Organisms evolve through gene regulation: who/what is the regulator?

[PIT2]

A tiny opossum's genome has shed light on how evolution creates new creatures from old, showing that change primarily comes by finding new ways of turning existing genes on and off.

"Evolution is tinkering much more with the controls than it is with the genes themselves," said Broad Institute director Eric Lander. "Almost all of the new innovation ... is in the regulatory controls. In fact, marsupial mammals and placental mammals have largely the same set of protein-coding genes. But by contrast, 20 percent of the regulatory instructions in the human genome were invented after we parted ways with the marsupial."

http://www.sciencedaily.com/releases/2007/05/070509205719.htm

Who or what regulates genes?
And does this falsify the view that random mutation (and selection) evolves organisms?

 

[Moridin]

Genes regulate genes. No, this does not falsify arbitrary mutations and/or natural selection.

 

[paralith]

Protein coding genes are often regulated by non-coding DNA sequences. These sequences are not transcribed. An example of a regulatory sequence would be a promoter, a site where proteins that aid in the transcription of a coding gene can bind prior to the actual act of transcription. Another regulatory sequence might sit between the promoter and the coding gene, to which a repressor protein might bind. The repressor protein gets in the way of transcription proteins bound to the promoter, so the coding gene can't be transcribed. These are simple examples; there are many types of regulatory sequences throughout the genome of an organism.

 

[PIT2]

... These are simple examples; there are many types of regulatory sequences throughout the genome of an organism.

So there are different regulatory sequences, which are affected by biological and environmental influences and cause evolution (?).

Doesnt this directly contradict the view that: a random mutation occurs and (over time) causes evolution?

 

[paralith]

Doesnt this directly contradict the view that: a random mutation occurs and (over time) causes evolution?

Not at all. Random mutations can occur in the regulatory sequences too. I think the point here is that evolution of regulatory sequences can potentially have a greater effect than evolution of coding sequences, because many regulatory sequences work with multiple coding sequences. However, whichever type of sequence you have, the ultimate end product is eventually a protein (or lack thereof), upon which natural selection can act.

 

[BoomBoom]

So there are different regulatory sequences, which are affected by biological and environmental influences and cause evolution (?).

Doesnt this directly contradict the view that: a random mutation occurs and (over time) causes evolution?

They both occur and both effect evolution along with gene duplications, alternative splicing, etc. etc.

 

[PIT2]

Not at all. Random mutations can occur in the regulatory sequences too.

The point is not that that could also happen and evolve organisms. The point is that that could also not happen, and still evolve organisms (through higher order gene regulation).

Take these statements for example:

Our report is not the first evidence of the existence of a specific mechanism directed toward genome rearrangements in stressed plants.

Our data suggests the existence of a specific, epigenetically controlled mechanism that promotes rearrangements in R-gene loci upon contact with a compatible pathogen.
http://nar.oxfordjournals.org/cgi/content/full/gkm029v1

Since epigenetics are "changes in gene function that occur without a change in the DNA sequence", the above link states, simply put, that there are mechanisms in those plants which are not controlled by gene mutations, yet do rearrange the genome. Basically, the plants detect environmental conditions that are unfavorable and then modify and reorganize specific parts of their genome in order to generate variations.

 

[Cincinnatus]

Changes in gene function due to epigenetics are still "genetic" in origin. Usually people refer to epigenetic regulation as any of the various chromosomal modifications that occur and can make transcription of certain genes more or less likely. The factors that affect these chromosomal modifications are themselves proteins coded for by DNA. So epigenetic regulators are just as subject to mutation as any other genes.

 

[BoomBoom]

So epigenetic regulators are just as subject to mutation as any other genes.

Perhaps even more so in many cases, as many essential genes to an organism's "fitness" become conserved and their exons are less subject to mutation than other regions of the genome.

 

[paralith]

Also, rearrangement alone has the potential to powerfully effect transcription levels. Many regulators function via their position in relation to the genes they regulate. This is in addition to the fact that, as Cinncinnatus wonderfully put it, mutations can still be at the root of epigenetic regulator evolution.

 

[BoomBoom]

Just FYI, but this week's Nature has a whole section of articles covering the topic of epigenetics...assuming one has access.

Nature 24 May 2007 Volume 447 Number 7143

Epigenetics p395
Alex Eccleston et al.

Perceptions of epigenetics p396
Adrian Bird

Transcription and RNA interference in the formation of heterochromatin p399
Shiv I. S. Grewal and Sarah C. R. Elgin

The complex language of chromatin regulation during transcription p407
Shelley L. Berger

Nuclear organization of the genome and the potential for gene regulation p413
Peter Fraser and Wendy Bickmore

Epigenetic inheritance in plants p418
Ian R. Henderson and Steven E. Jacobsen

Stability and flexibility of epigenetic gene regulation in mammalian development p425
Wolf Reik

Phenotypic plasticity and the epigenetics of human disease p433
Andrew P. Feinberg