AudioHelicase podcast: Ankur Jain on RNA clumps and the neurodegenerative diseases associated with them

This story is part of our series, Looking Beyond the Gene. Click here to see all stories in this collection. 

In this episode of AudioHelicase, Whitehead Institute Member Ankur Jain discusses how RNA can clump in cells and the diseases, such as Huntington's and amyotrophic lateral sclerosis (ALS), that are associated with these aggregations.

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Ankur Jain: The broad area that my lab is interested in studying is RNA aggregation. In my past research, I found that there are certain sequences, which are sticky, and they tend to act as tiny pieces of Velcro, if you may. And they like to stick to themselves and create aggregates. These are the sequences associated with certain neurodegenerative diseases, such as Huntington’s disease, or amyotrophic lateral sclerosis.

Lisa Girard: That was Ankur Jain, Whitehead Institute Member and an assistant professor of biology at MIT. And welcome to AudioHelicase, the podcast of Whitehead Institute, unwinding the science and the people behind some of the Institute’s most exciting discoveries. I’m Lisa Girard, director of communications at Whitehead Institute, and in this episode, I’ll be talking with Ankur about RNA aggregates and what they might mean for our understanding of certain neurodegenerative diseases.  As a postdoc in Ron Vale’s lab at UCSF, Ankur discovered that RNA sequences that contain repeated cytosines, or Cs, and guanines,  or Gs, can actually stick together and form membraneless blobs or “RNA gels” inside of the nucleus. He also noted that such repeats are found in the disease genes associated with certain neurodegenerative disorders. Ankur, what diseases are actually associated with these sticky RNA segments?

Jain: There are about 30 known diseases in this family collectively called the repeat expansion disorders. The cause of the disease here is an expanded repeat. There’s a stretch of sequence which gets copied too many times. Perhaps a better-known example is Huntington's disease, where there's a stretch the sequence CAG, which gets copied too many times in the Huntington gene. Normal or healthy individuals have anywhere between five to thirty copies of CAG in the Huntington gene. But in some families that number exceeds 40 or so. They have 40 times, 50 times, CAG repeated. That results in the disease onset. Similarly, there are other diseases, for instance, in certain forms of amyotrophic lateral sclerosis, or ALS, there's a sequence GGGGCC, which gets copied too many times in the intron of its cognate gene. And virtually all of these diseases have this peculiar characteristic that short repeats do not result in disease onset. But only when the number of repeats exceeds a certain critical threshold that results in disease manifestation.  

Girard: Why is the number of repeats so important?

Jain: How exactly these repeats are resulting in the disease is not known. What we know so far is that long repeats result in a disease, short repeats to not. There's another feature that the more the number of repeats, the sooner the disease hits. For instance, an individual carrying 50 repeats will likely get Huntington disease symptoms earlier than the individual carrying 45 repeats or 40 repeats only. And  again, it has remained mysterious why there is this anticorrelation between the number of repeats and the age of disease onset. And what we found is that these repeats essentially lead to aggregation of the RNA, which is produced out of these repetitive sequences. And that aggregation is a potential contributor to the disease.

Girard: How can a repeated RNA sequence actually create clumps in the cell?

Jain: The disease-associated RNA are GC-rich.  They are of the type CAG in Huntington disease repeated many, many times. And Gs and Cs can form base pairs. So you can think if you have CAG, CAG, CAG, repeated several times, this can stick to itself, and if you made those repeats longer, it also has the propensity to stick to other RNA molecules. So the situation is fairly analogous to these CAG repeats acting like tiny pieces of tapes. The short piece of tape can fold onto itself. If you make the tape longer and longer, it becomes more prone to getting entangled. If you have many such long pieces of tape in a bowl or in your hand, they're going to form a meshwork or a network. So these RNA molecules, which have CAG repeats, are prone to forming these network-like structures. And in a polymer science, these networks, where a single molecule binds to many, many other partners, which are interconnected, this network has been described as a gel. And this is essentially what we think is going on. These RNA are forming gels inside the cell. And this gel is the aggregated state of the RNA potentially contributing to the pathology.

Girard: And that cellular pathology, for example in neurons, could lead to neurodegenerative diseases like Huntington’s. But then I thought Huntington’s disease is primarily caused by the aggregation of proteins produced from the repeated sequences.

