Tuesday, October 16, 2012

So-called Junk DNA – Not Really Junk

In the year 2000 as a result of a momentous effort to define the human genome, the first complete sequence of human DNA was delineated.  From this work, it was determined that only about 3% of the entire DNA structure was relegated to the genes – containing the information for the structure of those proteins that help defines us as human.  It was assumed that the remaining 97% of the DNA played no important biological role and was determined to be "junk."


To some it seemed inconceivable that so much DNA real estate would serve no biological purpose.  As a consequence, a number of laboratories from around the world became involved in an ambitious joint project designed to determine the role, if any, of the non-gene parts of the entire human genome.  This work required a meticulous examination of extended sequences of DNA.  This endeavor was referred to as the Encyclopedia of DNA Elements (ENCODE).  The goal of this project was to find those portions of the non-gene DNA that had an identifiable purpose.


In 2007, ENCODE came out with its first preliminary report clearly showing that this part of the DNA contained many varieties of functional elements.  As a consequence of this work, a series of papers has been published in the September (2012) issue of the prestigious scientific journal, Nature detailing ENCODE's findings.


These extensive and exhaustive studies clearly demonstrate that large non-gene areas of the human genome contain information of functional significance.  ENCODE has catalogued an impressive inventory of hidden switches for the expression or suppression of encoded genes, signals –transcription factors - and signposts integrated throughout the length of the human genome.  In essence, it now appears that much of the DNA landscape is relegated to regulatory processes.  To place this in perspective, roughly 1.2% of the genome is involved in protein coding, while some 8 – 9% is involved in regulatory processes.  Furthermore, it seems that these regulatory elements are more susceptible to change – mutation - than the genes that they regulate; this fact has profound evolutionary implications.  Finally, it now appears that around 80% of the entire genome is actively transcribed into RNA; this is a remarkable finding that requires further elucidation.


In conclusion, it appears that the concept of "junk" DNA can now be effectively put to rest.  These results open up whole new vistas for further investigation.