How much of "junk dna" is actually on/off switches for gene regulation?

[PhilKravitz]

How much of "junk dna" is actually on/off switches for gene regulation?

 

[SW VandeCarr]

How much of "junk dna" is actually on/off switches for gene regulation?

The short answer is no one knows. It is known that at least some non-coding DNA is involved in gene regulation during development. Studies have shown that some non-coding DNA located next to coding genes can either enhance or block the transcription process of the coding gene. However, most of the human genome that is non-coding is still terra cognita.

http://www.psrast.org/junkdna.htm

A more recent update:

http://www.junkdna.com/

 

[mtc1973]

Let me precede this by saying - i am no geneticist! but I always thought that there may be an evolutionary benefit from junk dna. Think about a lizards tail! Now think about the rate of mutation -if mutation is random - there is more likelyhood it occurs in a non essential area if we have junk dna. if every bit of dna were vital - then we would breakdown function quickly - so i always like to think of it as equivalent to the lizards tail - dna we can afford to loose/mutate - the stuff we can afford to mess with without having detrimental effect on our essential function. And with epigenetic phenomenon - who knows what 'junk' really means?

 

[Ken Natton]

Huh. I have gathered that my posts are not appreciated here. But for the first time in a long time I have a perspective to offer that I believe is worthwhile.

Not all ‘junk’ DNA is entirely worthless. That isn’t to say that it has any influence at all on the phenotype of the species in which it exists, but a fair proportion of it is what Sean Carroll calls ‘fossil genes’. That is, stretches of DNA code that are not part of any active gene but were parts of active genes in the species’ evolutionary past. From these fossil genes comes much powerful evidence of the evolutionary past not just of the species to which those genes belong but also of other species that might have interacted with that species in significant ways.

 

[Quickless]

Just because very large segments of DNA do not code for a protein does not imply that the segments are of no value. These large segments still have to be continually processed. I suspect at the very least that part or all of what is being call junk DNA is performing some type of timing function. Even given, that when large portions of junk DNA are removed this seems to have no effect on the resulting organism, the effect maybe transgenerational.

 

[Pythagorean]

$$\frac{d[tf-a mRNA]}{dt} = \frac{k_max [TF-A]^2}{[TF-A]^2 +K_d} - k_degR [tf-a mRNA] + R_bas$$

is more interesting than on/off

 

[Delong]

What does that even mean?

 

[nobahar]

$$\frac{d[tf-a mRNA]}{dt} = \frac{k_max [TF-A]^2}{[TF-A]^2 +K_d} - k_degR [tf-a mRNA] + R_bas$$

is more interesting than on/off

I think you're marvelous, but I have to give you points for esotericism.

Let me precede this by saying - i am no geneticist! but I always thought that there may be an evolutionary benefit from junk dna. Think about a lizards tail! Now think about the rate of mutation -if mutation is random - there is more likelyhood it occurs in a non essential area if we have junk dna. if every bit of dna were vital - then we would breakdown function quickly - so i always like to think of it as equivalent to the lizards tail - dna we can afford to loose/mutate - the stuff we can afford to mess with without having detrimental effect on our essential function. And with epigenetic phenomenon - who knows what 'junk' really means?

I'm probably wrong but I do not understand this explanation. Each base has a certain probability of mutating. Having lots more bases does not alter the individual probability of any single base mutating, it just means there will be a greater number of absolute mutations in the genome. It will not decrease the chances of any particular base from mutating, or act as a 'buffer'. Apologies if I am wrong.

I think a consideration of Retrotransposons may be of some benefit; but again I don't know. Richard Dawkins discusses junk DNA in The Selfish Gene, but I can't remember what he wrote.

 

[Pythagorean]

It's the dynamical systems approach to modeling gene networks:

Modeling Transcriptional Control in Gene
Networks—Methods, Recent Results, and Future Directions
PAUL SMOLEN, DOUGLAS A. BAXTER AND JOHN H. BYRNE

http://www.springerlink.com/content/q85v357x0x414976/fulltext.pdf

^gives the background

"Frequency selectivity, multistability, and oscillations emerge from models of genetic regulatory systems" (same authors)

^tells more about the system itself and what it can do in terms of dynamics

Also, I learned about it in "from molecules to networks: an introduction to molecular neuroscience"

 

[SW VandeCarr]

I think you're marvelous, but I have to give you points for esotericism.



I'm probably wrong but I do not understand this explanation. Each base has a certain probability of mutating. Having lots more bases does not alter the individual probability of any single base mutating, it just means there will be a greater number of absolute mutations in the genome. It will not decrease the chances of any particular base from mutating, or act as a 'buffer'. Apologies if I am wrong.

To the extent that mutations are due the high energy particles (cosmic or local sources) the density of the particles is not related to the density of coding DNA. Due to folding, the much more common non coding DNA may block and protect the coding DNA. However, it's increasingly apparent that non-coding DNA has important functions.

The second link in post 2 refers to the new term "Hologenomics" which is supposed to have done away with the term "junk" DNA as of July 31,2008. Among other things, it now appears that the fractal type constructions such as CNS Purkinje cells are built up by feedback loops of proteins back to DNA; something that was forbidden by Crick's original "laws" of transcription.

 

[Pythagorean]

good links, SW