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Old 1st October 2008, 08:23 AM   #1
Darkhole
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Question about junk DNA.

I am a bit puzzled about this line in Wiki:

Quote:
While overall genome size, and by extension the amount of junk DNA, are correlated to organism complexity, it is not a solid rule of thumb. For example, the genome of the unicellular Amoeba dubia has been reported to contain more than 200 times the amount of DNA in humans.
Does this mean the Amoeba also has a comparable (or more) amount of junk DNA as humans have?
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Old 1st October 2008, 10:28 AM   #2
sanguine
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Originally Posted by Darkhole View Post
Does this mean the Amoeba also has a comparable (or more) amount of junk DNA as humans have?
I'm not specifically familiar with that example, but it may mean that the Amoeba in question has more non-gene-coding (i.e. "junk") DNA than a human cell would. There are a couple things to keep in mind here:

1. Organisms have different "ploidies" -- that is, they carry different numbers of copies of their individual chromosomes. A normal human cell has two copies of each autosome, as well as two chromosomes -- we'd say it's diploid, or that the ploidy is 2. Many organisms have higher ploidies, carrying quite a few copies of the same chromosomes. As far as I can tell from a quick review of genome databases and the biomedical literature, Amoeba dubia hasn't been sequenced, and it looks like the estimate of its genome "size" comes from an analysis of its biochemical composition. Thus, it's possible that A. dubia has more DNA per cell than a human cell would, but that that DNA comprises many copies of the exact same stuff. The net result would be more "junk" DNA in absolute terms than human, but perhaps less "junk" DNA per chromosome.

2. A. dubia hasn't been sequenced, so we have no idea how many genes it has. The ratio of gene-coding to non-gene-coding DNA varies from organism to organism. Bacteria are highly "efficient" in terms of having mostly coding DNA, for example, whereas humans have a lot of noncoding stuff in there. We won't know until dubia is sequenced what percentage of its DNA codes for genes, and what doesn't, so we can't say for sure that even with a bigger genome than a human cell (if that's true) that it'll have more "junk" DNA.

3. You'll notice I keep putting "junk" in quotes. As our understanding of biology grows, we see that more of the non-gene-coding parts of our DNA still do useful things. Some DNA may serve a direct structural role, keeping parts of the DNA "pinned" into regulatory units. Some DNA may code for hard-to-identify RNA genes. Some DNA is also pretty much "junk" in the sense that it's genes that have mutated such that they no longer function, or the skeletal remains of viruses that have infested us over the years. But our image of what is or isn't "junk" keeps changing over time, as new data falsifies old hypotheses and forces us to come up with more accurate models.
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Old 1st October 2008, 10:50 AM   #3
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Thanks Sanguine.

Quote:
A. dubia hasn't been sequenced, so we have no idea how many genes it has. The ratio of gene-coding to non-gene-coding DNA varies from organism to organism. Bacteria are highly "efficient" in terms of having mostly coding DNA, for example, whereas humans have a lot of noncoding stuff in there.
Do you know, generally speaking, does higher forms (primates, dolfins) make for more 'junk' DNA, or have lower forms equal amounts?


And, yes surfing the web I found 'Junk' doesn't always mean junk.
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Old 1st October 2008, 12:38 PM   #4
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Originally Posted by sanguine View Post
A normal human cell has two copies of each autosome, as well as two chromosomes
Oops. I meant to write "two sex chromosomes" here.
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Old 1st October 2008, 01:09 PM   #5
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Originally Posted by Darkhole View Post
Do you know, generally speaking, does higher forms (primates, dolfins) make for more 'junk' DNA, or have lower forms equal amounts?
First, you need to define what you mean by "higher" forms. It sounds like you're shooting for smarter animals, but that doesn't necessarily mean much of anything genetically.

The big divide of interest here is probably between prokaryotic organisms (bacteria and archaea, which are a lot like bacteria) and eukaryotic organisms (plants, animals, fungi). Speaking very generally, eukaryotes, us included, tend to carry a lot more "junk" than prokaryotes. We're still trying to figure out why this might be. A lot of ideas center around the idea that when you're a little bacterial cell struggling to survive in the world, there are a lot of serious energetic costs associated with making DNA that isn't doing anything for you. Mutations that "clip out" nonfunctional DNA may then be favorable. It's also worth mentioning that for any organism that reproduces sexually, it's significantly harder to make bulk changes in your genome (losing a bunch of "junk," e.g.) and still be fertile with another member of your species.

