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Second DNA code: Stunned scientists find ‘duons’ that control health, diseases

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A second DNA code, called “duons,” recently discovered by researchers shows that within the first DNA code there is a second DNA code that makes sense of health and diseases. “Since the genetic code was deciphered in the 1960s, scientists have assumed that it was used exclusively to write information about proteins,” reported Bioscience Technology on Dec. 13, 2013.

“For over 40 years we have assumed that DNA changes affecting the genetic code solely impact how proteins are made,” said Dr. John Stamatoyannopoulos.

However, a new research study has now discovered that DNA (Deoxyribonucleic Acid), which is present in the cells of all humans and most other living organisms, is not only used to write information about proteins but that it has a second set of instructions, a second DNA code, that cells use to control genes.

Dr. John Stamatoyannopoulos is the University of Washington associate professor of genome sciences and of medicine. He is the leader of the research team that discovered the second DNA code. The team’s findings was published in the Dec. 13 issue of Science and was part of the Encyclopedia of DNA Elements Project, also known as ENCODE.

For biology enthusiasts, the abstract provided by Science reads:

“Genomes contain both a genetic code specifying amino acids and a regulatory code specifying transcription factor (TF) recognition sequences. We used genomic deoxyribonuclease I footprinting to map nucleotide resolution TF occupancy across the human exome in 81 diverse cell types. We found that ~15% of human codons are dual-use codons (‘duons’) that simultaneously specify both amino acids and TF recognition sites. Duons are highly conserved and have shaped protein evolution, and TF-imposed constraint appears to be a major driver of codon usage bias. Conversely, the regulatory code has been selectively depleted of TFs that recognize stop codons. More than 17% of single-nucleotide variants within duons directly alter TF binding. Pervasive dual encoding of amino acid and regulatory information appears to be a fundamental feature of genome evolution.”

For non-enthusiasts, the key sentence in the above abstract is “we found that ~15% of human codons are dual-use codons (‘duons’) that simultaneously specify both amino acids and TF recognition sites.”

Since the genetic code was deciphered in the 1960s, researchers thought that the DNA code was used exclusively to write information about proteins. The genetic code, which uses a 64-letter alphabet, was called codons.

Now Dr. John Stamatoyannopoulos’s team discovered that about 15% of those codons have in fact two functions and called them “dual-use codons” or "duons."

The discovery of the second DNA code, or better second-function DNA code called "duons", is stunning scientists not only because they have missed it so far but also because "duons" instruct cells on how genes are controlled.

“Now we know that this basic assumption about reading the human genome missed half of the picture,” said Dr. John Stamatoyannopoulos.

“UW scientists were stunned to discover that genomes use the genetic code to write two separate languages. One describes how proteins are made, and the other instructs the cell on how genes are controlled. One language is written on top of the other, which is why the second language remained hidden for so long.”

Having discovered the second DNA code, or ”duons,” opens a new door for scientists to look at how genes are controlled. In regard to health and diseases, this is a ground-breaking discovery that can lead to new ways to treat patients.

About the significance of the discovery of the second DNA code, or "duons," Dr. John Stamatoyannopoulos commented that “the finding could have a significant impact on how scientists and doctors interpret a patient's genetic code and lead to new ways to diagnose and treat health problems.”

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