Finding on "junk DNA"

[Ocean]

Thought this was interesting.

http://www.nytimes.com/2012/09/06/s...-dark-matter-proves-crucial-to-health.html?hp

 

[natasa778]

Very interesting, thanks! Saw this on newstand this morning and missed the train!

 

[Tally]

This is great. And it just proves how little we still know.

This is why it upsets me so much when doctors run a few basic test and claim with certainty that we not physically ill. How are they so much not aware of how much there is still to discover about our bodies???

 

[natasa778]

Major scientific discovery sheds light on how environment rules over genes: "... The findings, which are the fruit of an immense federal project involving 440 scientists from 32 laboratories around the world, will have immediate application for understanding how alterations in the non-gene parts of DNA contribute to human diseases ... They can also help explain how the environment can affect disease risk. In the case of identical twins, small changes in environmental exposure can slightly alter gene switches, with the result that one twin gets a disease and the other does not. ..."

http://www.nytimes.com/2012/09/06/s...dna-dark-matter-proves-crucial-to-health.html


and guess what likes to insert close to gene switches and play with them!

 

[anciendaze]

The scale of the problem is what I find astonishing. The part of the genome which codes for proteins is about 2% of the total. The "junk DNA" found active in regulation is now put at 80%, 40 times the DNA most researchers have typically been studying.

One more point, one reason researchers labeled sequences as junk was that a high percentage resembled viral sequences. Some of these can be identified as retroviral sequences or retrotransposons (transposable elements). Surprisingly, other sequences are from viruses not known to be retroviruses. It appears that ordinary viruses can insert sequences if retroviruses or retrotransposons are also active. We find sequences from both DNA viruses and RNA viruses among the junk.

Autoimmune diseases have repeatedly been associated with evidence of reverse transcription. Others have imaged bodies resembling virions. Still others have found short sequences associated with retroviruses. What is lacking is a single species of complete virion which breeds true in the laboratory, without being attributed to contamination. We know of multiple experimental examples of helper viruses which provide functions missing in a single species of virus.

I'm still waiting for someone to explain why biological processes have to follow rules that humans find convenient.

 

[voner]

Here is some musing on the subject from Paul Whiteley, who writes the Questioning Answers blog.

http://questioning-answers.blogspot.com/2012/09/pcbs-pbdes-autism-15q11.html

Organophosphates and autism,DNA and methylation.

Makes one wonder.....

 

[alex3619]

This is something that was being intensely discussed in 2000 when I was studying biochem. Many thought it would turn out to be very significant - they were right. Classical genes are just protein instructions. Put a hundred thousand types of proteins in a pot, 21000 protein encoding genes, stir, and you don't get a human being. The rules for how to use those proteins, and other RNA that has been ignored to a large extent in research, is what makes much of the difference. Bye, Alex

 

[natasa778]

The scale of the problem is what I find astonishing. The part of the genome which codes for proteins is about 2% of the total. The "junk DNA" found active in regulation is now put at 80%, 40 times the DNA most researchers have typically been studying.

One more point, one reason researchers labeled sequences as junk was that a high percentage resembled viral sequences. Some of these can be identified as retroviral sequences or retrotransposons (transposable elements). Surprisingly, other sequences are from viruses not known to be retroviruses. It appears that ordinary viruses can insert sequences if retroviruses or retrotransposons are also active. We find sequences from both DNA viruses and RNA viruses among the junk.

So we are one small part humans and one big part a medley of zombie viruses. Add to that the fact that up to 3% of our DNA apparently is of Neandrethal origin, we are not left with much genuine material are we

I'm still waiting for someone to explain why biological processes have to follow rules that humans find convenient.

The Sun still revolves around the Earth it seems as far as genetics go.

 

[Mark]

This is something that was being intensely discussed in 2000 when I was studying biochem. Many thought it would turn out to be very significant - they were right. Classical genes are just protein instructions. Put a hundred thousand types of proteins in a pot, 21000 protein encoding genes, stir, and you don't get a human being. The rules for how to use those proteins, and other RNA that has been ignored to a large extent in research, is what makes much of the difference. Bye, Alex

Quite so. It seems that what this is looking like is the explanation for why there are unexpectedly few genes in the human genome: this additional layer of complex rules for how those genes are used is a whole other layer on top of the genome. Ever since I first heard the term "junk DNA" I've been waiting for the crucial role of "junk" DNA to be uncovered, and it always seemed that it would be roughly along these lines (as a programmer, the genes seemed rather like subroutines and I guessed that the "junk" might be the actual program) so this breakthrough isn't exactly a shock to me. But unravelling so much of the detail seems like a massively important development.

I've been trying to find time (largely unsuccessfully) to follow this MIT Biology lecture series:
http://ocw.mit.edu/courses/biology/7-014-introductory-biology-spring-2005/video-lectures/

It might be of interest to Alex and others, and I've picked up enough so far to be really intrigued by this comment in the NYT article about the 3D structure of DNA revealing how the 'junk DNA' switches tend to be close to the DNA they control: it demonstrates how viewing DNA as a straight linear sequence isn't really going to show you what is 'close' to what.

There is another sort of hairball as well: the complex three-dimensional structure of DNA. Human DNA is such a long strand — about 10 feet of DNA stuffed into a microscopic nucleus of a cell — that it fits only because it is tightly wound and coiled around itself. When they looked at the three-dimensional structure — the hairball — Encode researchers discovered that small segments of dark-matter DNA are often quite close to genes they control. In the past, when they analyzed only the uncoiled length of DNA, those controlling regions appeared to be far from the genes they affect.

I guess this also means that it really matters exactly where the gene sequences appear within the DNA: having "1 copy" or "2 copies" of a gene is one thing, but which copies, and where exactly, and do they fit into the 3D structure in such a way that they work correctly? Looking at that 3D structure of DNA with a new emphasis is presumably going to be a really big part of biochemistry from now on. How do you start to unravel how the 3D structure maps onto biological function? Is it too much to hope that there's some easy, discoverable structure there, even that areas will be found in the 3D structure that map nicely on to organs in the body, or provide a way to group the genes by functional areas?

Great stuff: thanks for posting, Ocean.

 

[alex3619]

There is not much body region gene clustering I think, and it would be largely due to chance I suspect. On the other hand, functional clustering is known, but the genome is still very scattered - it would only be partial clustering.

That is what systems biology is for: to create databases of clusters and pathways that work together. Its why I am so happy to see systems biology being used on ME.

Bye, Alex