So-Called Junk DNA – Genetic “Dark Matter” – Is Actually Critical to Survival in Mammals

Knocking out transposon promoter leads to pup death in mice; similar promoters found in many mammals.

Nearly half of our DNA has been written off as junk, the discards of evolution: sidelined or broken genes, viruses that got stuck in our genome and were dismembered or silenced, none of it relevant to the human organism or human evolution.

But research over the last decade has shown that some of this genetic “dark matter” does have a function, primarily in regulating the expression of host genes — a mere 2% of our total genome — that code for proteins. Biologists continue to debate, however, whether these regulatory sequences of DNA play essential or detrimental roles in the body or are merely incidental, an accident that the organism can live without.

A new study led by researchers at University of California, Berkeley, and Washington University explored the function of one component of this junk DNA, transposons, which are selfish DNA sequences able to invade their host genome. The study shows that at least one family of transposons — ancient viruses that have invaded our genome by the millions — plays a critical role in viability in the mouse, and perhaps in all mammals. When the researchers knocked out a specific transposon in mice, half their mouse pups died before birth.

This is the first example of a piece of “junk DNA” being critical to survival in mammals.

Viral elements called transposons have invaded mammalian genomes for millions of years and currently make up nearly half the DNA in the genomes of all living mammals. The image depicts species-specific transposon integrations as unique events in the evolutionary history of each species. Credit: UC Berkeley image by Kerry Lin

In mice, this transposon regulates the proliferation of cells in the early fertilized embryo and the timing of implantation in the mother’s uterus. The researchers looked in seven other mammalian species, including humans, and also found virus-derived regulatory elements linked to cell proliferation and timing of embryo implantation, suggesting that ancient viral DNA has been domesticated independently to play a crucial role in early embryonic development in all mammals.

According to senior author Lin He, UC Berkeley professor of molecular and cell biology, the findings highlight an oft-ignored driver of evolution: viruses that integrate into our genome and get repurposed as regulators of host genes, opening up evolutionary options not available before.

“The mouse and humans share 99% of their protein coding genes in their genomes — we are very similar with each other,” He said. “So, what constitutes the differences between mice and humans? One of the major differences is gene regulation — mice and humans have the same genes, but they can be regulated differently. Transposons have the capacity to generate a lot of gene regulatory diversity and could help us to understand species-specific differences in the world.”

Colleague and co-senior author Ting Wang, the Sanford and Karen Loewentheil Distinguished Professor of Medicine in the Department of Genetics at the Washington University School of Medicine in St. Louis, Missouri, agrees.

“The real significance of this story is it tells us how evolution works in the most unexpected manner possible,” Wang said. “Transposons were long considered useless genetic material, but they make up such a big portion of the mammalian genome. A lot of interesting studies illustrate that transposons are a driving force of human genome evolution. Yet, this is the first example that I know of where deletion of a piece of junk DNA leads to a lethal phenotype, demonstrating that the function of specific transposons can be essential.”

The finding could have implications for human infertility. According to first author Andrew Modzelewski, a UC Berkeley postdoctoral fellow, nearly half of all miscarriages in humans are undiagnosed or don’t have a clear genetic component. Could transposons like this be involved?

“If 50% of our genome is non-coding or repetitive — this dark matter — it is very tempting to ask the question whether or not human reproduction and the causes of human infertility can be explained by junk DNA sequences,” he said.

Embryo implantation

He, the Thomas and Stacey Siebel Distinguished Chair Professor at UC Berkeley, studies the 98% or more of our genome that does not code for proteins. For most of He’s career, she has focused on microRNAs and longer pieces of non-coding RNAs, both of which are potent gene regulators. Five years ago, however, her team accidentally discovered a microRNA regulator for a transposon family called MERVL (mouse endogenous retroviral elements) that was involved in cell fate determination of early mouse embryos. The unexpected abundance of transposon transcription in mouse embryos led He’s team to investigate the developmental functions of transposons, which have taken up residence in the genomes of nearly every organism on Earth.

