"So-called junk DNA plays critical role in mammalian development"

[thoughtful (Valerie (non-scientist))]

Ok, so this was another fascinating article about transposons, my favorite “junk DNA.” After the thread I most recently started, now I’m very curious how you feel about what these scientists said about “junk DNA.”

But I’m also very interested in the science too if you have any comments about that!

So-called junk DNA plays critical role in mammalian development

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.

https://www.cell.com/cell/fulltext/S0092-8674(21)01104-1?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867421011041%3Fshowall%3Dtrue

Retrotransposons mediate gene regulation in important developmental and pathological processes. Here, we characterized the transient retrotransposon induction during preimplantation development of eight mammals. Induced retrotransposons exhibit similar preimplantation profiles across species, conferring gene regulatory activities, particularly through long terminal repeat (LTR) retrotransposon promoters. A mouse-specific MT2B2 retrotransposon promoter generates an N-terminally truncated Cdk2ap1 ΔN that peaks in preimplantation embryos and promotes proliferation. In contrast, the canonical Cdk2ap1 peaks in mid-gestation and represses cell proliferation. This MT2B2 promoter, whose deletion abolishes Cdk2ap1 ΔN production, reduces cell proliferation and impairs embryo implantation, is developmentally essential. Intriguingly, Cdk2ap1 ΔN is evolutionarily conserved in sequence and function yet is driven by different promoters across mammals. The distinct preimplantation Cdk2ap1 ΔN expression in each mammalian species correlates with the duration of its preimplantation development. Hence, species-specific transposon promoters can yield evolutionarily conserved, alternative protein isoforms, bestowing them with new functions and species-specific expression to govern essential biological divergence.

[Spinosaurus-729]

“A conserved genetic element turned out to have a function? What a surprise! This definitely means that everything we knew about the genome is wrong!!”

[Rumraket (Mikkel R.)]

For every new thread of these you start, recall the hasty generalization fallacy. Some =/= therefore all.

[thoughtful (Valerie (non-scientist))]

Who made a hasty generalization fallacy? I don’t conclude “some, therefore all.” I believe the genome was designed for religious reasons, therefore these conclusions make a lot of sense in that paradigm. The question is, how much functional “junk DNA” is too much before scientists have to conclude the same?

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.

I know creationists are postulating this. Anyone besides him? Is this new or already somewhat accepted?

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.

“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.

I see design, you see what?

Also could transposons like this be an option to consider the limits of baramins?

Just some of the thoughts rumbling around in my head.

[Rumraket (Mikkel R.)]

@thoughtful

Who made a hasty generalization fallacy?

Wang when he 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.”

Yet he does no work to show that this particular transposon has ever been claimed to be junk. Thus he is the one making a hasty generalization fallacy (that because it has been inferred that most transposons are junk - therefore the people who inferred this must think all transposons must be junk) and you seem to be going along with it.
In fact I gather you’re not just falling for it, because you seem to be trying to make point of linking these trash articles as if your ability to keep finding examples of scientists committing this same basic fallacy somehow means you’re amassing lots of evidence.

@thoughtful

The question is, how much functional “junk DNA” is too much before scientists have to conclude the same?

The paper you linked suggests function for one transposon promoter, serving as a regulator of a conserved downstream gene.

One promoter found in a transposon.

And it’s only the promoter. Not everything found in the transposon.

A promoter can be as little as 6 basepairs long. There are multiple types of transposons, and their sizes range between hundreds to tens of thousands of bp. A typical fully intact retrotransposon can be ten-thousand basepairs, some times even more.

Please consider that speaking just of a particular type, there are over half a million LINE-1 retrotransposon copies alone in the human genome, most of which are showing varying degrees of degradation to mutations, as you would expect if some of them are more recent insertions, others are a bit older, and still others are much older and therefore more mutated and degraded. Suffice it to say, your ability to link one of these articles every month should keep you busy for longer than you think the entire universe has existed, so don’t hold your breath.

Nobody ever said ALL transposons will be nonfunctional junk. But they did say the majority, and that we can frequently tell them apart by their features, such as degree of conservation, and more specifically the specific types of mutations and overall state of degradation we find in them.

Finding that a promoter from a transposon serves as a regulator for a nearby gene does not transform the entirety of that transposon into a functional one. Not by a long shot.

