What does the pufferfish tell us about
junk DNA and dark matter?
A great moment from Dr. Jeffrey Bland on the Functional Forum.
Basically, the human genome in its entirety is huge compared to any other genome.
It dwarfed the... it makes the chimpanzee genome look just tiny in comparison.
And so all this other stuff that's in there,
all this other DNA that's in there - it's been a question mark for some time.
People knew it was in there, but because it didn't code for protein through normal mrna transcription
people said, well okay what are we gonna call it?
Let's just call it junk, because it must be remnants.
There's a lot of repeating units in there and a lot of redundancy.
And so it must be stuff that's not that important.
So we're just going to call it junk.
But I want to really remind us that...I know I'm giving a quick reminder of
maybe some things you prefer to forget.
But in the biology of the gene, the molecular biology,
the gene...remember that there are
these spacers in the genes.
And these are the introns, right.
And those have to be pulled out in the splicing to get rise,
to give rise into the genome.
That's going to do the other portion of the gene.
That's going to do the coding
for the protein.
So we assume for a long time that these green spots in there
were kind of like, just who knows what they were.
Like insulators or something, and they weren't providing any function.
Now as I'll go through, we recognize that they code for all sorts of information
pertaining to the regulation of how genes are expressed as families,
and we don't express genes one at a time.
You know that you have these families,
and that's what really differentiates
humans from others at the complexity of
how you
assemble and express these in groups.
So if I asked a simple question,
that kind of a statistical question...
How many permutations and combinations could you have of 22,000 genes?
Take multiple at a time. Ah ha.
Now we get into an infinite number virtually of possibilities, right?
And so that's the diversity of the human species.
The more ways they can be assembled intelligently,
the more diversity and control and fine structure you have.
So the puffer fish is an interest...I actually studied tetrodotoxin in the puffer fish.
I was doing neuroscience at one of my phases in my earlier life.
And it turns out the puffer fish genome is kind of interesting,
because it has ninety eight
percent of its DNA it codes for protein.
And so it's very efficient, but it
doesn't have much executive centers of
what used to be called junk DNA.
So exactly the reverse of the human genome
that's only two percent coding and
ninety-eight percent other stuff.
So what is this junk in hand? This is a wonderful book, by the way.
Nessa Carey is a really wonderful writer. She's a molecular geneticist in England.
So she talks about the fact that this junk DNA can contain within it
the promoter regions of genes, the long sequence non-coding RNAs telomeres,
which were going to talk about in a moment. Short inhibitory RNAs and micro RNA.
So they're all coated for the...out of the non-protein coding portion
of what used to be called junk DNA.
Okay, so as Nessa said in the Junk DNA book, I quote,
"One shot when the sequencing of the human genome was a realization that
the extraordinary complexities of human anatomy, physiology, intelligence, and
behavior
cannot be explained by referring to the classical model of the genes."
Wow, that's a pretty compelling statement, isn't it?
When we think of all the time we spent putting this stuff to memory,
thinking that we had answers that
we could reproduce on demand,
and it would be a value. Now we're saying,
well maybe it's only a limited value. That we need to be looking farther down the story.
So you look at the encode project. I don't know how many of you have followed this.
But the encode project is very fascinating, because it
started looking at the full complex of
information encoded in the genes - not
just the coding portion for protein.
And the the first published paper out of the encode project was in 2007,
in which they were able to do a complete decoding of only two percent of the human genome.
But in that two percent, they found all these regions of non-coding portions
of the genome that had functional characteristics, right?
Fun, I love this term, because functional genomics has emerged now as the frontier of this genomic space.
So if genes can't change but their expression does,
then the dark matter of the genome is what controls the expression of genes.
So if you look at that kind of mass of DNA sitting in there,
that's obviously not ready to divide. That's just kind of a distributed DNA.
There's a huge amount of that ninety percent.
It's related to regulation of how the message is going to be expressed
under different environmental circumstances.
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