The double meaning they are referring to relates to the fact that DNA not only encodes proteins (DNA > RNA > Protein), but also contains sections that are used as control sites for this production. That is, other proteins, known as transcription factors, bind to these complimentary regions and can turn genes off and on as well as altering the structure of the protein produced. They are the regulatory regions.
Consequently, this “double meaning” is nothing new. We have known about these regulatory elements – such as promoters and enhancers – for decades, although there is still much to learn about their complexity. And the study published today in Science that has given rise to these headlines provides new insights through the regulatory maze.
Researchers from the University of Washington have found that these regulatory regions are commonly found within the protein-coding regions themselves. It was previously believed that these two regions of DNA – regulatory and protein-coding – were spatially separated: transcription factors bound to regions upstream of the protein-coding sequence (known as an “exon”). Imagine a length of rope with bands of blue and yellow. The different colours are analogous to this simplified arrangement of regulatory sequences and axons: Blue, yellow, yellow, yellow = regulatory region, protein-coding, protein-coding, protein-coding This compartmentalised arrangement of regulatory region followed by exons (as the image above shows) was what I was taught as an undergraduate.
So, statements like this one published today are just downright erroneous (italicised words are my emphases. Then I went further and underlined them as well):
“The second one [regulatory regions], which was just discovered, codes information which tells the cell how to control genes”
Even the finding that these regulatory regions are embedded within protein-coding sequences is nothing new; they have been discovered in several studies since 1995. The main conclusions of this new study by Dr. John Stamatoyannopoulos and his colleagues is that these regions are more pervasively contained within coding-sequences than previously believed – 87% of genes (from the 81 cell types investigated) contained them. (And, perhaps they have coined the term “duons” for these genes – I’m not sure.)
Moreover, they found that these regulatory sequences determine the structure of proteins themselves by preferentially choosing some amino acids (the building blocks of proteins) over others. Consequently, if a mutation resulted in the selection of different protein structures, they have the potential to catalyze evolutionary change. Finally, with a large proportion of disease-associated DNA sequences being found within these duons, this study reveals a myriad of insights into the overlooked process of gene regulation within exons.
But – the take home message is that – the fundamentals of genetic function remain the same: there are regions that encode proteins and others that control this process. It’s just that “duons” are commonplace and they influence protein structure, evolutionary pathways, and perhaps certain diseases.
Stergachis, A.B., et al. (2013) Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution. Science.
Schematic from howardhughes.trinity.duke.edu