So how much more? A couple of hundred million times more should do it, for transposons. Then there’s pseudogenes…

@thoughtful

know creationists are postulating this.

No, creationists aren’t postulating this. They’re taking this from molecular and cell biologists and then just repeating it too. Creationists generally say all DNA is functional for whatever theological reasons, but usually stay away from even speculating on how other than by just aping the speculations of various molecular biologists.

@thoughtful

I see design, you see what?

I honestly don’t think you’re really "seeing design” as much as you’re just rationalizing something you don’t understand by wrapping it up in your theological views.

@thoughtful

Also could transposons like this be an option to consider the limits of baramins?

How would they?

Edit: Sorry for the big edit. I wrote this half asleep last night.

[dsterncardinale]

Wait, sequences in question are conserved? Seems like that’s important.

[thoughtful (Valerie (non-scientist))]

Thanks for the science you explained. I learned something.

@Rumraket

Suffice it to say, your ability to link one of these articles every month should keep you busy for longer than you think the entire universe has existed, so don’t hold your breath.

@Rumraket

In fact I gather you’re not just falling for it, but you seem to be trying to make point of linking these trash articles as if your ability to keep finding examples of scientists committing this same basic fallacy somehow means you’re amassing lots of evidence.

I just think it’s interesting that there are a handful of lay articles with quotes from professors who are heads of important labs, who get published in major journals who talk about non-coding DNA this way (as junk DNA) and many regulars of the forum get so annoyed by it. I just think it’s a popular way of speaking and it’s not that big of a deal, even though I like precise language. Definitions of words become what they are because of the way people use them.

I also think it just shows something about human nature. We like to use hyperbole to show off discoveries as unexpected. For instance, someone could be mining for gold and find some, and say, “No one ever thought of mining here. I wonder if there’s gold throughout this area!” I also think as humans we do find joy in things that appear to be designed to be functional and useful.

@Rumraket

They’re taking this from molecular and cell biologists and then just repeating it too.

Ok, that answers that question.

@Rumraket

The paper you linked suggests function for one transposon promoter , serving as a regulator of a conserved downstream gene.

One promoter found in a transposon.

And it’s only the promoter. Not everything found in the transposon.

A promoter can be as little as 6 basepairs long. There are multiple types of transposons, and their sizes range between hundreds to tens of thousands of bp. A typical fully intact retrotransposon can be ten-thousand basepairs, some times even more.

@Rumraket

I honestly don’t think you’re really "seeing design” as much as you’re just rationalizing something you don’t understand by wrapping it up in your theological views.

As I was going to respond to additional things you wrote, I went back and read the article again. After your explanation I understand it better, so thanks again.

But WOW. This.

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.

This tiny promoter sequence works its little tail off for 1 day. Only 1 DAY at a very specific time, or things go off the rails with implantation. If that is not design, what is? C’mon. That is freaking amazing.

@Rumraket

@thoughtful

Also could transposons like this be an option to consider the limits of baramins?

How would they?

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.

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.

I was thinking that if these transposons turned on before implantation are different for each species they looked at, perhaps the transposons would be the same within each baramin. I guess it’d be interesting to find out if it’s the same between humans and great apes. If it is the same, that kills that idea.

[Rumraket (Mikkel R.)]

@thoughtful

I just think it’s interesting that there are a handful of lay articles with quotes from professors who are heads of important labs, who get published in major journals who talk about non-coding DNA this way (as junk DNA) and many regulars of the forum get so annoyed by it. I just think it’s a popular way of speaking and it’s not that big of a deal

That’s weird because every other creationist I talk to seems to think it’s a really big deal, and that this way of talking somehow proves there’s no junk DNA.

@thoughtful

Definitions of words become what they are because of the way people use them.

Right, but if you’re going to call all non-coding DNA “junk” even though you don’t think it’s nonfunctional, what are you going to call actually nonfunctional DNA? It seems to me we already had two perfectly sensible words that describe the attributes we use to categorize them. Junk and non-coding.

@thoughtful

I also think it just shows something about human nature. We like to use hyperbole to show off discoveries as unexpected. For instance, someone could be mining for gold and find some, and say, “No one ever thought of mining here. I wonder if there’s gold throughout this area!” I also think as humans we do find joy in things that appear to be designed to be functional and useful.