In a paper appearing this week in the journal Cell, He and her team identify the key regulatory DNA involved: a piece of a transposon — a viral promoter — that has been repurposed as a promoter for a mouse gene that produces a protein involved in cell proliferation in the developing embryo and in the timing of implantation of the embryo. A promoter is a short DNA sequence that is needed upstream of a gene in order for the gene to be transcribed and expressed.

Wild mice use this transposon promoter, called MT2B2, to initiate transcription of the gene Cdk2ap1 specifically in early embryos to produce a short protein “isoform” that increases cell proliferation in the fertilized embryo and speeds its implantation in the uterus. Using CRISPR-EZ, a simple and inexpensive technique that Modzelewski and He developed several years ago, they disabled the MT2B2 promoter and found that mice instead expressed the Cdk2ap1 gene from its default promoter as a longer form of the protein, a long isoform, that had the opposite effect: decreased cell proliferation and delayed implantation.

The result of this knockout was the death at birth of about half the pups.

Modzelewski said that the short form of the protein appears to make the many embryos of the mouse implant with a regular spacing within the uterus, preventing crowding. When the promoter is knocked out so that the long form is present only, the embryos implant seemingly randomly, some of them over the cervix, which blocks exit of the fully developed fetus and sometimes kills the mother during the birthing process.

They found that within a 24-hour period prior to embryo implantation, the MT2B2 promoter ramps up expression of the Cdk2ap1 gene so much that the short form of the protein makes up 95% of the two isoforms present in embryos. The long isoform is normally produced later in gestation when the default promoter upstream of the Cdk2ap1 gene becomes active.

Working with Wanqing Shao, co-first author of the study and a postdoctoral fellow in Wang’s group at Washington University, the team searched through published data on preimplantation embryos for eight mammalian species — human, rhesus monkey, marmoset, mouse, goat, cow, pig and opossum — to see whether transposons are turned on briefly before implantation in other species. These online data came from a technique called single cell RNA sequencing, or scRNA-seq, which records the levels of messenger RNA in single cells, an indication of which genes are turned on and transcribed. In all cases, they had to retrieve the data on non-coding DNA because it is typically removed before analysis, with the presumption that it’s unimportant.

While transposons are generally specific to individual species — humans and mice, for example, have largely different sets — the researchers found that different species-specific transposon families were turned on briefly before implantation in all eight mammals, including the opossum, the only mammal in the group that does not employ a placenta to implant embryos in the uterus.

“What’s amazing is that different species have largely different transposons that are expressed in preimplantation embryos, but the global expression profiles of these transposons are nearly identical among all the mammalian species,” He said.

Colleague and co-senior author Davide Risso, a former UC Berkeley postdoctoral fellow and now associate professor of statistics at the University of Padua in Italy, developed a method for linking specific transposons to preimplantation genes so as to weed out the thousands of copies of related transposons that exist in the genome. This method is crucial to identifying individual transposon elements with important gene regulatory activity. 

“It’s interesting to note that the data that we used were mostly based on the previous sequencing technology, called SMART-seq, which covers the full sequence of the RNA molecules. The current popular technique, 10x genomics technology, would not have shown us the different levels of protein isoforms. They’re blind to them,” Risso said.

Viruses are evolutionary reservoir

The researchers found that in nearly all of the eight mammalian species, both short and long Cdk2ap1 isoforms occur, but are switched on at different times and in different proportions that correlate with whether embryos implant early, as in mice, or late, as in cows and pigs. Thus, at the protein level, both the short and long isoforms appear conserved, but their expression patterns are species-specific.

“If you have a lot of the short Cdk2ap1 isoform, like mice, you implant very early, while in species like the cow and pig, which have none to very little of the short isoform, it’s up to two weeks or longer for implantation,” Modzelewski said.

Wang suspects that the promoter that generates the long form of the protein could be the mouse’s original promoter, but that a virus that integrated into the genome long ago was later adapted as a regulatory element to produce the shorter form and the opposite effect.

