By apsmith, Section Commentary Posted on Tue Sep 21, 2004 at 05:53:14 AM PST
Returning yet again to the subject of junk DNA, a fascinating Scientific American article from the October issue (not yet online) is titled "The Hidden Genetic Program of Complex Organisms," by geneticist John Mattick. The essence of the new view seems to be that proteins are merely the mechanical components of the machinery of life, while the remainder of the genome encodes information that governs what the proteins do, via transcription into "micro-RNA's" and related regulatory signals.
The completion of the Human Genome Project a few years back left us with a rather disappointing count of just 25,000 or so protein-coding genes - hardly more than the number of proteins used by a simple roundworm. Mattick's article points out, however, that more complex organisms, while having almost the same number of protein-coding genes, tend to have larger and larger fractions of their DNA devoted to non-coding "introns," or what was once called "junk." For humans, only about 1.5% of DNA encodes proteins. For bacteria (prokaryotes) essentially ALL the DNA is transcribed to proteins, and there are no 'introns' - in part because bacteria lack a cell nucleus to separate transcription (from DNA to RNA) from translation (to proteins).
Which suggests a question: is all that non-coding DNA actually responsible for the complex structure that distinguishes multi-celled life (eukaryotes) from bacteria? And how does it do that?
One of the keys to organism complexity is differentiation - the process whereby cells in different regions of the organism express different genes and become physically different in character. For humans, 100 trillion cells are placed and differentiated into a large number of organs and regions with specific positions and functions. For each of these cells, what genes exactly it expresses or does not express is determined by the detailed structure of the chromosomes, the way the DNA material has been combined with proteins to open up some regions, and shut off others. Some experiments, according to Mattick, imply that these micro-RNA's are controlling this detailed structure directly.
The previously prevailing view, that proteins are in control, succumbs to a problem of "combinatorial complexity" - the more proteins involved, the proportion of the system devoted to regulation increases, and there's an intrinsic "complexity limit." The rise of multicellular organisms evidenced in the "Cambrian explosion" suggests a transition to a new control structure that could transcend previous limits - and this direct role for regulatory RNA could be the explanation.
Quoting Mattick:
The implications of this [...] are staggering. We may have totally misunderstood the nature of the genomic programming and the basis of variations in traits among individuals and species.
Biologists still have a lot of work to do to understand how life works!
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