Junk DNA – uh – What is it good for? Absolutely. . . something.

Ok, I’ve been looking for an excuse to post the music,  \”War, What is it good for?\” (War, Edwin Starr) so here it is: Junk DNA. What is it good for? Gene regulation.

To the uninitiated, it may be surprising that most of your DNA has heretofore been referred to as “junk”.  This is not because of any inherent qualities of the DNA itself, but rather due to the deficiencies in those studying it. For the longest time, no one could figure out what DNA did if it didn’t encode proteins (or even RNA), so, rather than reaching into their soul to find their own shortcomings, researchers projected these character flaws onto the DNA and called it “junk”.

Now, Lin et al., researchers from that blue-state, Iowa, finally report that “junk” DNAs regulate gene expression, and may be very important in tissue specific turning-on-and-off-or-how-much of specific genes.  From the PLoS advance press release  (which I get since, after all, I am a member of the fourth estate, same as anyone with a website and a keyboard):

Study finds value in “junk” DNA

For about 15 years, scientists have known that certain “junk” DNA — repetitive DNA segments previously thought to have no function — could evolve into exons, which are the building blocks for protein-coding genes in higher organisms like animals and plants. Now, a University of Iowa study has found evidence that a significant number of exons created from junk DNA seem to play a role in gene regulation. The findings, which increase understanding of how humans differ from other animals, are published October 17 in the open-access journal PLoS Genetics.

Nearly half of human DNA consists of repetitive DNA, including transposons, which can “transpose” or move around to different positions within the genome. A type of transposon called retrotransposons are transcribed into RNA and then reintegrated into the genomic DNA. The most common retrotransposons in the human genome are Alu elements, which have over one million copies and occupy approximately 10 percent of the human genome.
“Alu elements are a major source of new exons. Because Alu is a primate-specific retrotransposon, creation of new exons from Alu may contribute to unique traits of primates, so we want to better understand this process,” said the study’s senior author Yi Xing.

To study the impact of Alu-derived exons on human gene expression, the researchers used a high-density exon microarray. The technology has nearly six million probes for monitoring the expression patterns of all human exons. Using data generated by these microarrays, the scientists analyzed 330 Alu-derived exons in 11 human tissues. The team then identified a number of exons with interesting expression and functional characteristics.  “Hundreds of exons in the human genome were created from Alu elements. The whole-genome exon microarray allowed us to quickly identify exons that most likely contribute to the regulation of gene expression and function,” said Lan Lin, lead author of the study.

Analysis of one human gene, SEPN1, which is known to be involved in a type of muscular dystrophy, along with comparative data from chimpanzee and macaque tissues, suggested that the presence of a muscle-specific Alu-derived exon resulted from a human-specific change that occurred after humans and chimpanzees diverged evolutionarily.

“In this case, this exon is only expressed at a high level in the human muscle but not in any other human or non-human primate tissue, so this implies that the exon plays a functional role in muscle, and this role is human-specific,” Xing said.

http://dx.plos.org/10.1371/journal.pgen.1000225
Citation: Lin L, Shen S, Tye A, Cai JJ, Jiang P, et al. (2008) Diverse Splicing Patterns of Exonized Alu Elements in Human Tissues. PLoS Genet 4(10):
e1000225. doi:10.1371/journal.pgen.1000225
From OPEN-ACCESS JOURNAL PLoS GENETICS (www.plosgenetics.org) . PLoS Genetics is an open-access, peer-reviewed journal published weekly by the Public Library of Science (PLoS).

Probably the paper that held the most sway for the longest period of time was Roy J. Britten and Eric H. Davidson,” Repetitive and Non-Repetitive DNA Sequences and a Speculation on the Origins of Evolutionary Novelty,” The Quarterly Review of Biology, June 1971, vol. 46, no. 2, DOI: 10.1086/406830 (the link goes to citing references).  I wish I could remember an experiment I did relating to nuclear pore density and repetitive sequence copy number but alas, the company I worked for at the time bounced my paycheck, and so I quit, without ever giving this another thought until now.

Gene regulation, epigenetics, and non Mendelianism are turning out to be biggies. Here and here are previous posts relating to Indian corn and Keith Richards, both of whom probably exhibit epigenetic changes as a result of environmental challenges, particularly Mr. Richards, who seems to self-inflict said environmental challenges. My hunch is that “junk” DNAs probably shape-shift with environmental stimuli.