While that is definitely true, I wonder if you’d also be so charitable if you read pop-sci articles about evolution, or the origin of life, or whatever other topic you might think conflicts with religious or political views you hold.

@thoughtful

But WOW. This.

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.

This tiny promoter sequence works its little tail off for 1 day. Only 1 DAY at a very specific time, or things go off the rails with implantation. If that is not design, what is? C’mon. That is freaking amazing.

I agree that’s amazing just in and of itself, but that is really “just” environmentally sensitive gene-regulation. A genetic “switch” that responds to, and therefore is turned on or off for as long as some environmental condition is met, and once that condition dissipates it responds by switching back off/on again. Some respond to the presence of signaling molecules like hormones, some respond to metabolites, some respond to smells and certain foods (such as sugars), some respond to light of different wavelengths, etc. etc.

For anyone interested, there is good evidence for how promoter sequences evolve:

Random sequences rapidly evolve into de novo promoters - PubMed

And we even know how certain environmentally sensitive transcriptional regulators evolved:
https://www.sciencedirect.com/science/article/pii/S0092867414011143

[Michael_Okoko]

@thoughtful

@Rumraket

In fact I gather you’re not just falling for it, but you seem to be trying to make point of linking these trash articles as if your ability to keep finding examples of scientists committing this same basic fallacy somehow means you’re amassing lots of evidence.

I just think it’s interesting that there are a handful of lay articles with quotes from professors who are heads of important labs, who get published in major journals who talk about non-coding DNA this way (as junk DNA) and many regulars of the forum get so annoyed by it

It is surely interesting because it reveals the massive misunderstanding of the topic by the big heads running major research labs across the US and the world.

@thoughtful

and many regulars of the forum get so annoyed by it.

Its kinda hard not to.

@thoughtful

If that is not design, what is?

The classic God of the gaps.

[Rumraket (Mikkel R.)]

@Michael_Okoko

@thoughtful

If that is not design, what is?

The classic God of the gaps.

This isn’t even a gap. We know how these regulators evolve.

[thoughtful (Valerie (non-scientist))]

@Rumraket

For anyone interested, there is good evidence for how promoter sequences evolve:

They replaced a promoter sequence with another sequence - how is that showing de novo function of any random junk?

@Rumraket

I agree that’s amazing just in and of itself, but that is really “just” environmentally sensitive gene-regulation. A genetic “switch” that responds to, and therefore is turned on or off for as long as some environmental condition is met, and once that condition dissipates it responds by switching back off/on again. Some respond to the presence of signaling molecules like hormones, some respond to metabolites, some respond to smells and certain foods (such as sugars), some respond to light of different wavelengths, etc. etc.

So it’s not design because design happens all the time?

@thoughtful

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.

This is a lot of function to be gained and lost between common ancestors of all these species.

@thoughtful

“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.

Huh. Nope, not design.

[Mercer (John Mercer)]

@thoughtful

@Rumraket

For anyone interested, there is good evidence for how promoter sequences evolve:

They replaced a promoter sequence with another sequence - how is that showing de novo function of any random junk?

Because they replaced the functional promoter with random junk. It’s even in the abstract:

We studied de novo evolution of promoters in Escherichia coli by replacing the lac promoter with various random sequences of the same size (~100 bp) and evolving the cells in the presence of lactose. We find that ~60% of random sequences can evolve expression comparable to the wild-type with only one mutation, and that ~10% of random sequences can serve as active promoters even without evolution.

In what way is this unclear?

[Art (Arthur Hunt)]

@thoughtful

@thoughtful

“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.

Huh. Nope, not design.

Yup. No design. From the paper:

A hallmark of mammalian preimplantation embryos is the transient and robust retrotransposon induction, likely resulting from extensive epigenetic reprogramming (Tang et al., 2015).

In other words, the distinctive stage-specific expression of different retrotransposons is likely due to a global re-setting of epigenetic marks at this particular developmental stage. There isn’t anything special or unlikely going on. An LTR transposon (ALL active members of which carry promoters and cryptic splice sites) landed in the Cdk2ap1 gene in a way that allowed retention of the expression pattern of this gene. This can happen because of a coincidental overlap in the developmental epigenetic re-setting and the stage-specific expression of the gene.

No design needed. Just another example of how genetic carpet-bombing can occasionally yield interesting and positive outcomes.

[thoughtful (Valerie (non-scientist))]

@Mercer

In what way is this unclear?

