Old and slow isn’t always the winning combo for critical genes

New work upends paradigm that young, rapidly evolving genes can’t be essential; highlights importance of 'junk' DNA
Close-up of a man's face in front of brightly lit DNA sequencing data.
Close-up of a man's face in front of brightly lit DNA sequencing data. Getty Images stock photo

It’s generally thought that the more critical a gene is to cellular function, the more likely it is be an “old” part of DNA and relatively unchanged by evolution. But new work from scientists at Fred Hutchinson Cancer Research Center, published November 10 in the journal eLife, upends that belief by demonstrating that some essential genes are actually “young” and evolving rapidly.

“The big result from the paper is that [the strict dogma of] slow evolution and conservation as a proxy for functional importance is probably not true,” said Hutch evolutionary biologist and senior author Dr. Harmit Malik.

The findings also underscore the importance of repetitive stretches of chromosomes that mostly lack genes and were once dismissed as mere “junk” DNA. These areas, which are known collectively with their DNA packaging proteins as heterochromatin, help orchestrate critical cellular processes and can act as a cell’s “master puppeteer,” Malik said. The young and rapidly evolving genes that Malik and first author Dr. Bhavatharini Kasinathan identified perform their essential functions within heterochromatin, which itself changes dramatically between species.

The researchers hope that these insights into how genes rapidly acquire essentiality could help guide scientists looking to develop new therapies that target cancer cells while sparing normal cells, he said.

The paradigm

Malik explains the paradigm of old, unchanging and essential genes by comparing the cell to a mechanical Swiss watch. The design of a watch’s inner workings, which control its essential function — to tell time — haven’t changed in hundreds of years.

If you were to break any one component, you're likely to break the entire mechanism,” he said.

It was thought that essential cellular functions worked similarly to a Swiss watch’s innards, so indispensable genes were unlikely to change much over long stretches of time, even millions of years. Such genes are known to evolutionary biologists as “highly conserved.” Non-essential genes, the idea went, are more like the watch’s face: free to morph dramatically because their changes don’t affect the cell’s essential functions. The upshot of the paradigm is that, if a gene is young (evolutionarily speaking) and rapidly evolving, it was considered unlikely to encode a protein that carries out a necessary cellular function.

A Sikh man in a turban
Dr. Harmit Malik studies arms races that drive evolution. Photo by Robert Hood / Fred Hutch News Service

Findings from other scientists had hinted that the paradigm was not as solidly founded as previously thought — but the idea that essential genes may not always be highly conserved remained controversial. These studies relied on wide-scale surveys of genes’ essentiality and age. To tackle the question a different way, Kasinathan, while an M.D./Ph.D. student in Malik’s lab, decided to look at a group of related genes in more detail.

Working with Malik Lab technician Hannah McConnell and staff scientist Dr. Janet Young, and University of California, Berkeley collaborators Drs. Serafin Colmenares and Gary Karpen, Kasinathan chose to look at the largest class of transcription factors (proteins that turn other genes on) in insects, the ZAD-ZNF transcription factors.

“We knew from other people’s work that these transcription factors do not appear to be the same across insect species,” Malik said. “They appear to be quite variable. She wanted to understand the basis for this variability.”

Young genes can encode essential functions

Fruit flies in the genus Drosophila are commonly used by geneticists as model organisms used to help them understand the cellular functions encoded by specific genes. Genetic surveys of the ZAD-ZNF transcription factors that Kasinathan examined showed that some are young, having evolved recently, while others are old, and have changed little over time.

“She asked, are the genes that are more universally conserved in Drosophila more likely to encode an essential function?” Malik said.

Essential, in this case, meant required for fertility or embryonic viability. Kasinathan genetically manipulated each ZAD-ZNF transcription factor gene to prevent fly larvae from producing it, then looked at whether this prevented fly larvae from developing or adult flies from producing offspring.

“She found that there was no difference,” Malik said. “If you look at the young genes or the old genes, they were both just as likely to be encoding essential functions.”

Kasinathan also approached the question from a slightly different angle, comparing the essentiality of rapidly evolving and slowly evolving genes. Rather than seeing that slowly evolving genes were more often essential, she found the opposite: In D. melanogaster, the fruit fly species most often used in the lab, rapidly evolving ZAD-ZNF genes were more likely to encode essential functions than their slowly evolving counterparts.

Upending long-held dogmas about gene essentiality not only reveals novel biological insights, but also opens new avenues of research that could exploit the unique evolutionary trajectories of cancer genomes, Malik said.

This means that Kasinathan’s findings may have implications for human health. Cancer is largely driven by changes to our DNA, and DNA within tumors rapidly evolves, helping to spur tumor growth, progression and resistance to therapy.

