Podcasts

Dark Matter of the Genome, Pt. 1 (Base Pairs Episode 8)

Most of the genome is not genes, but another form of genetic information that has come to be known as the genome’s “dark matter.” In this episode, we explore how studying this unfamiliar territory could help scientists understand diseases such as ALS.

Could “genome” be a misnomer? The name implies that our genetic information is mainly genes, yet when the Human Genome Project was completed in 2003, it revealed that genes comprise a tiny minority. About 98 percent of the genome is something else—a kind of genomic dark matter.

We’re kicking off the second season of Base Pairs with a two-part series in which we explore this genomic dark matter. We start by talking with an astrophysicist-turned-genome-biologist, Assistant Professor Molly Hammell, about how the revelation that the genome is mostly not made of genes is similar to astrophysicists’ discovery that the universe is mostly not made of ordinary matter, and how she ended up studying a type of genomic dark matter called transposons. While they are not genes, transposons may play a role in a number of human diseases, including ALS, a focus of Hammell’s research. We also dig into the archives to hear from Barbara McClintock, the pioneering CSHL scientist who discovered transposons while studying corn way back in 1944.

Full transcript

BS: Welcome to season two of Base Pairs! We took a little break for the holidays, but we’re back with a two-part series for you all.

AA: And we need two episodes for this because—well, there’s a solid 98 percent of the genome that we haven’t even mentioned yet. And that’s what we want to tell you about.

BS: If you’re thinking, “That makes sense—there are thousands of genes, so of course they haven’t covered most of them yet,” you’re right. But that’s not what we mean.

AA: We’re talking about the part of the genome that’s not made up of genes at all: The “dark matter” of the genome. Because scientists are realizing that this strange, mostly uncharted genomic territory within all of our cells may lead us to new insights and possibly treatments for devastating diseases like Alzheimer’s, breast cancer, and Lou Gehrig’s disease—that’s the one we’re going focus on today. You may also know it as ALS.

BS: But we should back up a little—back to when scientists spelled out, or sequenced, the full human genome for the first time, an effort known as the Human Genome Project. They expected to find lots and lots of genes – the lowest estimates were around 100,000. Instead, what they found was a measly twenty thousand or so. And lots of what appeared to be genetic junk. Some scientists actually called it that, and kind of dismissed it.

AA: But they actually just didn’t understand what they were looking at.

MH: I think, with the sequencing and assembly of the human genome, we really changed our idea of what genes are, what we’re made of, and all of the things out there that we had no idea about—how little we actually knew about something we thought we knew a good deal about.

BS: That’s CSHL assistant professor Molly Hammell, and like other genome scientists, she no longer thinks about this mysterious majority of the genome as junk. Actually, a lot of scientists really object to the term “junk DNA” now.

AA: I can see why. In labs like Molly’s, the non-gene parts of the genome—which, again, make up about 98 percent of the genome—those are the focus, not some “junk” that gets in the way. She and other scientists have come to prefer looking at it as the “dark matter of the genome.” I talked to Molly to learn more about why that is.

BS: And she should know, after all, since before she began studying the genome, she worked in the field from which biologists borrowed the term “dark matter”: astrophysics.

MH: I used to go a couple of times a year up to a telescope, and I would be alone on a mountaintop, sleeping during the day, staying up all night, taking pictures of the sky.

AA: At first, when you hear Molly talk about what she studied as an astrophysicist, it sounds about as far away as you can get from genome biology.

MH: So I spent my nights on the mountaintop at the telescope, looking for the oldest clusters of galaxies, trying to figure out how they formed and if they could tell us how the universe was going to end—whether it was going to be this big bang where everything would come back to a point again or whether it would just expand forever into some cold dark world. And dark matter has a big role in that, in determining whether the universe is going to come back again or whether it’s going to expand forever.

BS: Wow, yeah, the scale of what she was thinking about as an astrophysicist is so big, but the entire genome is contained within each tiny cell in our body.

AA: Exactly. But when Molly starts talking about the discovery of dark matter, you can begin to see the analogy to her current work in biology.

MH: At the time when dark matter and now dark energy where discovered, we thought we had a good understanding of what the universe was made of, what our role in it was, and, you know, what the basic constituents of the universe were, right. And then these discoveries came about, showing us that not only were there these—all of these different types of particles that we had no idea about but also that they actually constitute more of our universe than the part we did know about.