I guess I have to explain with an analogy and then you can tell me where I don’t understand the science.

Basically they took a car, took off a tire, and said most of the time it figured out how to run the same way. That’s not the same as a bunch of junk car parts running like a car.

@Art

There isn’t anything special or unlikely going on.

I’m trying my best to learn and thank you all for bearing with me, but the truth of that sentence would be more obvious to me if I could fully understand the paragraph it was in, especially after reading it five times.

[Rumraket (Mikkel R.)]

@thoughtful

Basically they took a car, took off a tire, and said most of the time it figured out how to run the same way. That’s not the same as a bunch of junk car parts running like a car.

More like they took a lot of cars and removed a tire(promoter), then put random junk in it’s place, and 60% of random junk evolved back into a tire with just one mutation. Another 10% of random junk could function like a tire already.

[Mercer (John Mercer)]

@thoughtful

I guess I have to explain with an analogy and then you can tell me where I don’t understand the science.

Your analogy is not analogous to evolution.

@thoughtful

Basically they took a car, took off a tire, and said most of the time it figured out how to run the same way.

It “figured out” by evolution, which was not hard because a lot of random stuff works like a tire.

@thoughtful

That’s not the same as a bunch of junk car parts running like a car.

No one (other than creationists using the straw-man fallacy) is suggesting that evolution puts systems together all at once. It only can assemble them recursively, on time scales that are so long that they are almost beyond our human comprehension.

[CrisprCAS9]

@thoughtful

Basically they took a car, took off a tire, and said most of the time it figured out how to run the same way. That’s not the same as a bunch of junk car parts running like a car.

The analogy would be taking a car, taking the engine out, replacing it with some random dirt and rocks, and finding that 10% of the time it works immediately.

[Giltil (Gilbert Thill)]

@Rumraket

Please consider that speaking just of a particular type, there are over half a million LINE-1 retrotransposon copies alone in the human genome, most of which are showing varying degrees of degradation to mutations, as you would expect if some of them are more recent insertions, others are a bit older, and still others are much older and therefore more mutated and degraded. Suffice it to say, your ability to link one of these articles every month should keep you busy for longer than you think the entire universe has existed, so don’t hold your breath.

Nobody ever said ALL transposons will be nonfunctional junk. But they did say the majority

Are you sure that the majority of retrotransposons are nonfunctional junk?
For example, the paper below presents data that suggest « a general theme of genomic repeats in orchestrating the function, regulation and expression of their host genes ».
https://www.sciencedirect.com/science/article/pii/S2211124720302096

[Rumraket (Mikkel R.)]

@Giltil

Are you sure that the majority of retrotransposons are nonfunctional junk?

Yes I’m quite sure of that.

@Giltil

For example, the paper below presents data that suggest « a general theme of genomic repeats in orchestrating the function, regulation and expression of their host genes ».
Genomic Repeats Categorize Genes with Distinct Functions for Orchestrated Regulation - ScienceDirect

I don’t see anywhere in the paper where they make estimates of the fraction of transposons or repetitive elements that are functional, they just say particular types are more associated with expression of specific classes of genes.

It should not be a surprise that more similar sequences more often recruit the same transcription factors. This is entirely consistent with what we already know about the specificity and how transcription factors interact with DNA, also resulting in the phenomenon of pervasive transcription.

The idea that all or the vast majority of transposons and repetitive elements, which most significantly contribute to variations in genome size between species, should be functional, fails the onion test. It’s not clear why between two species of onion, one needs up to five times more putative enhancers than another(or more than humans), why between two virtually indistinguishable species of water flea one needs twice as many as the other, and even less so why a pine tree needs seven times more than humans.

Meanwhile there’s a perfectly good explanation for these large differences in numbers of repetitive and transposable elements in different species, tied directly to the intrinsic capacity for this DNA to, well, copy and transpose itself all over the genome. It immediately makes sense of why large variations in genome size primarily come from these types of DNA. It’s the sort of DNA that most easily can change in quantity. Now please think about this for just one moment. Transposons and retrotransposons are exactly the types of genes that can massively change their numbers basically on their own through their transpositional activity. Repetitive elements are very prone to truncation and amplification through unequal crossover-effects.

Why do we need another explanation again?

[CrisprCAS9]

Please quote from your citation where the authors say what you suggest they said.