Could an odd plant with a terrible name show us that “junk DNA” has value after all?

The carnivorous bladderwort plant, Utricularia gibba, is a lightweight in the genome game. It has about 80 million DNA base pairs. By comparison, its relatives the grape and tomato have about 490 and 780 million base pairs, respectively. (You and I have about 3.2 billion base pairs, but hey, we’re humans.)

Despite its small genome, the carnivorous bladderwort is a complicated plant. Disguised as a lovely flowering beauty, it actually traps organisms such as insects and small fish in a bladder-shaped trap on its water-soaked roots—for nourishment, of course. And while that’s exciting, a new study in Nature has scientists even more excited about the carnivorous plant.

“The big story is that only 3 percent of the bladderwort’s genetic material is so-called ‘junk’ DNA,” says study co-author Victor Albert. The human genome, in contrast, includes about 98% junk DNA. But what kind of “junk” are we talking about?

Junk in the Trunk

“When complete genomes were first being sequenced, it became clear that only a small fraction of the DNA could be assigned a specific function,” explains Brian Simison, curator and director of the Academy’s Center for Comparative Genomics. “The functional regions or genes are primarily those that produce proteins or ribosomes. It has been hypothesized that these vast regions of unknown function were the product of duplications followed by loss of function due to the accumulation of random mutations and/or the accumulation of exogenous DNA from viruses. The term ‘Junk DNA’ emerged from these hypotheses.

“However, research on junk DNA is shedding new insights into these regions,” Simison adds. Last fall, he spoke with Science Today correspondent Barbara Tannenbaum about the ENCODE project. Conducting a huge international effort to look more into the junk part of the human genome, researchers determined that 80% of our genome actually had some function.

Since that time, ENCODE has come under some scrutiny. “I think the ‘controversy’ is overblown,” Simison says. “ENCODE scientists presented a testable hypothesis and it should be pursued as such. My bet is that some junk DNA will, in fact, turn out to be useless baggage from historical genomic events while other bits will prove to be required for normal human functions.”

No Junk in the Trunk

If our junk DNA is worth having around, then why doesn’t a meat-eating plant like the bladderwort need it? “Based on the miniscule number of complete genomes sequenced, it is unusual that the genome of the carnivorous bladderwort is only 3% junk DNA,” Simison says. “It may reveal interesting information about the function and organization of genomes. However, the sample size of complete genomes is so incredibly tiny that junkless genomes may not be that uncommon.”

So what happened to the junk? “That is the big question. Did it get deleted or did the carnivorous bladderwort not have it to begin with?” Simison asks. “To answer this we need to understand more about the evolutionary history of genomes and, in particular, we need to know more about the genomes of this plant’s ancestors.”

The bladderwort’s lack of junk DNA only adds to the mystery. Scientists hope to learn more as additional organisms’ complete genomes are sequenced—and as more research is conducted on the function of junk DNA.

Image: Bruce Salmon/Wikipedia

An international consortium of researchers recently announced another milestone in the quest to unravel the genetic makeup of the human species. The project—ENCODE, for Encyclopedia of DNA Elements—is a collaborative effort among 440 researchers in 32 global institutions, coordinated by the National Human Genome Research Institute (NHGRI). The results of this international effort will stand alongside such research breakthroughs as Watson and Crick’s 1953 description of DNA’s double helix structure and the Human Genome Project’s 2003 complete sequencing of humanity’s 3.2 billion nucleotides.

ENCODE mapped more than four million non-coding regions of the genome that regulate and interact with protein-producing DNA. The scientific consortium also confirmed that 80 percent of the genome performs specific biological functions. This upends the previous consensus that long stretches of DNA were no more than “junk DNA.”

“This is one of the most important collections of information the world is trying to decode,” explains Brian Simison, head of the Academy’s Center for Comparative Genomics.

Not only does ENCODE solve a bit more of the human genome puzzle, but it offers the potential to accelerate medical research. “We’ve known for a long time that there is a genetic basis to many diseases,” says Simison. “What we didn’t realize is that the source of many diseases would be found in the vast regions of the genome previously known as junk DNA.”

While others describe the project as having found the on/off switches to our genes, Simison prefers the term ‘regulatory function.’

“We are learning that junk DNA has a regulatory role in dosage, duration, timing and other regulatory functions. Understanding these functions will transform Western medicine,” Simison adds. “ENCODE reveals that Western medicine is in its infancy.”

Simison points out that ENCODE is also altering our vision of the genetic composition of life. “Most people think all genetic material is passed down to us by our direct ancestors. Actually,” Simison explains, “the human species is filled with ‘fossil DNA’ transferred to us from viruses.”

As an example, Simison describes a retrovirus that has inserted its DNA into a person’s genome. These endogenous retroviruses (ERVs) are found throughout the genome and it is now believed that some of these have been repurposed.

Finally, Simison explains that it’s not just what ENCODE found but how they found it that is significant.

“The wow factor is enormous,” Simison laughs. As the National Institute of Health reports, hundreds of international researchers performed more than 1,600 sets of experiments on 147 types of tissue with technologies standardized across the consortium.

“Although technology has improved, no single institution could have analyzed the genome data on its own,” Simison remarks. “You need many people sifting through the many layers of data to decode the human genome.”

“I believe it is a positive development that so many nations are sharing this knowledge,” he said, lauding the consortium for its cooperative methods. “These illustrate how the path towards lofty ambitions is often as fruitful as the objectives themselves. Unlike the U.S. space program, the Human Genome Project and ENCODE were international projects where the benefits that emerge are shared with and benefit the world.”

ENCODE’s results were published last month in a wide range of scientific journals and posted online to ensure transparency and public access. To learn more, review the publications here.

Barbara Tannenbaum is a science writer working with the Academy’s Digital Engagement Studio. Her work has appeared in the New York Times, San Francisco Magazine and many other publications.