“So, what happened here is a rodent-specific virus came in, and then somehow the host decided, ‘OK, I’m going to use you as my promoter to express this shorter Cdk2ap1 isoform.’ We see the redundancy that’s built into the system, where we can take advantage of whatever nature throws at us and make it useful,” he said. “And then, this new promoter happened to be stronger than the old promoter. I think this fundamentally changed the phenotype of rodents; maybe that’s what makes them grow faster — a gift of having a shorter pre-implantation time. So, they probably gained some fitness benefit from this virus.”

“Whatever you look at in biology, you’re going to see transposons being used, simply because there are just so many sequences,” Wang added. “They essentially provide an evolutionary reservoir for selection to act upon.”

Reference: “A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development” by Andrew J. Modzelewski, Wanqing Shao, Jingqi Chen, Angus Lee, Xin Qi, Mackenzie Noon, Kristy Tjokro, Gabriele Sales, Anne Biton, Aparna Anand, Terence P. Speed, Zhenyu Xuan, Ting Wang, Davide Risso and Lin He, 12 October 2021, Cell.
DOI: 10.1016/j.cell.2021.09.021

Other co-authors of the study are Jingqi Chen, Angus Lee, Xin Qi, Mackenzie Noon, Kristy Tjokro and Anne Biton of UC Berkeley; Terry Speed of the Walter and Eliza Hall Institute of Medical Research in Melbourne, Australia; Aparna Anand of Washington University and Gabriele Sales of the University of Padua. The work was supported primarily by the Howard Hughes Medical Institute faculty scholar award and the National Institutes of Health.

Developmental BiologyDNAEvolutionGeneticsPopularUC Berkeley
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  • Alex

    So… Lemme get this straight: anything genetically active on the DNA level is a virus. JUNK DNA is a lot like a “BLACK” HOLE or (((DARRRK MATTER))). Don’t know what you are “truely” seeing so… invent a causal/effective link to a specialized sequence of DNA and a pathogen. So… Maybe one can conclude that we are 80+% viral “slime”: Much in common with common pond scum: Spirogyra (and not the Jazz/Fusion Group).
    If it works for you… BUT MAYBE… just maybe it is Genetic Memory: stored “solutions” to All Sorts (not the confection) of challenges, both physical and Intellectual, which were acquired in an evolutionary ascent: a kind-of Handbook for Survival, or a Symphonic Composition on the Theme(s) and Memes of the Living Quest. I would prefer to think of myself in those terms rather than a Publisher’s Clearinghouse of VIRAL DNA. It MIGHT not be Science but it works just as well as Speculation on FORM and FUNCTION which might just a TAD jaundiced i.e.: a dis-eased vector(hopefully eventually disabused) of and by its perceptions of life as a flawed MECHANISM.
    🙈

  • Fee

    Alex I try not to absorb value judgements on my genome based on the origins of its variations, viral or not. We did come from some primordial ocean scums millions of years ago anyways.. but I do think of the junk DNA as a sort of historical library of perhaps peace treaties or war stories between our immune system and the viruses that have besieged them over the eons of life. Perhaps it is like a museum and an archive or sorts, the spoils of war are that our immune systems may hoard what useful DNA and RNA viruses attacked us with, (such as when they are figuring out how to form antibodies. There must be some RNA transcribing and new protein coding or combining going on in our cells’ armory.) , (useful for normal human life, not necessarily super mutant powers lol) and we repurpose it if evolution finds it useful or beneficial to do so in the further generations. The viruses sort of get to live on inside us, but it’s like when an invading army is conquered by the native defenses, and we steal their own weapons and technology or battle choreography tactics for future trials.

