‘MERFISH’ method identifies thousands of unique RNAs in 10 rounds of imaging

Harvard researchers have developed a “cellular atlas” of the brain using a novel fluorescence imaging technique known as multiplexed error-robust fluorescence in-situ hybridization, or MERFISH, the Harvard Gazette reported early this month.

The MERFISH methodology, coined by Harvard Higgins Professor of Molecular and Cellular Biology Catherine Dulac and colleagues, grew from a fundamental need to better understand the molecular components of individual cells in the brain.

“If you really want to understand the brain, you need the spatial context, because the brain is not like the liver or other organs, where the cells are organized in a symmetrical way,” Dulac told the Gazette. “The brain is unusual in that it has this topological arrangement of neurons...so we want to be able to look at a section of the brain and see what cells are there, but also where they are and what types of cells are surrounding them.”

Enter MERFISH, which works by assigning “barcodes” to cells’ RNAs and hybridizing them with a library of DNA. Imaging determines the identity of unique RNA molecules.

In a 2-millimeter-by-2-millimeter-by-0.6-millimeter region of brain, Dulac’s team was able to employ MERFISH to identify more than 70 types of neurons, as well as where those cells were located and what their functions were.

“An amazing property of this method is the exponential scaling between the number of genes that can be imaged and the number of imaging rounds,” Dulac said. “If you wanted to look at 10,000 genes, you could try the brute-force approach and do it one at a time, but of course no one would ever try that. The MERFISH approach is very powerful because it allows us to image and distinguish thousands of different RNAs in just about 10 rounds of imaging.”

Read more about MERFISH and Dulac’s work at the link below.