Genome Complexity Unveiled: No Junk, Only Function

Any remaining doubts that the idea of “junk DNA” has itself been junked should vanish under the latest findings about genome complexity.  A number of recent news stories have revealed astonishing levels of regulation and organization in the non-coding regions of DNA.  It turns out that genes are not the only interesting things in the code.  A wealth of functions were uncovered in the non-coding regions formerly assumed to be useless.

1. Function Junk-tion:  Nature¹ published results from a consortium named ENCODE (Encyclopedia of DNA Elements).  Its pilot phase consisted of 35 groups examining 30mb of the human genome (about 1%) in unprecedented detail.  See EurekAlert for a summary of the consortium’s findings.
       Team members found, first of all, that most of the “junk” sections are “pervasively transcribed” despite lacking genes.  Surprisingly, some distant portions are linked into one transcript.  Second, they found a lot of overlap in the transcribed areas; some non-gene transcripts overlap those of genes.  Third, the structure of chromatin (protein around which DNA is wrapped) has been shown to interact with the ways DNA is transcribed and regulated.  Finally, only a few genes appear constrained by natural selection; many others vary widely between mammals.
       These initial results are starting to revolutionize our picture of the “functional landscape of the human genome,” the paper said.  They will undoubtedly reverberate through speculations about genome evolution as well.  For instance, the presence of wide variation in the non-coding transcripts between mammals suggested to the authors that a vast pool of neutral segments (of no immediate benefit to the organism) exists.  “This pool may serve as a ‘warehouse’ for natural selection,” they speculated, “potentially acting as the source of lineage-specific elements and functionally conserved but non-orthologous elements between species.” 
2. Comments One:  This interpretation, however, is disputed by others, Erika Check reported in a separate news article summarizing the results.².  Her analysis agrees with the sense of wonder over all the new-found complexity.  She mentioned one geneticist who feels we have been “vastly underestimating how much of the genome is functional.” 
3. Comments Two:  And that’s with just 1% of it analyzed in this detail.  John Greally, in another news report in the same issue,³, reminded his readers: “So although the glimpse we are provided by the ENCODE consortium into the ordered complexity of 1% of the human genome is tantalizing, the insights only confirm the challenges that lie ahead.”  He expressed the reversal in attitudes about these Cinderellas of the genome:
   

   We should have guessed that this was merely prima-donna behaviour on the part of narcissist genes when the sequencing of the human genome revealed that they comprise only a small percentage of the DNA.  And our confidence should have been shaken when some sequences located far from any genes were found to be strikingly conserved, indicating that they have some important function.  Now, on page 799 of this issue,¹ the ENCODE Project Consortium shows through the analysis of 1% of the human genome that the humble, unpretentious non-gene sequences have essential regulatory roles (Fig. 1).
       We are increasingly being forced to pay attention to our non-gene DNA sequences.

4. Comments Three:  Elizabeth Pennisi also commented on ENCODE’s findings in Science.⁴  She said it’s forcing us to rethink what it means to be a gene.  If genes only make up 2% of the genome, why is 80% of the DNA expressed?  This is upsetting our gene-centric perspective.  She quoted Francis Collins of the Human Genome Project, who appeared optimistic that “we’re beginning to understand the ground rules by which the genome functions.”  That implies we are not far beyond square one.  He said the gene concept is not going out of fashion; “It’s just that we have to be more thoughtful about it.”
5. Drosophila phenomena:  An article from Berkeley Lab indicated that fruit fly heterochromatin (large regions of chromosomes devoid of genes) is “far from junk” as earlier thought.  “Not so long ago, the difficult-to-sequence, highly repetitive, gene-poor DNA found in regions of chromosomes known as heterochromatin was called ‘junk.’  Like dark matter in the universe, the true nature of heterochromatin was unknown.”  It appears now that heterochromatin is essential for numerous functions, such as neutralizing transposons.  Some of it also codes for genes that were missed because they are separated by large, repetitive introns.  These and other functions were uncovered when the team decided to question the “junk DNA” paradigm: “We set out to see if there was any information in that junk,” one team member said.
6. Genetic Clockwork:  Of all things, a clock mechanism has been discovered for regulating genes.  Dr. Bert O’Malley at Baylor College of Medicine (see EurekAlert) found that 25,000 genes follow a clock controlled by master switches that turn gene expression on and off.  Ubiquitin molecules are added each time a gene is expressed.  When the number reaches five, the protein transcribed is destroyed.  This prevents too much of a good thing.
       Dave Scot wrote about this from an I.D. perspective on Uncommon Descent.  He likened the mechanism to a shift register in digital electronic devices.
7. Teeming with Significant Life:  Another article appeared on Science Daily about the ENCODE results.  It says that the human genetic deserts, once thought to be junk regions without function, are “teeming with significant life.”  Professor Alexandre Reymond said, “Our work has shown that the human genome is far more complex than anyone could have imagined, even ten years ago. Understanding these complexities is essential to the development of effective and safe genetic medicine in the future.”

Several other Intelligent Design commentators have given non-Darwinian interpretations of these findings.  See Evolution News and Uncommon Descent for examples.

¹The ENCODE Project Consortium, “Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project,” Nature 447, 799-816 (14 June 2007); doi:10.1038/nature05874.
²Erika Check, “Genome project turns up evolutionary surprises,” Nature 447, 760-761 (14 June 2007); doi:10.1038/447760a.
³John M. Greally, “Genomics: Encyclopaedia of humble DNA,” Nature 447, 782-783 (14 June 2007); doi:10.1038/447782a.
⁴Elizabeth Pennisi, “DNA Study Forces Rethink of What It Means to Be a Gene,” Science, 15 June 2007: Vol. 316. no. 5831, pp. 1556-1557, DOI: 10.1126/science.316.5831.1556.

Let us all, therefore, with solemnity and humility, lay to rest the dead theory of junk DNA.  “We should have guessed,” Greally said.  Indeed.  If they had just listened to creationists and intelligent design people saying for years that it isn’t junk, that there must be a reason for it, then the Darwinists wouldn’t have held back good science for so long.  Now it would be honorable if they would give credit to the ones who were headed in the right direction from the beginning.