  • Babu G. Ranganathan

    Babu G. Ranganathan*
    (B.A. Bible/Biology)

    THE NATURAL LIMITS TO EVOLUTION

    ONLY LIMITED EVOLUTION (micro-evolution or evolution within biological “kinds”) is genetically possible (such as the varieties of dogs, cats, horses, cows, etc.), but not macro-evolution, or evolution across biological “kinds,” (such as from sea sponge to human). All real evolution in nature is simply the expression, over time, of already existing genes or variations of already existing genes. For example, we have breeds of dogs today that we didn’t have a few hundred years ago. The genes for these breeds had always existed in the dog population but never had opportunity before to be expressed. Only limited evolution, variations of already existing genes and traits, is possible.

    The genes (chemical instructions or code) for a trait must first exist or otherwise the trait cannot come into existence. Genes instruct the body to build our tissues and organs. Nature is mindless and has no ability to design and program entirely new genes for entirely new traits.

    Evolutionists believe that, if given millions of years, accidents in the genetic code of species caused by the environment will generate entirely new code making evolution possible from one type of life to another. It’s much like believing that by randomly changing the sequence of letters in a romance novel, over millions of years, can turn the novel into a book on astronomy! Not to worry. We’ll address the issue of “Junk DNA” in a moment.

    WHAT ABOUT NATURAL SELECTION? Natural selection doesn’t produce biological traits or variations. It can only “select” from biological variations that are possible and which have survival value.

    HOW COULD SPECIES HAVE SURVIVED if their vital tissues, organs, reproductive systems, etc. were still evolving? A partially evolved trait or organ that is not complete and fully integrated and functioning from the start would be a liability to a species, not a survival asset. Plants and animals in the process of macro-evolution would be unfit for survival. For example, “if a leg of a reptile were to evolve (over supposedly millions of years) into a wing of a bird, it would become a bad leg long before it became a good wing” (Dr. Walt Brown, scientist and creationist). Survival of the fittest actually would have prevented evolution across biological kinds!

    NEW SPECIES BUT NOT NEW DNA: Although it’s been observed that new species have come into existence, they don’t carry any new genes. They’ve become new species only because they can’t be crossed back with the original parent stock for various biological reasons. A biological “kind” allows for new species but not new genes. Nature has no ability to invent new genes for new traits. Only limited variations and adaptations are possible in nature, and all strictly within a biological “kind” (i.e. varieties of dogs, cats, etc.).

    Dr. Randy J. Guliuzza’s extensive research points to a better explanation than natural selection for variation and adaptation in nature. Dr. Guliuzza explains that species have pre-engineered mechanisms that enable organisms to continuously track and respond to environmental changes with system elements that correspond to human-designed tracking systems. This model is called CET (continuous environmental tracking). His research strongly indicates that living things have been pre-engineered to produce the right adaptations and changes required to live in changing environments. It’s much like a car that’s been pre-engineered so that the head lights turn on automatically when day changes to night.

    What about genetic and biological similarities between species? Genetic information, like other forms of information, cannot happen by chance, so it is more logical to believe that genetic and biological similarities between all forms of life are due to a common Designer who designed similar functions for similar purposes. It doesn’t mean all forms of life are biologically related! Only genetic similarities within a natural species proves relationship because it’s only within a natural species that members can interbreed and reproduce.

    Many people have wrong ideas of how evolution is supposed to work. Physical traits and characteristics are determined and passed on by genes – not by what happens to our body parts. For example, if a woman were to lose her finger this wouldn’t affect how many fingers her baby will have. Changing the color and texture of your hair will not affect the color and texture of your children’s hair. So, even if an ape or ape-like creature’s muscles and bones changed so that it could walk upright it still would not be able to pass on this trait to its offspring. Only changes or mutations that occur in the genetic code of reproductive cells (i.e. sperm and egg) can be passed on to offspring.

    What about the new science of epigenetics? Epigenetics involves inheritable factors which can turn already-existing genes on, but epigenetics doesn’t create new genes.

    Most biological variations are from new combinations of already existing genes, not mutations. Mutations are accidents in the genetic code caused by nature (i.e. environmental radiation), are mostly harmful, and have no capability of producing greater complexity in the code. Even if a good accident occurred, for every good one there would be hundreds of harmful ones with the net result, over time, being harmful, even lethal, to the species. Even if a single mutation is not immediately harmful, the accumulation of mutations over time will be harmful to the species resulting in extinction. At very best, mutations only produce further variations within a natural species.

