Building a multicellular organism, even a fruitfly, is kind of like assembling a complicated piece of Ikea furniture.
As with furniture, you have to assemble it in the right order. "There are many moving parts, many cell types, many organs, and the sequence and timing of events really matters," says Philippe Batut, assistant professor of genetics and development at Columbia University Vagelos College of Physicians and Surgeons. "Genes have to be turned on at the right time and the right place, or you're not going to get anywhere."
New research from his lab now reveals a surprising way that developing Drosophila embryos keep track of time and control gene activity with previously overlooked RNAs. The findings, published in Science, could have implications for human health and disease.
"Because many mutations disrupt when and where our genes are active, the work may lead to a deeper understanding of a vast array of human diseases and help identify new therapeutic strategies," says Batut.
Illuminating the dark genome
The research stretches back to a question that has intrigued biologists since the human genome was first sequenced more than two decades ago. Our genes contain the instructions for building the proteins that make our bodies work, but the first map revealed that genes only make up 2% of the human genome. The rest was dubbed "the dark genome."
One portion of the dark genome grabbed Batut's curiosity: About a decade ago, researchers discovered that regulatory regions known as enhancers give rise to mysterious noncoding RNAs.
Enhancers are well-known as sequences that act as switches, increasing or decreasing gene activity. But it was anyone's guess what the enhancers' noncoding RNAs were up to. As a postdoctoral fellow at Princeton and then in his own lab, Batut wondered if the enhancers' RNAs were functionally relevant during animal development, or merely spurious.
To find out, he developed real-time visualization techniques to watch endogenous noncoding RNAs and genes at work in developing fruit fly embryos, which share many biological processes with humans.
The initial analysis revealed a large set of noncoding enhancer RNAs appear at precise locations and times in the developing embryo, and seemed to orchestrate the activation of a set of crucial developmental regulators called HOX genes.
| Watching enhancer RNAs (magenta dots) in developing fly embryos helped reveal how the non-coding RNAs control when genes are turned on, a phenomenon that may also play a role in human health and disease. Video provided by Philippe Batut. |
Enhancer RNAs control timing
To understand what the enhancer RNAs were doing, the team edited the embryo's DNA to prevent one HOX gene's enhancer from creating noncoding RNA. They expected that would turn off the HOX gene or at least reduce its activity. Instead, they saw the HOX gene turned on in the right place, but at the wrong time, causing telltale changes in the embryo's morphology.
"This showed us that these noncoding RNAs are not controlling whether the gene is switched on, but rather when it is switched on," Batut says. Through a series of additional experiments, the investigators showed that activation of these important genes relies on a carefully coordinated "launch sequence," triggered by the noncoding enhancer RNA.
Although the study focused on fruit flies, similar enhancer RNAs are prevalent across the animal kingdom, including humans. "Their role in controlling timing is probably far more widespread than a couple of exotic genes," says Batut.
Because enhancers can be very far from the genes they regulate in the genome sequence, the folding of DNA is often important to bring together enhancers and genes separated by thousands or millions of bases on a chromosome. "One aspect of how these noncoding RNAs work is that they seem to regulate the formation of these long-range DNA loops, which then controls the timing of gene expression," says Batut.
New insights into health and disease
In his new lab at Columbia, Batut is now exploring exactly how enhancer RNAs help coordinate gene activity. "It's not just structural proximity between enhancers and genes, they are probably doing other interesting things as well, and those are questions we're trying to disentangle," says Batut.
A better understanding of enhancer RNAs could eventually provide new insights into health and disease. Genetic dysregulation is already known to drive numerous human diseases, ranging from developmental defects to cancer, and noncoding RNA is likely involved in many of those pathogenic processes.
"That's why basic research is so wonderful; not only is it intellectually fascinating, it's also helps us understand how things break down and potentially how to fix them," says Batut.
