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Gene regulation in humans is closer than expected to simple organisms
by PHYSORG
Reposted from:
http://www.physorg.com/news107617460.html
Using a novel method developed to identify reliably functional binding motifs, researchers from the Weizmann Institute of Science in Israel have performed a genome-wide study of functional human transcription factor binding sites that encompasses nearly ten thousand genes and four hundred known binding motifs. The study appears in the Aug. 29 issue of the online, open-access journal PLoS ONE.
Gene networks are some of the most basic features of a living organism. An external or internal stimulus activates some genes, which in turn control others genes whose activity turns on or off various biological processes (such as the cell cycle, energy production, DNA repair, cellular suicide etc).
Many of the regulatory functions are controlled by attachment of special proteins (transcription factors) to 6 - 10 nucleotide long binding sequences located on the DNA, activating or suppressing expression of the regulated gene. Our ability to identify these binding sites is essential to understand the way biological networks operate.
As the genomes of various organisms became known, it turned out that complex and simple organisms differ less than anticipated in the sizes and makeup of their genomes; complexity of an organism is now believed to be reflected mainly in the manner in which expression is regulated. According to consensus, transcription of human genes is regulated predominantly by factors that bind to sites whose distances from the transcription start site may vary widely and reach tens of thousands of base pairs.
To test the validity of this belief/consensus, researchers from the Weizmann Institute of Science in Israel have performed a genome-wide study of functional human transcription factor binding sites that encompasses nearly ten thousand genes and four hundred known binding motifs. Using a novel method that was developed to identify reliably functional binding motifs, they discovered that in human (and mouse) a surprisingly large fraction of the functional binding sites was concentrated very close to the transcription start site. Hence on the basis of currently available data it seems that the most basic underlying principles and strategies used by the genomes of higher organisms to regulate gene expression are quite close to those used by simple organisms like bacteria and yeast.
The discovery and the method will allow more focused and reliable search for transcriptional binding sites and hence may turn into a major tool to be used in the quest for the transcriptional networks whose function governs all cellular processes, and whose breakdown causes complex diseases. It will generate progress in establishing the design principles used by the transcription process in high organism, and allow a more focused search for the origins of their complexity.
Source: Public Library of Science
http://www.physorg.com/news107617460.html
Using a novel method developed to identify reliably functional binding motifs, researchers from the Weizmann Institute of Science in Israel have performed a genome-wide study of functional human transcription factor binding sites that encompasses nearly ten thousand genes and four hundred known binding motifs. The study appears in the Aug. 29 issue of the online, open-access journal PLoS ONE.
Gene networks are some of the most basic features of a living organism. An external or internal stimulus activates some genes, which in turn control others genes whose activity turns on or off various biological processes (such as the cell cycle, energy production, DNA repair, cellular suicide etc).
Many of the regulatory functions are controlled by attachment of special proteins (transcription factors) to 6 - 10 nucleotide long binding sequences located on the DNA, activating or suppressing expression of the regulated gene. Our ability to identify these binding sites is essential to understand the way biological networks operate.
As the genomes of various organisms became known, it turned out that complex and simple organisms differ less than anticipated in the sizes and makeup of their genomes; complexity of an organism is now believed to be reflected mainly in the manner in which expression is regulated. According to consensus, transcription of human genes is regulated predominantly by factors that bind to sites whose distances from the transcription start site may vary widely and reach tens of thousands of base pairs.
To test the validity of this belief/consensus, researchers from the Weizmann Institute of Science in Israel have performed a genome-wide study of functional human transcription factor binding sites that encompasses nearly ten thousand genes and four hundred known binding motifs. Using a novel method that was developed to identify reliably functional binding motifs, they discovered that in human (and mouse) a surprisingly large fraction of the functional binding sites was concentrated very close to the transcription start site. Hence on the basis of currently available data it seems that the most basic underlying principles and strategies used by the genomes of higher organisms to regulate gene expression are quite close to those used by simple organisms like bacteria and yeast.
The discovery and the method will allow more focused and reliable search for transcriptional binding sites and hence may turn into a major tool to be used in the quest for the transcriptional networks whose function governs all cellular processes, and whose breakdown causes complex diseases. It will generate progress in establishing the design principles used by the transcription process in high organism, and allow a more focused search for the origins of their complexity.
Source: Public Library of Science
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Posted: Thursday, August 30, 2007 | PermalinkComments 1 - 23 of 23 |
Reload Comments | Back to Top | Page Numbers2. Comment #66540 by Richard Morgan on August 30, 2007 at 10:54 am
pewkatchoo! Shame on you! You mean you didn't notice the "d" word in this article?It will generate progress in establishing the design principles used by the transcription process in high organism, and allow a more focused search for the origins of their complexity.Not to mention "origins" and "complexity". OK, I didn't really understand this article, but these are words that make me very, very suspicious.