But again, these are all in the idea stage (and are great fun to think about).

Within eukaryotes, some of the single-cell ones, like yeast, have less non-protein-coding DNA than their multicellular brethren. Once we get into multicellular beasties, however, all bets are off. We just don't have enough annotated sequences to say anything meaningful about their genes-to-other-stuff ratios.

So, other than the fairly sharp structural divide between bacterial and eukaryotic genomes, there's not much we can say about where "junk" DNA does or does not turn up.
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Old 1st October 2008, 05:20 PM   #6
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Another idea is that higher eukaryotes have a greater percentage of "junk dna" because, in fact, it is not junk but complex regulatory mechanisms. We just ain't got enough genes to 'splain the complexity.

http://currents.ucsc.edu/05-06/07-25/genome.asp

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Old 1st October 2008, 05:34 PM   #7
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Originally Posted by Paul C. Anagnostopoulos View Post
Another idea is that higher eukaryotes have a greater percentage of "junk dna" because, in fact, it is not junk but complex regulatory mechanisms. We just ain't got enough genes to 'splain the complexity.

http://currents.ucsc.edu/05-06/07-25/genome.asp

~~ Paul
I was trying to hint at that above -- basically, we've called some stuff "junk" in the past, then said, "Oh, wait hey..."

Part of this may be RNA-based regulatory mechanisms; part of it is also probably the kind of physical thing I mentioned above. Years ago, I worked on "boundary elements" -- that is, parts of DNA that seemed to mark off DNA zones, where regulatory mechanisms worked within a zone, but didn't transit out of the zone. These elements of the DNA, while they do not code for any product that we know of, nonetheless have a profound regulatory effect on crosstalk between genes, effectively defining individual DNA sandboxes where only certain subsets of the whole genome really interact.

Advances in bioinformatics have inclined us to think of DNA as a big text string, but it's important to recall that it's a physical entity. It has to be managed, moved around, unwrapped for access and then wrapped up again for normal storage, etc. Noncoding elements are almost certainly key players in all this.

Of course, I work primarily in microbes, and I find them relatively beautiful and elegant for lacking many of these issues, but it's fascinating either way.
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Old 2nd October 2008, 02:27 PM   #8
Darkhole
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Thank you, I own you a beer.
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Old 3rd October 2008, 01:07 PM   #9
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Originally Posted by Darkhole View Post
I am a bit puzzled about this line in Wiki:


Does this mean the Amoeba also has a comparable (or more) amount of junk DNA as humans have?
:: Amoebas
A. dubia has 670 billion base pairs.
A. proteus has 290 billion base pairs.

I wasn't able to locate the number of genes in the above Amoebae spp, but closely related spp A. dictyostelium has approximately 12,500 genes. [source]

:: Humans
H. sap has 3 billion base pairs.

H. sap has just under 20,000 genes.


:: Inference
I think it's reasonable to interpret this to mean that Amoeba spp have a lot more junk DNA than humans, both in real terms, and proportionally. Assumption is that average gene size is the same across phyla.
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Old 3rd October 2008, 04:58 PM   #10
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Originally Posted by blutoski View Post
:: Amoebas
A. dubia has 670 billion base pairs.
A. proteus has 290 billion base pairs.

I wasn't able to locate the number of genes in the above Amoebae spp, but closely related spp A. dictyostelium has approximately 12,500 genes. [source]

:: Humans
H. sap has 3 billion base pairs.

H. sap has just under 20,000 genes.


:: Inference
I think it's reasonable to interpret this to mean that Amoeba spp have a lot more junk DNA than humans, both in real terms, and proportionally. Assumption is that average gene size is the same across phyla.
Were you able to find a ploidy for the Amoebas? I wasn't. Without that, it's hard to say.
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Old 4th October 2008, 09:16 AM   #11
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Originally Posted by sanguine View Post
Were you able to find a ploidy for the Amoebas? I wasn't. Without that, it's hard to say.
Amoeba ploidy varies with life stage.

