‘Junk DNA’ made visible before the final cut

Jan. 7, 2013 Research findings from the University of North Carolina School of Medicine are shining a light on an important regulatory role performed by the so-called dark matter, or "junk DNA," within each of our genes.

The new study reveals snippets of information contained in dark matter that can alter the way a gene is assembled.

"These small sequences of genetic information tell the gene how to splice, either by enhancing the splicing process or inhibiting it. The research opens the door for studying the dark matter of genes. And it helps us further understand how mutations or polymorphisms affect the functions of any gene," said study senior author, Zefeng Wang, PhD, assistant professor of pharmacology in the UNC School of Medicine and a member of UNC Lineberger Comprehensive Cancer Center.

The study is described in a report published in the January 2013 issue of the journal Nature Structural & Molecular Biology.

The findings may be viewed in terms of the film industry's editorial process where snippets of celluloid are spliced, while others end up unused on the proverbial cutting room floor.

Taken from a DNA point of view, not every piece of it in each human gene encodes for a functional protein; only about 10 percent does, in coding regions called "exons." The other 90 percent of the stuff that fills the intervening regions are longer stretches of dark matter known as "introns."

But something mysterious happens to introns during the final processing of messenger RNA (mRNA), the genetic blueprint that's sent from the cell's nucleus to its protein factory. Only particular exons may be included within the final mRNA produced from that gene, whereas the introns are cut out and destroyed.

It's therefore easier to understand why more scientific attention has been given to exons. "When people are looking at the genetics of a disease, most of the time they're looking for the change in the coding sequence," Wang said. "But 90 percent of the sequence is hidden in the gene's introns. So when you study gene variants or polymorphisms that cause human disease, you can only explain the part that's in the exon. Yet the majority remains unexplainable because they're in the introns."

Following completion of the genome sequencing projects, subsequent DNA and RNA sequencing revealed the existence of more than one splice variant, or isoform, for 90 percent of human genes. During messenger RNA processing, most human genes are directed to be cut and pasted into different functional isoforms.

In a process called alternative splicing, a single gene could code for multiple proteins with different biological functions. In this way, alternative splicing allows the human genome to direct the synthesis of many more proteins than would be expected from its 20,000 protein-coding genes.

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'Junk DNA' made visible before the final cut