done, but it does seem like it’s going through an appropriate course correction.