BS: Ah, so, kind of like the way we look at the genome nowadays.

AA: Molly finished her Ph.D. in 2003—the same year that the Human Genome Project was completed. And as she was getting her professional scientific career started as an astrophysicist, biologists were learning all of this shocking stuff about the human genome.

MH: What we figured out was that most of the genome is actually not genes—not in the way we think about them. In fact, only 2 percent of the genome was genes and 98 percent of this was this other stuff, and we didn’t know what it did, if it exerted its influence on the genes that we have, and this was really similar. And I found this idea fascinating.

BS: And that was it? Then she just decided to leave that telescope on a mountaintop for a microscope at a lab bench? How many biologists do we know who have done research using the Hubble Space Telescope?!

AA: Yeah, pretty amazing.

BS: How was she able to make such a huge leap?

AA: Well, the dark matters of universe and of the genome have something else in common, too. Scientists can use a lot of the same mathematics to analyze data about them.

BS: I guess that makes sense when you think about how there are billions of stars in a galaxy, and billions of base pairs in a genome. Looking for patterns in such huge datasets like that is a skill that doesn’t change very much even when you switch from galaxies to genomes.

AA: Yeah, that’s a good way to think about it. Now, Molly’s research is focused on a particular kind of genomic dark matter known as transposons. In the human genome, most transposons are the remains of ancient viruses—they’re fossil viruses, essentially.

MH: So a transposon itself is very, very similar to, like, a viral sequence. So these viruses, they come in, they infect the cell, some of them actually insert themselves into our genome in order to take over the cell and start using it for the purpose of the virus. — So half our genomes—fifty percent—are these transposon sequences

BS: Fifty percent?! We’re half virus graveyard?

AA: Yes, fifty percent of our genome is basically an ancient graveyard for viruses and other transposons, millions of them. They’ve inserted themselves into the genomes of our ancestors, gotten passed on from generation to generation, and most of them are truly dead after all of this time—but there are a few zombies out there.

MH: 99 percent, almost all of them, are nonfunctional, because they’ve accumulated mutations or for some other reason they don’t work anymore, right? But there’s one percent that are still capable of being active and doing damage. And because that one percent is one percent of millions, it’s actually thousands of these things.

BS: Aren’t these the things that Barbara McClintock discovered? Back in the 1940s. I’ve been here at the Laboratory long enough now to know that about transposons.

AA: She did discover transposons, and so much more that we won’t have time to get into today. And she made the Nobel Prize-winning discovery of transposons during the 50 years she spent here at Cold Spring Harbor Laboratory, so she’s a particularly big name around campus. Part of what made this discovery so remarkable is that back when she was starting out in biology, next to nothing was known about the human genome.

BS: What’s next to nothing?

AA: I’ll let Barbara give you an idea. For reference, she was born in 1902.

BM: Well between, say 1875 and 1900, there was a burst, one of those wonderful periods in biology when so much was learned. We learned about the nucleus. I say we because I just am so enthused about what—I just feel that I’m in on it! We discovered chromosomes. We discovered how the chromosomes divided. We discovered the numbers of chromosomes. We discovered what happened with the chromosomes to make the gametes. We knew what happened when fertilization occurred.

BS: So this is really the basic, fundamental stuff in biology—what kids learn about in high school or maybe even middle school biology now.

AA: Pretty much. No one was even certain that genes were contained within chromosomes until McClintock proved it more than thirty years later. There was a lot she didn’t know, but she was incredibly astute in her observations of the corn plants that she bred.  She was still pretty modest about this discovery, though. Here’s what she said in an essay for the Nobel Prize committee. She wrote, “I doubt if this could have been anticipated before the 1944 experiment. It had to be discovered accidently.”

BS: What did she mean by that? I’ve seen the corn with all of the colorful, streaky kernels in a library exhibit here. I know that had something to do with it…

AA: Yes! We’ll put a photo of this corn cob up on our LabDish blog, but say a little more about what you remember that corn looking like.

BS: There are some kernels that are a dark bluish color, and some that are more of a red or a burgundy, and some that are more of a normal light yellow color. But then, some of those yellow kernels have these blue streaky splotches, and some have red ones.

AA: So those streaks and splotches are caused by transposons, which are also known as “jumping genes.” Even though they’re not exactly genes, it’s helpful to think of them this way. And I should mention that most of the transposons in corn and other plants didn’t come from viruses. They’re a bit different from human transposons in that way, but the important part is that transposons do this “jumping” thing, whether they’re in plants or in people.

