UMass Team Develops Technique to Visualize RNA Inside Living Cells

Chemists at the University of Massachusetts Amherst have created a new approach to visualize messenger RNA (mRNA) activity inside living mammalian cells using a three-color imaging system. The method enables scientists to tag different RNA molecules with distinct colors and follow their movements in real time, offering a clearer view of how RNA contributes to essential cellular functions. The method was recently published in Nature Methods.

“There are many diseases that result from something going wrong with RNA,” said lead author Daisy Pham. “And RNA plays a crucial role inside our cells: it’s the messenger that tells the cell how to make the proteins for which DNA is the master blueprint, they can turn on and off specific genes, they can organize and shape cellular structures, and other functions that need to happen perfectly for our cells to remain healthy.”

Jiahui (Chris) Wu, the paper’s senior author and a fluorescent microscopy specialist, noted the challenge of studying these processes: “The big question is how do you actually study them? The best answer is to actually observe them inside a living cell, but they’re tiny.”

Until now, scientists largely relied on the “RNA hairpin method,” which attaches fluorescent protein tags to target RNA strands. Wu and Pham have advanced this approach by refining how the fluorescent signal is produced and detected. They designed proteins that bind to a specific segment of RNA and only emit light once attached, preventing unwanted background glow that can cloud imaging results.

The researchers also engineered three distinct fluorescent proteins that light up in green, red, and far-red colors. Each one attaches to a specific type of RNA involved in different cellular roles, allowing scientists to watch multiple RNA processes unfold simultaneously inside living cells. “We can now watch as different kinds of RNA in action inside a living cell,” said Pham, “and we can better understand how they do what they do.”

The team has made their method available for public use, expanding the research toolkit for studying RNA dynamics.