Researchers Capture High-Resolution 3D Images of Human Chromosomes Genetic

A team of scientists at Harvard University have developed new imaging technology to visualize the organization of chromatin, a substance in a chromosome made up of DNA and proteins, at multiple scales in single cells at high throughput genomics.

“It is very important to determine the 3D organization to understand the molecular mechanisms underlying the organization and also to understand how this organization regulates the function of the genome,” said lead author Professor Xiaowei Zhuang, researcher at the Howard Hughes Medical Institute, in the Department of Chemistry and Chemical Biology, and in the Department of Physics at Harvard University.

With their new imaging method, Professor Zhuang and his colleagues began to construct a chromosome map from wide-lens images of 46 chromosomes and close-ups of a section of a chromosome.

To imagine something that is still too small to imagine, they captured connected points – genomic loci – along each DNA chain.

By connecting a lot of dots, they could form a complete picture of the structure of chromatin.

“But there was a catch. Previously, the number of points we could image and identify was limited by the number of colors they could image together: three. Three points cannot give a complete picture, ”noted Professor Zhuang.

Thus, the researchers proposed a sequential approach: image three different loci, turn off the signal, then image three more in rapid succession. With this technique, each point receives two identification marks: the color and the round image.

“Now we actually have 60 loci simultaneously imaged and located and, most importantly, identified,” Prof Zhuang said.

Yet to cover the entire genome, the authors needed more – thousands – so they turned to a language already used to organize and store huge amounts of information: the binary.

By printing binary barcodes on different chromatin loci, they could imagine many more loci and decode their identities later. For example, a molecule imaged in the first round but not in the second round gets a barcode starting with 10.

With 20-bit barcodes, the team could differentiate 2,000 molecules in just 20 imaging cycles.

“In this combinatorial way, we can increase the number of molecules that are imaged and identified much faster,” said Prof Zhuang.

With this technique, the team imagined about 2,000 chromatin loci per cell, an increase of more than ten times over their previous work and enough to form a high-resolution image of what the structure of chromosomes looks like in their cell. original habitat.

They also imagined transcriptional activity – when RNA replicates the genetic material of DNA – and nuclear structures like nuclear speckles and nucleoli.

With their high-resolution images, Professor Zhuang and his co-authors determined that areas with a lot of genes tend to flow to similar areas on any chromosome. But areas with few genes only come together if they share the same chromosome.

One theory is that gene-rich areas, which are active sites for gene transcription, come together like a factory to allow more efficient production.

While more research is needed before this theory can be confirmed, one thing is now certain: the local chromatin environment has an impact on transcription activity. Structure influences function.

The team also found that no two chromosomes are the same, even in cells that are otherwise identical.

Finding out what every chromosome in every cell in the human body looks like will take a lot more work than a lab can do on its own.

“It will not be possible to rely solely on our work. We have to rely on the work of many, many laboratories in order to have a global understanding, ”said Professor Zhuang.

The team’s results were published in the journal Cell.

_____

Jun-Han Su et al. Genome-wide imaging of 3D organization and chromatin transcriptional activity. Cell, published online August 20, 2020; doi: 10.1016 / j.cell.2020.07.032