BS: Ok, just to recap a little, most of the transposons in people are basically these fossils of viruses. They’re viruses that came along thousands or even millions of years ago, infected our ancestors by inserting their own viral genome into the human genome, and 99 percent basically died there in the human genome…

AA: …which leaves one percent of transposons that still have a little bit of life in them. Those are the jumping genes—the “zombies” we talked about earlier.

MH: One of the things that they can do is that they can cut themselves out of the particular piece of the genome they inserted into, and then insert themselves somewhere else. And if they do, they’ll probably break the gene next door to wherever they inserted, right?

AA: In the case of McClintock’s corn kernels, transposons were jumping around and “breaking” the genes for the colorful pigments that make the kernels look red or blue. By “breaking,” I mean interrupting and disturbing their function.  Since the transposons are breaking those genes kind of haphazardly, there are patches and streaks where the genes are left intact—they’re still able to produce the red or blue pigment. That’s the only way that McClintock could think of what would explain these bizarre patterns.

BS: So McClintock discovered this whole phenomenon of transposons because she was trying to explain this weird coloration in corn.

AA: Right. And this where the connection to diseases like ALS comes in. Basically, the idea is: What if some of the symptoms of ALS are caused by transposons that have been jumping around and breaking important genes? Molly started to really consider this idea after talking with a CSHL colleague named Josh Dubnau, who has recently moved to Stony Brook University. Josh was studying a protein called TDP-43.

MH: The thing about this protein was that we knew that if it wasn’t functional, that if this protein wasn’t working properly, that it actually causes specific a neurodegenerative disease called ALS, right? So one of the things that had happened is that Josh got a hint that TDP-43 might actually be binding to and regulating transposons.

BS: Wait, what is TDP-43 doing to transposons?

AA: It’s fighting the zombies. That dangerous one percent of transposons—the ones that are STILL able to jump around the genome—need to be kept under control. Our bodies actually devote a lot of resources to preventing a kind of zombie apocalypse from happening in our cells. And TDP-43 might be part of that effort.

MH: We think it’s possible that when it’s now not regulating these transposon sequences, those things could be escaping and wreaking havoc in our genomes. We started a collaboration together to look and see if this could be possible—that this ALS-related protein might also be moonlighting in regulating transposons, and that possibly that could be related to the disease.

BS: What causes ALS, anyway?

AA: That’s the thing. No one really knows yet exactly how ALS starts in the very beginning. I also asked this question when I was talking to Molly, and she told me about the bits and pieces scientists have learned from studying patients with the disease.

MH: We do know that patients develop these clumps of TDP-43. We know that if TDP-43 doesn’t function in a mouse model of this disease (AA: those are mice are genetically engineered such they can’t produce working TDP-43) that the mice will get motor neuron defects and neurodegenerative disease just like the patients do. When the neurons start to lose function because of TDP-43 not doing its job, then the muscles themselves waste away because they don’t get used. It’s a really fast-progressing disease. The time from symptom onset to sort of the end stage of the disease is, in general, about two years. It’s really—it’s quite sad.

BS: What an awful disease. It takes away a person’s ability to walk, talk, breathe, swallow—anything that we voluntarily control with our muscles. I met someone who lost her mother to the disease over the summer. She was actually a grad student here, named Lisa Krug, and she worked with Molly and Josh to figure out whether transposons might play a role in this disease that took her mother. She wrote about her experiences and research for our LabDish blog.

AA: Molly told me that since she started doing this research, a lot of people she already knew started telling her about loved ones they had lost to ALS. Suddenly, it felt like ALS was everywhere—it was just hard to realize before because these people are prisoners of their bodies. Leaving the house is incredibly difficult, even with help, and so ALS patients become kind of invisible.

MH: We think of this as kind of rare but I think this is much more common than we realize and that people are finally really paying attention to ALS and realizing that we really need more research to understand it better so that we can have a hope of some kind of treatment for these patients, which right now, there’s nothing, there’s nothing that can be done—it’s awful.

BS: The Ice Bucket Challenge that happened a few years ago definitely helped a lot with awareness. Remember that?

