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Rethinking junk DNA

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Teleological
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« Reply #30 on: July 24, 2009, 10:12:44 AM »


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ScienceDaily (June 6, 2009) — What was once thought of as DNA with zero value in plants--dubbed "junk" DNA--may turn out to be key in helping scientists improve the control of gene expression in transgenic crops.


Quote
That's according to Agricultural Research Service (ARS) plant pathologist Bret Cooper at the agency's Soybean Genomics and Improvement Laboratory in Beltsville, Md., and collaborators at Johns Hopkins University in Baltimore, Md.

For more than 30 years, scientists have been perplexed by the workings of intergenic DNA, which is located between genes. Scientists have since found that, among other functions, some intergenic DNA plays a physical role in protecting and linking chromosomes. But after subtracting intergenic DNA, there was still leftover or "junk" DNA which seemed to have no purpose.

Cooper and collaborators investigated "junk" DNA in the model plant Arabidopsis thaliana, using a computer program to find short segments of DNA that appeared as molecular patterns. When comparing these patterns to genes, Cooper's team found that 50 percent of the genes had the exact same sequences as the molecular patterns. This discovery showed a sequence pattern link between "junk" and coding DNA. These linked patterns are called pyknons, which Cooper and his team believe might be evidence of something important that drives genome expansion in plants.

The researchers found that pyknons are also the same in sequence and size as small segments of RNA that regulate gene expression through a method known as gene silencing. This evidence suggests that these RNA segments are converted back into DNA and are integrated into the intergenic space. Over time, these sequences repeatedly accumulate. Prior to this discovery, pyknons were only known to exist in the human genome. Thus, this discovery in plants illustrates that the link between coding DNA and junk DNA crosses higher orders of biology and suggests a universal genetic mechanism at play that is not yet fully understood.

The data suggest that scientists might be able to use this information to determine which genes are regulated by gene silencing, and that there may be some application for the improvement of transgenic plants by using the pyknon information.
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Teleological
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« Reply #31 on: August 03, 2009, 08:36:21 AM »

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Although repetitive elements pervade mammalian genomes, their overall contribution to transcriptional activity is poorly defined. Here, as part of the FANTOM4 project, we report that 6-30% of cap-selected mouse and human RNA transcripts initiate within repetitive elements. Analysis of approximately 250,000 retrotransposon-derived transcription start sites shows that the associated transcripts are generally tissue specific, coincide with gene-dense regions and form pronounced clusters when aligned to full-length retrotransposon sequences. Retrotransposons located immediately 5' of protein-coding loci frequently function as alternative promoters and/or express noncoding RNAs. More than a quarter of RefSeqs possess a retrotransposon in their 3' UTR, with strong evidence for the reduced expression of these transcripts relative to retrotransposon-free transcripts. Finally, a genome-wide screen identifies 23,000 candidate regulatory regions derived from retrotransposons, in addition to more than 2,000 examples of bidirectional transcription. We conclude that retrotransposon transcription has a key influence upon the transcriptional output of the mammalian genome.


Retrotransposons...junk DNA? Guess not...
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Mefiante
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« Reply #32 on: August 03, 2009, 11:49:44 AM »

*Yawn*  “Well, I can’t explain it, therefore a greater intelligence must be at work.”

What a tired little joke.


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« Reply #33 on: August 03, 2009, 15:45:03 PM »

Don't worry, the wabbit can handle straw....


Luckily "junk" tunes your gene activity....
Saved By Junk DNA: Vital Role In The Evolution Of Human Genome
Quote
ScienceDaily (May 30, 2009) — Researchers at K.U. Leuven and Harvard University show that stretches of DNA previously believed to be useless 'junk' DNA play a vital role in the evolution of our genome. They found that unstable pieces of junk DNA help tuning gene activity and enable organisms to quickly adapt to changes in their environments. The results will be published in the journal Science.
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rwenzori
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« Reply #34 on: August 03, 2009, 18:13:47 PM »

You know what really sucks for you TeleMechanoPhroneBone? Even if a function is found for EVERY little bit of human DNA, you still won't be able to demonstrate that Bebeh Jebus is behind it all!  LOL!
 Grin Grin

PS Nice kitteh.
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cyghost
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« Reply #35 on: August 03, 2009, 18:45:57 PM »

And this is where this thread needed to be - seeing as it lacks a sub-forum "rubbish bin" and all.   Cheesy
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« Reply #36 on: August 03, 2009, 20:56:35 PM »


'Luthon64
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