Not So Junky DNA and Beware the Genome SPace INvaders

Decoding the human genome found that only about 10 percent of the 3 billion or so base pairs of the DNA in the human genome consists of genes that code for proteins. The remaining 90 percent didn't have any obvious function, so researchers called it "junk DNA."

A new report in Genome Research by researchers at the Genome Institute Singapore find that it's not so "junky" after all:

Using the latest sequencing technologies, GIS researchers showed that many transcription factors, the master proteins that control the expression of other genes, bind specific repeat elements. The researchers showed that from 18 to 33% of the binding sites of five key transcription factors with important roles in cancer and stem cell biology are embedded in distinctive repeat families.

Over evolutionary time, these repeats were dispersed within different species, creating new regulatory sites throughout these genomes. Thus, the set of genes controlled by these transcription factors is likely to significantly differ from species to species and may be a major driver for evolution.

This research also shows that these repeats are anything but "junk DNA," since they provide a great source of evolutionary variability and might hold the key to some of the important physical differences that distinguish humans from all other species.

In other words, these apparently long boring stretches of repeat DNA base pairs are central to determining which genes turn on when and by how much. In addition, some of these DNA repeats jump around inside genomes changing the expression of genes and the course of a species' evolution.

University of California, San Francisco neurologist Raymond White speulates:

"This hypothesis for formation of new species through episodic distributions of families of gene regulatory DNA sequences is a powerful one that will now guide a wealth of experiments to determine the functional relationships of these regulatory DNA sequences to the genes that are near their landing sites. I anticipate that as our knowledge of these events grows, we will begin to understand much more how and why the rat differs so dramatically from the monkey, even though they share essentially the same complement of genes and proteins."

Even more amazingly, biologist Cedric Feschotte and his colleagues at the University of Texas in Arlington have found that some DNA repeats have actually jumped between mammalian and other tetrapod species including African clawed frogs, anole lizards, South American opposums, brown bats, mice and rats. This kind of horizontal interspecies DNA exchange happens among single-celled organisms all the time, but biologists find it very surprising that it can happen between large multicellular species. The repeat sequences have been dubbed "SPace INvaders" or SPIN transposons and may have been carried into these animal genomes by a virus 45 to 15 million years ago.

And this SPace INvasion may have been responsible for a mass mammalian extinction. According to The New Scientist: 

The team thinks that the hAT transposon invasion occurred about 30 million years ago and spread across at least two continents. "It's like a pandemic, and one that can infect species that weren't genetically or geographically close. It's puzzling, scary almost," Feschotte says.

It may not be a coincidence that the time of the invasion coincides with a period in evolutionary history that saw mass mammal extinctions. This is usually attributed to climate change, Feschotte says, but it is not crazy to suppose that this type of invasion could contribute to species extinction.

The hAT transposon does not occur in humans, but some 45% of our genome is of transposon origin.

Feschotte's work on the hAT transposon is the first time that a "jumping gene" has been shown to have entered mammalian genomes, and the first time it has been shown to do so in at around the same time, in a range of unrelated species, in different parts of the world.

Feschotte admits that we cannot rule out another transposon offensive occurring in mammals….

Whole press release on junk DNA's new usefulness here. New Scientist report on SPIN here.