We must be vigilant - they're getting in everywhere!!!
(And we gits must stick together!)
Other Comments by Richard Morgan
3. Comment #66550 by jonecc on August 30, 2007 at 11:35 am
Well I thought it was fascinating. In particular, the conclusion.... the most basic underlying principles and strategies used by the genomes of higher organisms to regulate gene expression are quite close to those used by simple organisms like bacteria and yeast.
In fact I was so engrossed my dinner is now stuck to the bottom of the frying pan. Mind you, I've read similar things before, so I'm not sure how groundbreaking it is, but you can't beat some extra supporting evidence.
Most of you probably know this already, but if you like this kind of thing, can I recommend the excellent Science Blogs (http://scienceblogs.com/)
It isn't just about atheism, after all.
Other Comments by jonecc
4. Comment #66556 by Corylus on August 30, 2007 at 12:00 pm
I can see why the world 'design' rings bells RichardM, (the needless attribution of agency worries me too) but I read this is a totally different fashion.This strikes me as a bit of a smack in the teeth for the ID mob. E.g. the "It's so darn complicated I guess a magic man did it". If instead you concentrate on simplicity...
the most basic underlying principles and strategies used by the genomes of higher organisms to regulate gene expression are quite close to those used by simple organisms like bacteria and yeast.
Then the argument of irreducible complexity really does not wash. What you are faced with instead is a small amount of simple processes where the illusion of complexity is provided by the fact that:-
An external or internal stimulus activates some genes, which in turn control others genes whose activity turns on or off various biological processes.
By that analysis one understands complex things in terms of simple things working in an interactive and algorithmic fashion.
Sod it - what do I know!! I'm an arts type. Doubtless talking out of my backside: happens alot sad to say.
Jonecc have I totally misunderstood?
Other Comments by Corylus
5. Comment #66559 by Buddha on August 30, 2007 at 12:12 pm
The way I read it is that this is a bit more evidence that indicates that 99.9999% of the genetic scaffolding and processes that it takes to make us mammals was formulated in the slime-ponds of the primordial earth. Makes sense as the majority of our planet's history has been ruled by single-celled organisms - still is in some respects.I don't think there is any need for paranoia about the use of the word "design". I think it's just the usual inadvertant teleology that creeps in with sloppy journalism.
Other Comments by Buddha
6. Comment #66561 by jonecc on August 30, 2007 at 12:26 pm
I'm kind of an enthusiastic amateur myself, Corylus, but as I understand it you're correct. DNA is kind of like a computer program, where operations are handled by subroutines, and the 'control' code, like control genes, says which subroutines are run, what order they're run in, how many times they're repeated, and so on.This doesn't of course help the ID position, because an intelligent designer would design more often from scratch, rather than editing subroutines or control patterns from previous programs. The fact that we share so much of our DNA with yeast could in itself be offered as evidence for evolution through natural selection.
Which is a bit like saying that the physics of lightning is an argument against the existence of Thor. It's true, but meteorologists would find it tiresome to have to keep saying so. The persistence of ID is such a nuisance mainly because it distracts from the really interesting stuff like this.
Other Comments by jonecc
7. Comment #66563 by mdowe on August 30, 2007 at 12:29 pm
It is interesting to those of us with related backgrounds, and has implications for evolutionary biology. But I don't think more scientific evidence is really going to matter much to the blindly religious, and so I don't really see a connection on that front. I'm taking it as a general-interest science article for biologists.On a completely irrelevant note, I just have to say I love open-access journals. These are among the best the things the internet has brought us.
Other Comments by mdowe
8. Comment #66570 by BicycleRepairMan on August 30, 2007 at 1:13 pm
Fail to see the relevance??? whaaaa?? isnt this bloody richarddawkins.net????!! You know his LATEST book is called "The God Delusion" but, you know, he's known to have written some other stuff to.. like, I dunno, an 650-pages long backwards history on all this gene-stuff called "The Ancestor's Tale" pictured on the right hand sider here.. He's also written 4 or 5 other books almost entirely related to this article, but maybe that doesnt count? Other Comments by BicycleRepairMan
9. Comment #66572 by RickM on August 30, 2007 at 1:20 pm
I think Buddha got the right idea.Interesting article; forced me to look up "binding motifs".
Other Comments by RickM
10. Comment #66587 by mdowe on August 30, 2007 at 2:25 pm
RE: Comment #66556 by CorylusIf you are interested enough that you want some basic background on this topic, the "lac operon" is the classic example of gene regulation taught in biology classes. If you can get by all the jargon and acronyms, you'll find the basics are simple enough -- even an artsy-type can understand it =)
http://en.wikipedia.org/wiki/Lac_operon
Other Comments by mdowe
11. Comment #66590 by pewkatchoo on August 30, 2007 at 2:38 pm
BicycleRepairManGet over yourself. I have read 3 other Dawkins books and find them fascinating stuff. This sort of article is quite mundane stuff by comparison.
