Junk DNA

… evidently it’s not all junk, after all. (I’m not surprised.)

http://www.usatoday.com/news/health/story/2012-09-05/junk-dna-disease/57604346/1?csp=34news

Evidently, the latest research on the human genome shows that what we used to call “junk DNA” isn’t meaningless. Perhaps we should have called it “noncoding”. It affects gene expression, and even takes part in chemical activity in the nucleus.

Do DNA clocks use “junk DNA”, or just “DNA synonyms”? If the former, wouldn’t this finding impact the validity?

BTW, I would expect there to be a certain amount of junk in DNA. I was just surprised that we thought that most of it is junk (what, 98%?)

There’s probably plenty of ignorance embedded in my post already. Please feel free to fight it. In any case, I’m interested in what you all think about the significance (or lack thereof) of this finding.

From the perspective of a biologist, I’ll just say this is really really old news to us. I’ve said before that whoever coined the term “junk DNA” should be shot. It’s led to a lot of bad assumptions and misconceptions in the public mind. We’re finding that the genome is far more complicated in both structure and function than we initially thought. This really shouldn’t be a surprise.

Not a biologist, and not surprised either. The classical model of a set of genes never looked like enough information to me.

Even though some of the non-coding DNA serves a regulatory function, isn’t it still pretty damn sure that quite a lot of our DNA is simply non-functional?

For example, wouldn’t the set of genes that are supposed to make the chemical called Vitamin C in humans, be called “junk”? What about all those retroviral insertions?

As a non-biologist, I’m not surprised either - it’s a hugely complex system, and studying it is essentially a Herculean task of reverse-engineering analytics - it’s not surprising at all that we keep on finding stuff we didn’t already know about it.

However, there has to be a fair amount of slack, redundancy and clutter in there, just because of the way DNA genomes all came about, and the way in which they are modified. If everything in there perfectly served a function, it would start to look like evidence of intelligent design - and it would not be as readily mutable as we know it to be.

As a card* carrying geneticist, I remember the department chair teaching about junk DNA. It was accepted as a given, part of the central dogma of genetics, that non coding DNA was junk and not necessary. Challenging the dogma was clearly relayed as not an effective way to have a career.

Oh how thinks have changed.
As to the OP…

DNA mutations in mitochondrial DNA are sometimes examined to clock the time since populations separated, something quite useful in studying evolutionary relationships. Mitochondrial DNA is thought to have a much lower proportion of non-coding “junk” DNA than nuclear DNA. Still, much of the DNA clock testing focuses on the small proportion of non-coding DNA in the mitochondria.

Mitochondria are thought to be prokaryotic cells which were incorporated into eukaryotic cells in some progenitor species. Mitochondria have their own small bit of DNA which is quite separate from nuclear DNA. Mitochondrial DNA is inherited only from the mother. Sperm do not contribute mitochondria.

  • diploma carrying, to be precise

It’s about time we came to our senses. I was studying organic chemistry with an interest in genetics back in the mid-90s (never finished the degree) and remember it was being taught as dogma that most of the genome was meaningless junk with no function. Depending on the professor, this was usually followed by a tangent on what all this junk “proved” about evolution, the presence of ancient retroviruses, etc, etc. and I remember thinking “We haven’t even proved it’s junk yet. Let’s keep the horses out in front until we’ve at least completed the genome project.”

I haven’t yet attempted to digest the new ENCODE findings, but here are my reactions to the “80% of genome is actually functional after all!” headlines:

  1. “Functional” can range from “absolutely critical” to “almost, but not quite entirely dispensable”.
  2. Some of those critical functions can include “filler”, i.e. controlling gene expression by separating powerful regulatory elements with 100 kb of random DNA.
  3. Even then, there’s plenty of bloat and redundancy in the human genome – other organisms have approximately comparable regulatory sophistication with far more compact genomes.
  4. But some of that bloat and redundancy is probably critical for human evolution.
  5. Holy crap this is a lot of data. The bioinformaticists are going to be chewing through this for years…

ETA:
6. It was definitely a mistake to equate “noncoding” with “junk”.