Jain: The primary job of the messenger RNA is to guide the synthesis of proteins. The CAG codes for an amino acid, glutamine. And if you have CAG repeated many times, it will encode for several glutamines. And as a result, the cellular machinery will produce a polyglutamine-containing protein. Now it's known that polyglutamines themselves can be toxic to the cells. And in fact, one proposed disease mechanism in Huntington's disease is the formation of these polyglutamine aggregates. Now, over the last 10 or so years, it has become increasingly evident that aggregation of polyglutamine is perhaps not the entire story. There are several reasons to believe that. Number one, there are other defects which have been observed primarily in RNA processing in these disorders. Second, besides Huntington disease, which is caused by a CAG expansion in a gene, is a very similar disease known as Huntington disease-like 2. Now this disease has very similar clinical symptoms, like Huntington disease, but it is caused by completely different mutation in a functionally unrelated gene. The mutation here is a CTG expansion in the noncoding part of a different gene. So the CTG expansion would not encode for polyglutamine but instead make a different protein. However, this expansion is outside the canonical protein-coding regions. So in fact, it should not be producing any protein, and it still results in a very similar clinical manifestation. So that has been puzzling and it's not clear why these two different expansions resulting in different proteins will produce similar disease symptoms. And what we think is potentially going on is that besides protein aggregation, there can be parallel disease mechanism. The RNA itself could be aggregating, and it could be another driver for the disease. Up to what extent RNA aggregation contributes and to what disease it still remains to be explored.

Girard: Do you think the detrimental effects of RNA aggregation are actually limited to repeat expansion diseases like Huntington’s?

Jain: What we think is that these diseases may just be the tip of the iceberg. There may be many, many other diseases associated with the RNA aggregation, or it could be a broad phenomenon, which somehow has not garnered sufficient scientific attention so far. And now we're actively looking into what other RNA aggregation diseases can be there. How does the cell prevent aggregate formation under healthy conditions or normal physiological conditions?

Girard: Could these RNA aggregates play a role in normal cell function as well?

Jain: Indeed a corollary of our work is that RNA can assemble into higher order structures inside the cell. They can self-assemble by the virtue of forming based pairing interactions, and it is very tantalizing to think that cells may make use of this self assembly of RNA for their advantage, for instance, in egg cells or oocytes. The egg cell transmits certain RNA to the single-celled zygote, and the maternal RNA is stored in something called the “germ granule.” Similarly in neurons and the synapses, there are neuronal granules which held local protein production at the synapses. And similarly, there are about 10 to 20 other RNA-containing bodies, which have been observed in cells. And so far the attention in the literature or in the community has been on the proteins that are present in these bodies. What our work shows is that perhaps RNA could also be a driver for these bodies. The sequences of RNA in these bodies can play an important role in their assembly. A part of my lab is actively working on figuring those roles out.

Girard: It seems like we know a lot more about proteins than we do about RNA. Where is the field of RNA research compared to the field of protein research?

Jain: Over the last 20 or so years, we've gotten really good at handling proteins and, for instance, purifying proteins, obtaining their structures, tagging them with a fluorescent proteins and visualizing where they are. And that has a lead to a revolution in our understanding of cell biology. Proteins do perform a large number of cellular functions. The tools to study RNA have in certain senses lagged behind and there was a need to develop new technologies, and I think that'll help us appreciate this molecule more. It has already surprised us several, several times. For instance, the discovery of RNAi, or RNA interference, the discovery of splicing that these RNAs can catalyze their own reactions – the discovery of ribozymes – I think it still hold a few more surprises up its sleeve.

Girard: That was Ankur Jain, a Member of Whitehead Institute and an assistant professor of biology at MIT. You can learn more about Whitehead science on our website at And you can listen to other AudioHelicase episodes on SoundCloud and iTunes, as well as our website. For Whitehead Institute, I’m Lisa Girard. Thanks for listening.



Produced by Nicole Giese Rura

Original music by Chocolat Billy. CC BY-NC-ND 4.0


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Ankur Jain’s primary affiliation is with Whitehead Institute for Biomedical Research, where his laboratory is located and all his research is conducted. He is also an assistant professor of biology at Massachusetts Institute of Technology.

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