Making sense of repetitive DNA

This story is part of our series, "Unsung cellular heroes." To read more stories in the series, click here. To read our cartoon explainer of repetitive DNA, click here.

The English language contains 26 letters, and those letters can be combined in an infinite number of ways to make up sentences just like this one. Our genomic language contains only four letters—four types of molecules: adenine, cytosine, guanine, and thymine (in DNA)—and yet that small set of building blocks gives rise to tens of tens of thousands of unique genes. However, not every region of our genomes is so richly varied. In some regions, the same sequence is repeated over and over again, and much like someone might look at a paragraph consisting of a single word repeated hundreds of times in a row and assume that it is nonsense, so some scientists assumed that certain regions of repetitive DNA were useless or “junk” DNA. Other types of repeating DNA sequences code for useful cellular machinery or occur within genes, where they may contribute to diseases. Whitehead Institute researchers are investigating some of these different types of repeats in our genomes in order to learn more about what they do in cells and how they contribute to health and disease.

More than junk

One type of repetitive DNA that had been thought of as junk is called satellite DNA. Satellite DNA makes up more than ten percent of our genome, and it does not contain any genes, only strings of repeating sequences. Whitehead Institute Member Yukiko Yamashita and colleagues have shown that satellite DNA is far from junk; rather, it plays pivotal roles in the cell and in evolution.

Yamashita and former postdoctoral fellow Madhav Jagannathan, currently an assistant professor at ETH Zurich, showed that satellite DNA helps to keep cells’ chromosomes together in a single nucleus. Proteins that specifically bind to satellite DNA gather all of the chromosomes’ satellite DNA together, which keeps the chromosomes corralled in the same place, the way binding keeps the pages of a book together. When the researchers removed one of these proteins in fruit flies, some chromosomes ended up in a separate micronucleus, and this was often lethal to the cells and flies. If the full set of chromosomes is the operations manual for a cell, this is the equivalent of some of the pages getting torn out and set aside so that the manual is missing key instructions and can’t be followed.

The researchers found that the same defects occurred in the hybrid offspring of two closely related fly species. Based on this work, they propose that the role satellite DNA plays in keeping chromosomes together may contribute to speciation—when two populations diverge to the point that they can no longer create viable offspring, and so become two distinct species. Satellite DNA mutates and evolves quickly. The researchers propose that as satellite DNA changes, populations of organisms must rapidly evolve new proteins to bind to the changing satellite DNA and keep chromosomes together in the nucleus. Over time, the protein that one population has won’t work on another’s satellite DNA, as the researchers saw in the hybrid flies. The populations become unable to interbreed–-they become distinct species.

These discoveries showed that satellite DNA is hardly junk, and in fact is critical for keeping the chromosomes in the nucleus together and defining species.

Repeats and disease

Repetitive DNA like satellite DNA does not contain any genes. However, genes can contain stretches of repetitive DNA. When mutations result in the same short sequence getting repeated too many times within a gene, this can contribute to disease. Whitehead Institute researchers are discovering more about how DNA repeats may contribute to disease, and developing potential strategies to treat diseases based on these insights.

Whitehead Institute Member Ankur Jain studies how repetitive sequences within RNA can contribute to repeat expansion disorders. This set of neurological disorders includes ALS and Huntington’s disease, and can cause a range of problems including neurodegeneration, muscular dystrophy, and intellectual disability. Each disorder is associated with excessive repeats of a short DNA sequence in the disease gene, such as the repeated sequence CAG in the case of Huntington’s.

In these disorders, the repeat-containing DNA gets read into repeat-containing RNA, which in turn makes faulty proteins that can contribute to the disorder. Jain and graduate student Michael Das found evidence that the repeat-containing RNA may also contribute directly to problems in the cell. The repeats in the RNA make it more likely to tangle up, the way a long piece of tape is more likely to get stuck to itself than a short piece. As multiple RNAs tangle up together, they form clumps. Researchers knew that in repeat expansion disorders, RNA clumps up like this in the nucleus where it is made. However, the clumps there did not seem to do much harm to the cell.

Jain and Das found that some of the repeat-containing RNA leaves the nucleus and goes into the cytoplasm, or main body of the cell, where it gets made into faulty proteins and then tangles together with those proteins to form gel-like solid clumps. These solid RNA and protein clumps in the cytoplasm do appear to harm the cell. They push on the nucleus from the outside, deforming it. They also trap other proteins so that those proteins cannot get to where they are needed in the cell to do their jobs. These findings reveal how repeat-containing RNA may be toxic to cells. They also suggest a possible treatment for repeat expansion disorders: using drugs that keep the RNA clumps in the nucleus, where they do less harm.

Targeting repeats for treatment

Fragile X syndrome is an incurable genetic disorder that causes intellectual disability, most commonly in males. It happens when the FMR1 gene is off in neurons—meaning the neurons do not produce the protein that the gene encodes. The DNA sequence of FMR1 contains a repeated three-nucleotide sequence: CGG. The number of CGG repeats present determines a person’s risk of developing Fragile X Syndrome, with 200 or more repeats leading to the disorder. Research from Whitehead Institute Founding Member Rudolf Jaenisch and former Jaenisch lab postdoc Shawn Liu determined how to turn the critical gene back on in neurons in the lab, laying the foundation for a possible treatment for the disorder.

Researchers already knew that Fragile X Syndrome is caused when a chemical tag attaches to the repeats in FMR1 and causes the gene to turn off, a process called methylation. Liu and colleagues created a version of the CRISPR/Cas9 gene editing tool that can remove methylation from a gene, rather than editing the DNA sequence itself. The researchers applied this tool to Fragile X neurons, and they found that removing the methylation from FMR1’s repeats turned on the gene and returned the neurons to normal function.

The work confirmed the role of the excessive CGG repeats in Fragile X Syndrome. It also suggests that targeting the repeats and removing their methylation may be an avenue for treating Fragile X.

In each of these cases, Whitehead Institute researchers have found that there is more to repetitive DNA than meets the eye. There is a lot left to explore about how DNA’s repeating elements can give rise to useful—or detrimental—properties within cells, and Whitehead Institute researchers continue to explore the unknown aspects of these DNA sequences. To learn more about repetitive DNA, read our cartoon explainer.