One of my bioinformatics guys said that if we stopped all sequencing cold NOW, we’d still have enough data already collected to keep everyones’ careers going for a generation.

Not really a surprise. I always figured the idea that so much of it was ‘useless junk’ was in itself, useless junk.

Coincidentally, there’s a good piece at Ars Technica that clears up some of the sloppy misconceptions in popular reporting of the Encode project. That author does a rather solid job of expounding on some of the ideas I tossed out (and most biologists were thinking).

As a physical scientist with a strong interest in genetics, I always thought it was absurd to consider “junk DNA” to be useless. Maybe some, but all? Hard to imagine anyone would assume that.

As far as I can tell, none of this even relates to issues like epigenetic changes or even the influence of interference RNA.

This is where reading SF can get your ass edumacated at the forefront of some fields. Greg Bear’s Darwin’s Radio talked about some real life and proposed functions of ‘junk’ DNA. He also covered how viruses get permanently written into genetic code.

What I read there spurred me to get up to date on genetics (the last stuff I’d read seriously was back in high school) and I found that virtually all of the science he mentioned was real. While the speculative virus and subsequent mutations were obviously fantastic, the backing science was about 99% solid, with only a sprinkling of fact-twisting to get to where he wanted his plot to go.

Actually, epigenetics and small RNA elements are a huge part of the ENCODE project. DNA methylation, chromatin modifications, DNA binding proteins, and a whole host of other things are being mapped on a whole-genome scale. And on the RNA end, there’s experiments to find all the small RNAs, and all the RNA that is bound to interesting proteins (including the silencing complex).

What I meant was, how are those processes coded? Obviously the RNA has to be coded somewhere. And the “logic” I guess you’d call it for how and when to methylate or phosphorylate a section of coding DNA has to reside someplace too.

Thank you for this graf. Would all dopers, myself included, take the time every now and then.

According to this study, 20% is still nonfunctional. One example of nonfunctional DNA is a segment of coding DNA that gets duplicated (a common replication error) and then mutated into a noncoding segment.

Thanks for your post.

Just to nit-pick, most mitochondria are inherited from the mother, via the egg, which has hundreds of thousands. Few mitochondria are from the father, as a sperm cell has only enough mitochondria to power it as it matures and for its journey. Normally, the sperm mitochondria get selected out. However, the resulting fertilized egg, with DNA from both parents, might be incompatible with the egg’s mitochondria and compatible with the sperm’s, leading to mitochondria inherited mostly from the father. (Nuclear DNA produces the precursors that are used in mitochondrial processes, and thus the nuclear DNA has to be compatible with the mitochondrial DNA. Mitochondrial DNA has been stripped down to the bare minimum required to regulate energy production.) My understanding comes mostly from the book, “Power, Sex, and Suicide”. I am not a biologist. :wink: Anyway, I bet you knew this but were keeping it simple. I couldn’t resist, since I think mitochondria are fascinating.

In any case, if mitochondrial DNA clocks are based on noncoding DNA, and that DNA serves a vital function, then this could explain some discrepancies.

Excellent points. If #2 accounts for a lot of the noncoding DNA, then it wouldn’t affect molecular clocks much.

Thanks – I look forward to reading it.

As an aside, several folks above mentioned embedding of viral DNA.

I remember learning Java and contrasting its pure-class system from C++. In C++, an object class can “inherit” properties from any number of other object classes. In Java, it can inherit from at most one.

Pondering this distinction, I came up with only one good case in the real world where inheritance is single: that of (eukaryotic) species.

And as it turns out (thanks to embedding of viral DNA), I was wrong about that one!

Ain’t biology grand? There’s always a fly in the ointment. And dammit, the fly usually makes the ointment work better!