Other Comments by pewkatchoo
12. Comment #66611 by Corylus on August 30, 2007 at 3:32 pm
Thank you mdowe - working my way through :) Other Comments by Corylus
13. Comment #66624 by dhweaver on August 30, 2007 at 4:03 pm
Once again, I can hear the southern baptist preacher on Sunday:"You hear what them scientist types are sayin now. All life is made of the same guts. Hehehe. Well Mr. Scientist I had a steak for dinner last night, and it didn't taste nothin like my salad. Am I right...Praise the lord!
Other Comments by dhweaver
14. Comment #66626 by BMMcArdle on August 30, 2007 at 4:36 pm
Bacteria and yeast gave rise to Man...or was it Eve?Other Comments by BMMcArdle
15. Comment #66679 by robotaholic on August 30, 2007 at 11:09 pm
dude, I think it's yeast that rises- Other Comments by robotaholic
16. Comment #66686 by hungarianelephant on August 31, 2007 at 1:00 am
jonecc - I don't think the ID brigade will see it that way. Programmers do frequently use the same code over and over again for very different purposes, especially object-oriented code which is perhaps more closely analogous to genetic code. Typically you would not rewrite unless there's a pressing need. Minor inefficiencies are tolerable - you wouldn't bother rewriting a clumsy function which did the job unless you were calling it many times over and it was causing a noticeable performance hit. And you probably wouldn't take redundant or non-useful functions out of your code either. No point deleting the function MakeAppendix, or the line which calls it, unless keeping it is materially damaging to the program. (Yes, I know the appendix might have a function in developing the immune system of an infant. Can't think of a better analogy at the mo :)) Lazy design, perhaps, but it doesn't exclude intelligence.Of course, the closeness in genetic "design" of modern mammals to ancient simple organisms doesn't sit too comfortably with the alleged specialness of humans which IDers also believe in. But since when were they consistent? They'll now go elsewhere to find "irreducible complexity". It's like pushing down bubbles under the wallpaper.
Other Comments by hungarianelephant
17. Comment #66689 by epeeist on August 31, 2007 at 1:33 am
Comment #66686 by hungarianelephant
Programmers do frequently use the same code over and over again for very different purposes, especially object-oriented code which is perhaps more closely analogous to genetic code.
Perhaps the closest analogy is the idea of "design patterns" (http://en.wikipedia.org/wiki/Design_Patterns) in which complex programs are built from simple recurring elements. Design patterns in software are derived from the ideas of pattern languages put forward by architect Christopher Alexander (http://en.wikipedia.org/wiki/Christopher_Alexander)
Other Comments by epeeist
18. Comment #66712 by Yorker on August 31, 2007 at 5:07 am
16. Comment #66686 by hungarianelephant In my code that would be HungarianElephant in keeping with proper use of hungarian notation.
Let all those who use underscores shrivel up and die!
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19. Comment #66714 by epeeist on August 31, 2007 at 5:12 am
Comment #66712 by Yorker
Comment #66686 by hungarianelephant
In my code that would be HungarianElephant in keeping with proper use of hungarian notation.
usHungarianElephant surely. Other Comments by epeeist
20. Comment #66718 by BillySands on August 31, 2007 at 5:39 am
It's not very new. We have known for some time that altered temporal and spatial regulation of Hox genes can radically alter body plan. That's a boot in the nuts for the creationists though. They seem to think you need massive ammounts of new DNA inserted into organisms to suddenly evolve an eye in a single step Other Comments by BillySands
21. Comment #66720 by hungarianelephant on August 31, 2007 at 6:00 am
Never did I think I'd start a debate about underscores! Can't stand the things myself.HungarianElephant(as should be, but didn't think at the time)
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22. Comment #66760 by Yorker on August 31, 2007 at 8:43 am
21. Comment #66720 by hungarianelephant "Never did I think I'd start a debate about underscores! Can't stand the things myself."
No debate, they're a complete waste of space and serve no useful purpose not already better served by you-know-what!
Other Comments by Yorker
23. Comment #67395 by logical on September 3, 2007 at 8:55 am
Nice to read that most people here are familiar with the latest news in genetics.To an old hag like me it was a reminder of the infamous Singer debate - the furor around philosopher (and fellow atheist) Peter Singer, and the term "speciesism" he created.
http://www.princeton.edu/~psinger/books.html
If this is no longer a debate and we laugh off the faithheads who will be uncomfortable to be called "close" to one-cell organisms, there has been progress since the 1980ies.
Other Comments by logical
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1. Comment #66533 by pewkatchoo on August 30, 2007 at 10:27 am
It is difficult to see of what relevance it is.
Other Comments by pewkatchoo