“We already know that cancer breaks many of the rules of essentiality,” Malik said. “Have we really considered the possibility that, just like in other species — which is what a cancer cell is, effectively — maybe there are genes that are absolutely not essential in the human genome, but actually essential to the cancer genome? And some of these genes might not even exist [in normal cells]. They might be formed by the process of innovation that exists in the cancer genome.”

'Junk' DNA drives genetic innovation

Having demonstrated that certain genes flouted the prevailing dogma left Kasinathan with a big question: how and why did they do it?

“We said, ‘Okay, let's look at the subset of genes that break this dogma, that are both rapidly evolving and yet essential,’ ” Malik said.

Kasinathan chose a little-studied ZAD-ZNF gene she dubbed Nicknack, after a villain from a James Bond film. (The name was inspired by a neighboring ZAD-ZNF gene, Oddjob, also named after a Bond villain.) Nicknack is one of the most rapidly evolving genes in D. melanogaster.

First, Kasinathan used genetic manipulations to confirm that Nicknack is essential for fruit fly larval development.

As a first step to understanding Nicknack’s function, she looked at where Nicknack spent most of its time within the cell. Here again, Nicknack upended expectations.

Despite the fact that transcription factors’ primary function is to turn genes on, Kasinathan found that the Nicknack protein clustered in regions known as heterochromatin. These gene-poor regions of DNA are tightly bundled with DNA packaging proteins. Originally dismissed as mere “junk” DNA because it contains so few genes, heterochromatin is rich in repetitive stretches and transposable elements that can move around within and between chromosomes. This type of DNA is also found in a critical area of the chromosome, called the centromere, where the molecular pulleys that separate chromosomes during cell division attach.

Heterochromatin is the “ugly stepsister” of genetic analysis, Malik said, as scientists have mostly focused their studies on the areas of DNA where genes are clustered and loosely packed to facilitate expression, known as euchromatin.

But that’s proven to be shortsighted — heterochromatin is now known to influence many cellular functions. It can regulate whether genes in other areas are turned on and off, and some of the rare genes located in heterochromatin are indispensable to the cell’s well-being. It also varies widely between species, which suggested to Kasinathan and Malik that the rapid evolution of ZAD-ZNF transcription factors like Nicknack may be driven by their need to interact with fast-evolving components of heterochromatin.

This idea was supported by experiments in which Kasinathan swapped in Nicknack from a different fruit fly species (D. simulans, whose heterochromatin is separated from D. melanogaster’s by 2.5 million years of evolution). While female melanogaster flies with simulans Nicknack appear to be normal, melanogaster males flies with simulans Nicknack are inviable.

Malik and Kasinathan believe that because simulans Nicknack hasn’t evolved to interact optimally with melanogaster heterochromatin, the large amount of heterochromatin on the Y-chromosome overwhelms it and prevents it from carrying out all of its essential functions.

“Whereas in females, there is actually not that much difference in the amount of heterochromatin, so you're still able to rescue some sort of functionality [with simulans Nicknack],” Malik said. “This drives home the idea that differences in heterochromatin are requiring this innovation just to maintain life.”

An arms race within the cell

To explain why genetic innovation and rapid evolution may go hand-in-hand with essentiality, Malik draws inspiration from another area of study: the genetic arms race between pathogens (like viruses) and their hosts (like us).

Now, host-pathogen interactions are this perfect example of where you need innovation. Because you need to keep pace with the pathogens. But [anti-viral genes] are not essential except in the face of an infection,” Malik said. “But what if, what you're in an arms race with, is actually part of the same genome?

That appears to be the case with Nicknack and the heterochromatin components with which it interacts.

Unlike in euchromatin, where the gene environment stays more or less stable over billions of years, in heterochromatin, the gene is there, but its neighborhood constantly shuffles over,” Malik noted. Nearby mobile DNA elements come and go.

The rapid innovation of transcription factors like Nicknack reflect these changes as well as some function of the heterochromatin, Malik believes. It’s not yet clear whether that function relates to the essential genes within heterochromatin, or the mobility of many DNA elements found in it, Malik said.

Either you need this constantly innovating signpost that tells you where all the essential genes that are buried in heterochromatin are, or you need a way to suppress all of these bad actors [like transposable elements] that are jumping into heterochromatin that are going to control the rest of the genome,” he said. “It’s an important clue that, in fact, evolutionary innovation of these internal conflicts, that are waged by heterochromatin, are really important for essentiality.”

The work was supported by the National Institutes of Health and the Howard Hughes Medical Institute.

Sabrina Richards, a staff writer at Fred Hutchinson Cancer Center, has written about scientific research and the environment for The Scientist and OnEarth Magazine. She has a PhD in immunology from the University of Washington, an MA in journalism and an advanced certificate from the Science, Health and Environmental Reporting Program at New York University. Reach her at srichar2@fredhutch.org.

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