Tracking RNAs: A glowing story of man-made fireflies

In between lab measurements, I found myself dazing off…“Above the polar circle in the vast alleys of Cellsland, the subjects had not yet discovered light and darkness reigned perpetually for months on end. Within this one-of-a-kind kingdom, the inhabitants, a myriad of tiny creatures, relentlessly joined forces to keep their home up and running throughout the tough months of winter. The ruler of the kingdom, Nucleolus sent coded duties to selected individuals day and night. No one really knew how he assigned a complex network of tasks and to whom or even how they intertwined all together to create a functioning habitat."

“The kingdom thrived and happiness prevailed until a gloomy turning point. An avalanche engulfed a few of the key code-readers who suddenly stopped carrying on with their daily tasks. Chaos overtook the kingdom. Not a single creature could pinpoint the source of the problem. Nucleolus thought if he could only light-up the little hard workers in this pitch-dark environment in order to recognize who performed which tasks, where and with whom. Nature could brilliantly provide with a flying answer: Fireflies! What if these light-emitting insects could get somehow attracted to and remain bound to the workers for a decent amount of time in order to reveal their actions?” ……..

I opened my eyes and observed that the persistent glowing RNA fragments sat still next to me on the microscope slide. I smiled. When bound to an RNA fragment of interest, my man-made ‘firefly’ bricks – or fluorogenic dye in scientific terms – emitted quantifiable light for quite some time to the outside cell world. This could finally become a valid research tool for scientists who wish to track RNAs. Eureka!

RNAs are best known as the molecules responsible for translating genetic code into proteins within our cells – a known biological fact. For some time, however, scientists believed that RNAs only existed inside cells. It turns out that they were wrong, and the rather recent discovery of extracellular RNAs – or simply exRNAs – has shaken the entire scientific community. These exRNAs can travel throughout the body via the bloodstream in tiny little fat bags – a puzzling encapsulated wonder. Today, scientists pursue the quest to understand why cells release RNAs in a first place and what could these molecules be telling us when it comes to the health of an individual. As you may have guessed by now, RNAs, -- extracellular and cellular ones -- are more than ever on the spotlight. When it comes to studying the implications of such molecules within a biological molecular path, this research may bring tremendous value.

Let’s go back to the kingdom of Cellsland. Cellular RNAs are just like its small inhabitants transporting messages from one place to another in a bleak environment. Lighting them up is necessary to follow their interactions with other molecules so scientists can unravel important biological communications, which in the long run could be part of the puzzle in detecting the early onset of a disease, for example. The main goal of my research; however, is to develop this new cellular RNA imaging tool. The techniques used up to date are not as efficient as a researcher would like for two reasons: little contrast, high fluorescent background and incompatibility with small cellular RNAs (MS2-GFP technique); in addition, they cannot be used in a live functioning cell (FISH technique).

With that being said, I use a cool microfluidic technology to scan around 10^6 RNA fragments/hour that are able to specifically interact with fluorogenic dyes. These dyes are not emitting light in a free state; that is, when not bound to a specific RNA, they would be much like a faded firefly. Yet they light up when bound to an RNA that accepts them, chemically-speaking. The cellular RNA, and therefore its cascade of interactions, can be tracked down over time in a cell, as the RNA-dye complexes can display a fluorescent signal in vitro for around 30 minutes. Is it not, literally, brilliant? (Pause for groans or chuckles). In the future, scientists should be able to light up their molecules of interest more efficiently and for a longer period of time with these smaller RNA-dye complexes. Seeing is indeed believing, as one says!

I am Farah Bouhedda, and I am a freshly graduated PhD student affiliated with the ‘Architecture et réactivité de l'ARN’ group with Prof. Michaël Ryckelynck as supervisor. The group is part of the ‘Institut de Biologie Moléculaire et Cellulaire’ at the University of Strasbourg. The research described above is supported by funding from the French National Research Agency (ANR).

Text by Fernanda Haffner

Illustration by Marion Couturier