Scientists utilize RNA to map neural networks

An innovative use of RNA sequences has allowed scientists from Cold Spring Harbor Laboratory (CSHL) to track connections between individual neurons in the brain, according to a study published in Neuron.

Developed by Anthony Zador, MD, PhD, biology professor at New York’s CSHL, the technique is called Multiplexed Analysis of Projections by Sequencing (MAPseq).

Current methods of tracing neuronal connections are limited to whole regions, rather than individual neurons. For example, a common method uses a fluorescent protein that is injected into the brain and transported between neurons. While this technique can determine all of the regions the neurons project to, it can’t tell scientists if two adjacent neurons projected to different places or if they are sending signals to the same spot.

Instead, using RNA sequences allowed Zador and his team to precisely track neurons.

“The RNA sequences, or 'barcodes,' that we deliver to individual neurons are unmistakably unique," Zador said, "and this enables us to determine if individual neurons, as opposed to entire regions, are tailored to specific targets.”

The RNA molecules are delivered to the neuron by a deactivated virus containing a massive pool of unique RNA barcodes. Each barcode comprises strings of 30 nucleotides—meaning that there are many more sequences (10¹⁸) than neurons in the brain, allowing for easy identification once the RNA has traveled downstream through synapses to other neurons.

The brain is dissected two days after the injection, and the RNA is gathered and sequenced. RNA barcodes at the source are matched to other sites throughout the brain, giving researchers more specific information about connectomes than was ever available before.

MAPseq is a “simple, rapid and inexpensive approach to determining the projection patterns of myriad single neurons at one or more injection sites,” wrote Zador et al.