Cysts are tetranucleated, but their ploidy is 1n or 2n, depending on species.

Adult stage is 1n. Polynucleation is common.

Reproductive stage is 2n or 4n, depending on species, and polynucleation is highly variable.

The base pair count reported in the previous post is from adult stage, single nucleus. I don't know if it's 1n or 2n. But either way, it's fairly contrastable to H. sap adult genome.
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Old 4th October 2008, 09:23 AM   #12
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Just one more thought about the high volume of dna in Amoeba species: this gribblie does a lot of phagocytosis. It's sop is to absorb the dna of its prey through a digestive vacuole, but it's entirely reasonable to imagine an event where the prey's nucleus is not digested enough, and the dna is absorbed across the cell membrane mostly intact.

Consequently, we would predict a lot of this stray dna would find its way into nuclei and be mistaken for damaged host dna and 'repaired' back into the genome.

This hypothesis is supported by the nature of the junk dna. In eukaryotes, a lot of junk dna is repeated sequences, currently best explained by retrotransposon activity. However, Amoeba junk dna has proportionally less retrotransposon signature, and a lot of evidence of lateral transfer instead.
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Old 4th October 2008, 04:25 PM   #13
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Originally Posted by blutoski View Post
Just one more thought about the high volume of dna in Amoeba species: this gribblie does a lot of phagocytosis. It's sop is to absorb the dna of its prey through a digestive vacuole, but it's entirely reasonable to imagine an event where the prey's nucleus is not digested enough, and the dna is absorbed across the cell membrane mostly intact.

Consequently, we would predict a lot of this stray dna would find its way into nuclei and be mistaken for damaged host dna and 'repaired' back into the genome.

This hypothesis is supported by the nature of the junk dna. In eukaryotes, a lot of junk dna is repeated sequences, currently best explained by retrotransposon activity. However, Amoeba junk dna has proportionally less retrotransposon signature, and a lot of evidence of lateral transfer instead.
I like it. It's a reasonable mechanism.
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Old 6th October 2008, 08:09 AM   #14
Darkhole
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Blutoski, can you translate this in ordinary English?

Quote:
:: Humans
H. sap has 3 billion base pairs.

H. sap has just under 20,000 genes.
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Old 6th October 2008, 12:39 PM   #15
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Originally Posted by Darkhole View Post
Blutoski, can you translate this in ordinary English?
I can tackle that one for you.

DNA is a polymer made up of very similar units, each of which has a sugar, a phosphate, and a component called a "base". The bases encode the information in DNA that is says which part of the DNA is a gene, what proteins the cell should make, and so forth. The full structure of DNA is actually an entwined pair of these polymers -- the sugar and phosphate form the backbone of each polymer. The bases from each polymer point in toward the middle, linking together like a giant zipper. We say that the bases "pair" when they join in this way -- A joins to T, G joins to C.

As a consequence, when we say that the human genome has 3 billion base pairs, we're saying that each polymer has 3 billion elements on it, and a matching polymer with another 3 billion elements that are all exactly matched up to it.

(Note that the human genome is actually split across 22 autosomal and 2 sex chromosomes, so there's more than one giant polymer. The basic point stands.)

Since eukaryotic DNA is always a double helix, rather than say that a genome has "3 billion nucleotides" or similar, we say that it has "3 billion base pairs."

For the second part, that's just saying that our current estimate of the number of protein-coding genes in the human genome is about 20,000. Before we finished sequencing the human genome, our best estimates humans would have many more protein-coding genes than that, but the reality has been a much lower number. Note that this remains an estimate because we haven't checked to see that each and every one of these 20,000 or so possible protein-coding genes actually leads to a protein.

I also refer to them as "protein-coding" genes because there are genes that just code for RNA, and those are significantly harder to find based on their sequence alone. Some "junk" DNA may actually include various RNA-coding genes, for example.

But the short form is that Blutoski was saying that the Amoeba genomes are about 200 times bigger in terms of pure length of sequence than humans, and it's perhaps unlikely that they have 200 times as many genes as humans do.
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Old 6th October 2008, 12:56 PM   #16
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Maybe their spiritual creatures.
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Old 13th October 2008, 12:10 PM   #17
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Thanks, got it now.
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