(CLIPS FROM ICE BUCKET CHALLENGE YOUTUBE VIDEOS)

AA: The Ice Bucket Challenge really did raise the profile of ALS. And, as silly as it seems, it helped research a lot, too. The campaign raised over $115 million for ALS research and development of new treatments, and may help support Molly’s future research. Like she said, right now there are no treatments for ALS. Researchers have already looked through the genes of ALS patients and so far have discovered no obvious avenues for treatment. That’s what makes it so exciting that this largely unknown world of transposons might be involved in ALS. There’s hope that this new territory will offer some solutions that would have otherwise seemed ridiculous—like treating ALS with antivirals.

BS: You mean the kinds of drugs that we’re given to treat, say, the flu?

AA: Yes. Because, remember, many transposons were once viruses. That dangerous one percent of transposons that can still jump around the genome, they’re acting as if they were still normal viruses.

MH: They haven’t figured out that they’re not really viruses any more, they’re now these pro-viral sequences that exist in our genome, but they’re still trying to act like they are, right? And if we can block them, if we can slow them down, and if that has an impact on patients’ lives, that would be fantastic. We have an idea about how this could lead to a potential therapy, in the sense that some of these transposon sequences are still similar enough to viral sequences that the antiviral drugs we have are actually effective in slowing them down and inhibiting their activity.

BS: That’s amazing! That would mean that if someone has non-functional TDP-43, leaving transposons to run amok as Molly and her team suspect, then it may still be possible to stop those transposons from causing ALS by simply giving them an antiviral drug.

AA: That’s the idea!

BS: How close is this idea to becoming a treatment that’s ready to give to patients?

AA: It’s a work in progress, for sure. This is still such a new idea, and so little is known about how transposons effect our health in general, much less in the specific context of ALS. Right now, Molly and her team are working on building up the knowledge needed to take that next step of developing a new treatment. One way that they’re doing this is by looking at the genetic sequences of people with and without ALS.

MH:  We get samples from patients with ALS disease and samples from patients who definitely don’t have any kind of neurodegenerative disease, and we’re usually just cross-comparing what’s different, right. Do we see the transposons coming up only in the patients and never in the controls?

BS: Ah, because if the transposons are only active in the ALS patients, that’s a clue that they could be involved in causing the disease.

AA: Right. Molly uses algorithms and other mathematical tricks from her astrophysics days to uncover those clues within vast datasets filled with genetic information. Once she finds a solid clue, the next step is to find out whether there’s any causation behind that correlation by doing experiments on cells very similar to neurons that can be grown in a dish. That’s where they are for the moment: uncovering little clues about how TDP-43 might work to keep transposons under control, and how symptoms of ALS emerge when that control system goes haywire.

BS: This really shows the importance of sharing knowledge between different scientific disciplines—that the mathematics that astrophysicists and computer scientists use can help biologists explore a new avenue for treatment of a deadly disease. And we know about transposons in the first place because of work done in plants!

AA: True! Barbara McClintock in particular always liked to remind people of the contributions that plant science has made to biology.

BM: The plants are just as significant as animals when it comes to genomes, and the operation of the genomes—the operation of the genome is just like that in animals. The plants really offer very special conditions for studying genetic phenomena.

AA: When McClintock first discovered transposons in 1944, relatively few took notice. She didn’t even get her Nobel Prize until nearly 40 years later, in 1983. But as knowledge and technology advanced, the importance of her discovery became more apparent. And that realization is still going on today, now that we can easily sequence the genome and the many transposons within it.

MH: You know, at the time when Barbara McClintock was working, she was really inferring this huge, vast existence of these transposon sequences without a picture of what the genome itself actually looked like, right. Now that we have the tools to look at these things, we can really go out and see how many human diseases could be potentially related to these things becoming unregulated and escaping. This is the tip of the iceberg.

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Extras for Episode 8:

These corn specimens helped Barbara McClintock make her Nobel Prize-winning discovery of transposons. They are now kept in CSHL’s library.

After her mother was diagnosed with ALS, Lisa Krug decided to devote her Ph.D. work at the Watson School of Biological Sciences to studies of this disease. She worked closely with Molly Hammell, who we hear from in this episode, to better understand how transposon activity might contribute to ALS. She wrote about her experiences with ALS, in the lab and at home, for LabDish last summer.

Molly Hammell participated in a huge group “Ice Bucket Challenge” (she’s somewhere in the “E”) held by ALS Ride for Life, an inspiring organization started by an ALS patient who travels for miles in his motorized wheelchair to raise funds for research. Some of those funds have gone toward supporting the research in Hammell’s lab.

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