DNA-Based Tool Designed to Map Wiring of Whole Brain

A new and possibly groundbreaking way of obtaining a neuronal connectivity map (or the connectome) of the whole brain of the mouse is now in the planning stages.

A report on the technology was published October 23, 2012, in the open-access journal PLOS Biology. The investigators, led by Prof. Anthony Zador, PhD, of Cold Spring Harbor Laboratory (Cold Spring Harbor, NY, USA), have an objective of providing a detailed map of neural connectivity. Currently, the only way of getting this information with high precision involves studying individual synapses in electron microscopes. However, such methods are slow, labor-intensive, and expensive.

Prof. Zador and colleagues instead propose to tap high-throughput DNA sequencing technology to explore the connectivity of neural circuits at the resolution of single neurons. “Our method renders the connectivity problem in a format in which the data are readable by currently available high-throughput genome sequencing machines,” said Prof. Zador. “We propose to do this via a process we’re now developing, called BOINC [barcoding of individual neuronal connections].”

The approach comes at a time when a number of scientists in the United States are advancing in the technology of mapping connections in the mammalian brain. These efforts use injections of tracer dyes or viruses to map neuronal connectivity at a “mesoscopic” level--a mid-range resolution that makes it possible to follow neural fibers between brain regions. Other groups are developing approaches based on electron microscopy.

The investigators are trying to trace connectivity further than the mesoscopic, at the scale of synaptic contacts between pairs of individual neurons, throughout the brain. The BOINC barcoding technique, now undergoing proof-of-concept testing, will be able, according to Prof. Zador, “to provide immediate insight into the computations that a circuit performs.”

Most neural computations are not currently understood at this level of precision, most because detailed circuit data are not yet available for mammals. The BOINC technology has the potential to be much more rapid and less expensive than applications based on electron microscopy.

The BOINC method comprises three steps: First, each neuron is labeled with a specific DNA barcode. A barcode consisting of just 20 random DNA “letters” can distinctively label a trillion neurons--many more than exist in the mouse brain. The second step looks at neurons that are synaptically connected, and links their particular barcodes with one other. One way to do this is by exploiting a virus such as the pseudorabies virus, which can move genetic matter across synapses. “To share barcodes across synapses, the virus must be engineered to carry the barcode within its own genetic sequence,” explained Dr. Zador. “After the virus spreads across synapses, each neuron effectively ends up as a bag of barcodes, comprising its own code and those from synaptically coupled partners.”

The third step of the BOINC method involves joining barcodes from synaptically connected neurons to make individual pieces of DNA, which can then be read by way existing high-throughput DNA sequencing techniques. These double-barcode sequences can then be assessed computationally to reveal the synaptic wiring diagram of the brain. Combined, reported Prof. Zador, if BOINC is effective in its current proof-of-concept testing, it will offer a drastically inexpensive and fast way of building a connectome, even of the complicated brain circuitry of mammals.

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Cold Spring Harbor Laboratory