    All species of plants and animals in the fossil record are found complete, fully formed, and fully functional. This is powerful evidence that all species came into existence as complete and fully formed from the beginning. This is only possible by creation.

    God began with a perfect and harmonious creation. Even all the animals were vegetarian (Genesis 1:30) in the beginning and did not struggle for survival nor kill and devour each other. Macro-evolutionary theory does not begin with a perfect and harmonious creation as the Bible states. The Bible and macro-evolutionary theory cannot both be true.

    All the fossils that have been used to support human evolution have been found to be either hoaxes, non-human, or human, but not non-human and human (i.e. Neanderthal Man was discovered later to be fully human).

    There has never been unanimous agreement among evolutionary scientists on ANY fossil evidence that has been used to support human evolution over the many years, Including LUCY.

    The actual similarity between ape and human DNA is between 70-87% not 99.8% as commonly believed. The original research stating 99.8% similarity was based on ignoring contradicting evidence. Only a certain segment of DNA between apes and humans was compared, not the entire DNA genome.

    Also, so-called “Junk DNA” isn’t junk. Although these “non-coding” segments of DNA don’t code for proteins, they have recently been found to be vital in regulating gene expression (i.e. when, where, and how genes are expressed, so they’re not “junk”). Also, there is evidence that, in certain situations, they can code for protein.

    ARE FOSSILS REALLY MILLIONS OF YEARS OLD? (Internet article by author)

    Visit my latest Internet site: THE SCIENCE SUPPORTING CREATION (This site answers many arguments, both old and new, that have been used by evolutionists to support their theory)

    Author of popular Internet article, TRADITIONAL DOCTRINE OF HELL EVOLVED FROM GREEK ROOTS

    *I have given successful lectures (with question and answer period afterwards) defending creation before evolutionist science faculty and students at various colleges and universities. I’ve been privileged to be recognized in the 24th edition of Marquis “Who’s Who in The East” for my writings on religion and science.

  • Stark

    So just still figuring out how it even goes together and here we are editing it..

  • Jeffrey Sussman, MD

    This is all very fascinating. So, maybe we need to think of viruses as the plasmids of eukaryotic cells. An evolutionary method of exchanging or modifying DNA and survival solutions between a species or sometimes a related species. It’s funny, as a physician I always thought of viruses as some external invader, a vector of illness and even death, an entity unto themselves. But really, if I am interpreting this article correctly, then viral infection or pandemics may be a method of mass communication between eukaryotic organisms to exchange information. Sometimes with good results sometimes not….

  • Deborah Wheeler Morales

    Duh! The ‘junk’ DNA perspective has been ‘de-junked,’ as in debunked, for quite a while. They’re saying 98% at least and most likely 100% of our DNA is NOT JUNK. Also, I note you mentioned the percentages of protein building have been greatly reduced from a previous value of 12 to 15% and thus the remainder being relegated to junk by a simple subtraction approach as opposed to the/an actual legitimate process for that information. I have learned to put those approaches under outline portion dedicated to wishful thinking/agenized make believe.

    DNA is no longer fit to be categorized by your Granny’s approach anymore…………… and the BIG present under the tree that I am so excited about is epigenetics!!1

  • Wil

    This really isn’t showing us anything new. I have always considered that what is important isn’t only coding sequences, but ALL genetic sequences that show high conservation across many generations, particularly if the degree of conservation is higher than natural mutation rates would produce. This would indicate a selective pressure against changes, which indicates to me that these sequences probably have some function, even if it remains undetermined.

    Promoters, however, are old news; at least 20 years old. It’s kind of strange to see this discussed as though it were a recent discovery.

  • Kiesha

    Junk DNA is just a part of evolution. It will be replaced in generations if no one will disturbe it.