DNA Dumpster Diving


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By Elsa Youngsteadt

With the foundation of molecular biology in the 1950's, geneticists proposed a certain tidy flow of information from the DNA molecule to the phenotype of the living organism. This so-called central dogma—that DNA codes RNA, RNA codes proteins, and proteins do the work that makes life function—turns out to be only part of the story.

Some 96% of human DNA does not code for proteins, and alternative explanations could account for the existence of this surplus DNA. It could really be neutral junk—neither beneficial, nor harmful enough to be removed by selection. Alternatively, it could regulate the expression of protein coding genes and other cellular functions in more subtle ways currently understood. Or it could be some combination of the two.

Two papers published during the week of July 9, 2007, examine the roles of specific bits of junk DNA. One finds the junk sequence to be useful, while the other, investigating a different sequence, declares its junk neutral.

The useful-junk paper, led by scientists at the University of California, San Diego, appears in the July 13 issue of Science. The research examined a DNA sequence called a SINE (short interspersed elements) that was once believed to be junk. They found, however, that the sequence SINE B2 played an important role in regulating growth hormone genes in mice. At certain times during the mouse lifetime, SINE B2 was transcribed to RNA, but never translated to protein. The transcription of SINE B2 changed the structure of the chromosome around the SINE as well the neighboring genes for growth hormone, and allowed the growth hormone gene to be expressed. In this case, the authors liken the junk DNA to punctuation marks that organize coding genes.

The neutral-junk paper, based on research conducted primarily at Johns Hopkins medical institute and published in PLoS Genetics, examines a different kind of repeated DNA sequence, the so-called numts (nuclear mitochondrial-like sequences). None of these sequences coded for protein, nor did they apparently regulate nearby genes. Furthermore, they were far more abundant in primates than in other mammals. By comparison of human numt sequences with those of other animals, they estimated when the numt sequences first appeared. They concluded that the human numts originated some 54 million years ago, at the time that primates first appeared. They propose that neutral junk like numts are most likely to spread or disappear at the time of new species formation, when species numbers are small and genetic drift can have a large effect on neutral or nearly-neutral sequences.

These two papers address outstanding questions in molecular evolution, demonstrating how the DNA molecule participates in the evolutionary process and highlighting changes in evolutionary thinking since the field of molecular biology was founded.
Useful Junk

Science Magazine for original paper (July 13, 2007)
Lunyak, V. V., et al, 2007. Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis. Science, 317: 248-251.

University of California San Diego news release about Science paper

Neutral Junk
PLoS Genetics for original paper (Gherman et al., July 2007)

Johns Hopkins news release (picked up by PhysOrg.com)—about PLoS paper

Related Reading
Gibbs, W. W., 2003. The unseen genome: Gems among the junk. Scientific American, 289: 46-53.
This article is available to subscribers through the Scientific American website; free copies can also be found online.

Wikipedia on Junk DNA

Questions for review and discussion

1. What is junk DNA? What function could it have under the DNA to RNA to protein paradigm?

2. What function did the Science paper describe for SINE B2 junk DNA? How does this differ from traditional explanations of junk DNA?

3. What function did the PLoS paper describe for a different junk sequence? Does it prove that numts have no function?

4. Do the two papers contradict one another? Explain your answer.

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