Using a new CRISPR-based technique, researchers are examining how the position of DNA within the nucleus affects gene expression and cell function.
Quanta Magazine said:The nucleus of a cell has something in common with a cardboard box full of kittens: People get so fascinated by the contents that they overlook the container. The nucleus itself is often treated as no more than a featureless membranous bag for holding the vitally dynamic genetic material. Yet in fact it has specialized parts and an internal architecture of its own, and scientists have long speculated that precisely how the DNA positions itself with respect to those parts might matter a great deal.
Now a team of researchers is finding credible evidence that this is true and possibly an important influence on gene expression. Using a new technique based on the genome-editing tool CRISPR, they artificially pinned parts of a cell’s DNA to different regions in the nucleus and observed what happened. The work, published last month in Cell, has begun to yield intriguing insights into how various nuclear neighborhoods may relate to gene expression, as either cause or facilitator.
The 6 feet of DNA intricately bundled within a human cell’s tiny nucleus can look as chaotic as a ball of spaghetti or a tangle of thread. But how that DNA gets situated in three-dimensional space is critical — and not at all random. The degree of packing and folding enables genes to be accessible in the right place at the right time, so that the cell’s machinery can find and decode them, dial their activity up or down, and keep everything working as it should. Those rearrangements also put specific parts of the genome near or far from landmarks within the nucleus.
There’s been tantalizing evidence that the positioning of DNA at those nuclear locations may not be coincidental. Tightly wound, silent genes tend to be located toward the periphery of the nucleus, while open, active DNA makes its home toward the interior. During development, as cells differentiate, the DNA reorganizes itself: As some genes shift from a repressed state to an active one, they’ve also been found to move away from the periphery. That said, some other gene regions usually found near the periphery aren’t there all the time, and when they do move, they still show the same levels of activity.
Biologists have therefore debated how DNA’s condensed structure and expression relate to its nuclear location, and what might be cause rather than effect. Inactive genes with a certain profile might get drawn to the periphery, or the periphery itself may be responsible for silencing them. Those considerations get even more complicated toward the center of the nucleus, which comprises many different domains defined by a variety of nuclear bodies, such as the nucleolus (which assembles ribosomes for protein production) and Cajal bodies (which help to splice RNA). Their functions, too, have been difficult to tease apart: Once again, correlations abound, but pinning down causality is a different story.
“These have been the questions at the epicenter of the studies on the relationship of genome organization and nuclear structure and gene regulation for decades,” said Mitchell Guttman, a biologist at the California Institute of Technology.
And so for the past four years, Stanley Qi, a bioengineer at Stanford University, and his colleagues have been working on paving a way for scientists to start answering those questions. They turned to CRISPR, a system that has been used widely to edit genes, regulate transcription and take images of cellular processes. Now they’ve innovated a way to harness it for spatial control over the genome. They’ve dubbed the process CRISPR-GO (the GO stands for “genome organization”). “It’s a broad expansion of the CRISPR technology,” Qi explained, “which started five years ago and is still not slowing down.”
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