The Deep Genome: Hidden Files--Forbidden Access

Understanding the genome sometimes feels like peeling an onion. Beneath the surface layer, lurks another layer of function and control. And beneath that . . .

...before transcripts can guide protein synthesis or take on regulatory functions, they have to undergo a strict mRNA surveillance system that degrades defective, obsolete, and surplus transcripts. In their study, published in the Dec. 28 issue of Cell, the scientists zoomed in on a specific subclass of transcripts that are under the control of the exosome, a molecular machine in charge of controlled RNA degradation.

“We found evidence for widespread exosome-mediated RNA quality control in plants and a ‘deeply hidden’ layer of the transcriptome that is tightly regulated by exosome activity,” says Joseph R. Ecker, Ph.D., professor in the Plant Biology Laboratory and director of the Salk Institute Genomic Analysis Laboratory.

...Since the common notion is that the exosome plays a central role in bulk RNA turnover, the researchers say, they expected to find the levels of all transcripts increasing when they inactivated the exosome complex. “But not everything is going up, instead the exosome mechanism seems to be very tightly regulated,” says Ecker. “We didn’t see regions that are known to be silenced to go up, instead we found a very specific group of transcripts that are regulated in this way.”

Among them are regular protein-coding RNAs, RNA processing intermediates and hundreds of non-coding RNAs, the vast majority of which hadn’t been described before. “These strange transcripts are associated with small RNA-producing loci as well as with repetitive sequence elements,” says Gregory. “They are under very tight regulation by the exosome, but we still don’t know exactly what this means.”

“It is likely that these RNAs that are usually ‘deeply hidden’ become important for genome function or stability under some circumstances”, adds co-first author Julia Chekanova, an assistant at the University of Missouri-Kansas City. “We need to do more work to figure out what these circumstances are.”

Physorg

Understanding how genes turn on and off is the key to stem cell research, gene therapies, and regenerative medicine. Being able to insert genes into the genome, for example, is easier than making sure the new genes work only as intended. There is still a lot to learn about the deep web of transcriptome control.

In modern biological research, there is no shortage of data or data analysis tools. But the limited human brain is beginning to run into the incredible complexity of not only the data itself, but the data analysis.

Due to the lack of training in "lateral thinking" and creative analysis, many scientists are at a loss when attempting to interpret the mountain of data returned from even fairly simple experiments.

It should not be surprising then to see one conclusion reported in the headlines, only to read a startlingly contradictory claim the next day. You know that if scientists are a bit overwhelmed by the complexity of the task, that journalists are at a total loss.

It is often quite amusing to watch news anchors and talk show hosts interview "science" journalists about the latest findings in science. Like the movie Idiocracy: "it's got what plants crave--electrolytes!" But then, sometimes the simplest explanations are the best.