Chromosomes look different than you think

In high school textbooks, human chromosomes are depicted as Winky X, as if two hot dogs had eaten together. But those images are far from accurate. “For 90 percent of the time, chromosomes aren’t like that,” said Jun-Han Sue.

Last year, before Sue graduated with a PhD, she and three current Ph.D. Graduate School of Arts and Sciences candidates Z Pu Zheng, Sion Kinorot and Bogdan Bintu obtained high-resolution 3-D images of human chromosomes, complex houses for our DNA. Now, those images can provide enough evidence to turn those Xs into more complex but much more specific symbols that will not only teach the next generation of scientists but also help the current generation generate uncontrollable secrets about how chromosome structure is affected.

All living things, including humans, must create new cells to replace the very old and worn-out spaces in order to function. To do that, cells divide and mimic their DNA, which is wrapped in labyrinthine libraries inside chromatin, the material inside chromosomes. Expanding in a straight line, DNA in a single cell can reach up to six feet, all wrapped up in tight, complex structures within the cell structure. Just a mistake of copying or re-winding that genetic material can alter or deform a gene.

It is difficult to zoom in closely to see the chromatin structure. But it is even more difficult to see both the constitution and the function. Now, in a paper published in August Cell, Zhuang and his team report a new method of simultaneously constructing the structure and behavior of chromatin, to determine how the points affect each other to maintain proper function or to cause disease.

“It is very important to determine the 3-D organization,” said David B. Arnold, junior professor of science, Zhuang.

With their new high-resolution 3-D imaging method, the team began creating chromosome maps from wide-lens images of all 46 chromosomes and close-ups of one section of a chromosome. To create something that is still very small in the image, they captured points (“genomic loci”) connected to each DNA chain. By connecting several points, they can form a comprehensive picture of the chromatin structure.

But there was a snag. Previously, Zhuang said, the number of dots they could show and recognize was limited by the number of colors they could image together: three. Three dots cannot create a comprehensive picture.

So, Zhuang and his team came up with a sequential approach: pictures of three different Loki, hiding the signal, and then giving the other three the impression of succession. With that technique, each dot gets two identifying marks: color and image round.

“Now we really have 60 Loki simultaneous images and localization and, importantly, recognition,” Zhuang said.

Still, to cover the whole genome, they need more – thousands so they turned to a language that is already used to organize and store huge amounts of information: binary. By placing binary barcodes on different chromatin loci, they can create an image of even more loci and decode their identities later. For example, an atom gets a barcode from “10” but not in two rounds in one round. With 20-bit barcodes, the team can isolate 2,000 atoms in just 20 rounds of imaging. “In this combination, we can increase the number of molecules we have imagined and identified more quickly,” Zhuang said.

With this technology, the team envisioned about 2,000 chromatin loci, ten times more than their previous work and creating a high-resolution image of what the chromosome structure looks like in its original habitat. But they didn’t stop there: they also envisioned transcription activity (when RNA mimics genetic material from DNA) and molecular structure such as atomic speckles and nucleoli.

With their 3-D Google Maps of the genome, they will be able to begin analyzing how the structure migrates over time and how regional movements help or damage cell division and replication.

Researchers already know that chromatin is broken down into different areas and domains (such as desert versus cities). But what those regions look like in different cell types and how they work is still unknown. With their high-resolution images, Zhuang and team determined that areas with too many genes (“gene-rich”) would move to the same areas on any chromosome. But fields with few genes (“gene-weak”) converge only if they share the same chromosome. One theory is that areas rich in genes, which are active sites for gene transcription, come together like a factory to enable more efficient production.

While more research is needed before confirming this theory, one thing is now certain: the local chromatin environment affects transcription activity. Structure performance functions. The team also found that no chromosomes look alike, even in cells that are otherwise identical. To find out what every chromosome in every cell of the human body looks like, a lab alone will do much more than take it alone.

“It won’t be possible to build on our work alone,” Zhuang said. “We need to build the work of many, many laboratories to gain a comprehensive understanding.”