A New Kind of Cycling

What am I looking at?

This video shows 8 different proteins within a hippocampal slice of a mouse brain. Each of the proteins is color-coded, and the color key can be seen in the top right corner of the video. As the video progresses, it zooms in on different sections of the tissue, highlighting where the different proteins are concentrated within the hippocampus. The spatial resolution of this imaging technique is good enough that we can even see the locations of protein densities within single cells and their nuclei when zoomed in.

Biology in the Background

Researchers at HHMI’s Janelia Research Campus wanted to understand where and how genes are expressed as RNA and proteins in the cell during development and how this organization controls developmental progression. To do this effectively they needed to image hundreds of RNA molecules in a thick tissue sample.  However, while there were microscopy techniques that could image many RNA molecules at once and those that could visualize fluorescent tags in thick tissue samples, there was not a single technique that could do both at high resolution. So, they created a new technique to satisfy their needs.

This new technique, known as cycleHCR, uses a DNA barcode system to track hundreds of RNA and protein molecules in single cells within thick biological samples. This allowed the researchers to observe how these targets are expressed and organized inside tissue samples. This technique will not only be useful to track the 3D positions of RNA molecules and proteins within single cells and tissue samples in the context of basic research but could also be used as a diagnostic tool to track gene expression and protein localization in human tissues being tested for specific diseases.

The cell bodies of the individual cells in this video are around 20 micrometers across, roughly 3.5 times smaller than the width of a human hair.

Technique

This video was created using a type of fluorescence microscopy called cycleHCR.