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Dark matter

Riley Hoonan

At first the remarkable role of Xist as a lncRNA was considered an exception, but soon more lncRNAs were suspected to have crucial functions. Despite the debate about lncRNAs’ significance, it was generally agreed that all noncoding regulatory elements acted on the same chromosomes on which the RNA’s own sequences were located: They acted in cis, from Latin for “the same side.”

In 2007, however, Rinn, then a postdoctoral fellow under Howard Chang at Stanford University School of Medicine, and his colleagues were astonished to discover a lncRNA that worked in trans—on a different chromosome. They had identified a lncRNA called HOTAIR in developmentally important HOX gene clusters. HOX clusters, from A to D, contain genes that define the body plan from head to toe, as reflected in the progressively detailed features of a growing fetus. HOTAIR is located near the HOXC cluster on chromosome 12, so Rinn thought that by deleting its DNA he could see whether one of the nearby HOXC genes would be affected. The deletion did have an impact, but on HOXD13 on chromosome 2.

Here, too, what first seemed like an exception—to the rule of in cis regulatory elements—now appears more common, and in trying to determine how such elements might wield their influence from afar, researchers have also had to rethink other basic assumptions. For example, they had typically thought of the genome as a linear sequence of DNA bases (A, T, C and G) that align in a long chain, with various sections spelling out instructional recipes for proteins. But the reality turns out to be much more complex.

“You can think of the genome as having three layers of information,” says Job Dekker, a biochemist and molecular pharmacologist at the University of Massachusetts Medical School. The first layer involves the familiar linear DNA sequence. But if all of the DNA in the genome sequence were straightened out, it would extend to six feet. How does that long strand get squeezed inside a cell nucleus that’s a mere 10 to 20 microns (millionths of a meter) in diameter without becoming hopelessly entangled? How do the various factors that switch on a gene find their target? “That’s the biggest challenge for cells,” Dekker says, “and for a very long time we weren’t able to figure out how they solve it.”

The solution lies in how the DNA is tightly wound around spools called histones, which are packaged with a coating of chemicals called chromatin. Chromatin is decorated with “flags” indicating where genes, lncRNAs and other regulatory elements are tucked away inside—and that system comprises the second layer of genomic information. It enables other molecules to locate those elements, causing the chromatin to open or close depending on whether an element needs to be activated or silenced.

This layer of information is tied to the third layer, which concerns how the chromosomes themselves fold and loop within the cell nucleus. That looping can bring genes and noncoding regulatory elements that lie far apart in the linear sequence (and even on different chromosomes) into close proximity and even physical contact. That three-dimensional physical interaction (the third layer), in turn, may change the chromatin configuration (affecting the second layer) and thus influence the activity of genes (written in the first, linear layer of information).

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What Is Genetic Dark Matter?

Researchers are only beginning to understand genetic dark matter's many mysteries.


1. “Genome Regulation by Long Noncoding RNAs,” by John L. Rinn and Howard Y. Chang, Annual Review of Biochemistry, July 2012. The authors, who have made major contributions to the understanding of long noncoding RNAs, review technologies enabling these studies and highlight emerging themes.

2. “The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb,” by James P. Noonan et al., Cell, July 3, 2013. Noonan describes enhancers associated with the embryonic development of the distinctive human hand and foot.

3. “Xist RNA Is a Potent Suppressor of Hematologic Cancer in Mice,” by Jeannie T. Lee et al., Cell, Feb. 14, 2013. Some breast cancers have extra copies of the X chromosome, suggesting that these cancers may have malfunctioning Xist, a long noncoding RNA responsible for silencing the second X chromosome in females. Here, Lee and colleagues investigate whether Xist dysregulation might cause cancer, using blood cancer in mice as a test case.

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