"Junk DNA" was a term introduced to describe DNA sequences with no known function, steming from the surprising finding that much of higher eukaryotic genomes contain few "exonic" regions, i.e. DNA encoding for protein. Humans contain about ~95% junk DNA much of which is rather worryingly obsolete virus material, thought to have arisen from germline integration of viruses, retrotransposons and other transposable selfish elements (McClintock's "jumping genes"
The C-value paradox is a description of early genome work that somewhat surprisingly, say the corn plant (Zea mays) has more genomic DNA than a human, whereas any reasonable measure of biologic complexity, such as, the number of mRNA transcripts (protein coding RNA from exonic DNA) generated by the compared species shows humans to be vastly more complex genetically.
Exciting and profound new work shows that the non-coding/"junk" DNA has important roles in gene regulation and the transposable elements provide many binding sites for transcription factors.
"Junk" DNA which was always meant to be a red rag to a bull as molecular biologists were not happy with 95% non-functional and is a good example of nomenclature provoking a useful reaction experimentally. It took a lot longer than thought but it now appears "junk" DNA is a major driver of evolution. Exciting stuff. Below is a copy and paste that is going up on sites all over the place. Abstract is here: http://genome.cshlp.org/content/current
In a paper published in Genome Research on Nov. 4, scientists at the Genome Institute of Singapore (GIS) report that what was previously believed to be "junk" DNA is one of the important ingredients distinguishing humans from other species.
More than 50 percent of human DNA has been referred to as "junk" because it consists of copies of nearly identical sequences. A major source of these repeats is internal viruses that have inserted themselves throughout the genome at various times during mammalian evolution.
Using the latest sequencing technologies, GIS researchers showed that many transcription factors, the master proteins that control the expression of other genes, bind specific repeat elements. The researchers showed that from 18 to 33% of the binding sites of five key transcription factors with important roles in cancer and stem cell biology are embedded in distinctive repeat families.
Over evolutionary time, these repeats were dispersed within different species, creating new regulatory sites throughout these genomes. Thus, the set of genes controlled by these transcription factors is likely to significantly differ from species to species and may be a major driver for evolution.
This research also shows that these repeats are anything but "junk DNA," since they provide a great source of evolutionary variability and might hold the key to some of the important physical differences that distinguish humans from all other species.
The GIS study also highlighted the functional importance of portions of the genome that are rich in repetitive sequences.
"Because a lot of the biomedical research use model organisms such as mice and primates, it is important to have a detailed understanding of the differences between these model organisms and humans in order to explain our findings," said Guillaume Bourque, Ph.D., GIS Senior Group Leader and lead author of the Genome Research paper.
"Our research findings imply that these surveys must also include repeats, as they are likely to be the source of important differences between model organisms and humans," added Dr. Bourque. "The better our understanding of the particularities of the human genome, the better our understanding will be of diseases and their treatments."
"The findings by Dr. Bourque and his colleagues at the GIS are very exciting and represent what may be one of the major discoveries in the biology of evolution and gene regulation of the decade," said Raymond White, Ph.D., Rudi Schmid Distinguished Professor at the Department of Neurology at the University of California, San Francisco, and chair of the GIS Scientific Advisory Board.
"We have suspected for some time that one of the major ways species differ from one another – for instance, why rats differ from monkeys – is in the regulation of the expression of their genes: where are the genes expressed in the body, when during development, and how much do they respond to environmental stimuli," he added.