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What causes alleles to become dominant or recessive?


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#1 Itoero

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Posted 6 October 2016 - 10:59 AM

What causes alleles to become dominant or recessive?
How does RNA 'know' which allele is dominant and which is recessive? How does itbind with the correct one?

If a recessive allele causes the fittest phenotype then the recessive allele will become dominant(after a long time)...this causes the huge variation.
How is this possible?
Alleles which become dominant have the most interactions with RNA.
Can RNA alter the dominance/recessiveness?
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#2 Ophiolite

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Posted 6 October 2016 - 02:02 PM

I asked a similar question on this or another forum and the simplified answer appeared to be "shit happens". The real answer is more complex.


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#3 StringJunky

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Posted 6 October 2016 - 03:14 PM

 

This is where dominant and recessive come from. Some proteins are dominant -- they win out over their fellow proteins, just like dominant athletes win against their competitors.

 
The simplest situation of dominant and recessive alleles is if one allele makes a broken protein. When this happens, the working protein is usually dominant. The broken protein doesn't do anything, so the working protein wins out.
 
A great example of a recessive allele is red hair. There's a protein called MC1R, and one of its usual jobs is to get rid of red pigment. When it isn't working, you get a buildup of red pigment and end up with red hair.
 
All it takes to keep from having red hair is a little bit of MC1R protein. So it's easy to see why red hair is recessive. As long as you have one working MC1R gene, you won't have red hair. The working protein picks up the slack. If both copies of your MC1R gene code for broken proteins, then you'll have red hair.
 

I recommend reading the whole answer to this question; it's interesting. This is the layman version. If you want to go more technical then search for 'haplosufficiency' and 'haploinsufficiency'.


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#4 CharonY

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Posted 6 October 2016 - 04:43 PM

I asked a similar question on this or another forum and the simplified answer appeared to be "shit happens". The real answer is more complex.

 

Not entirely wrong. But basically you can boil it down to the following: alleles usually code for different varieties of proteins. The proteins are associated with a given set of phenotypes. If you mix them, they do their thing, If a given mixture always results in a given trait, the protein(s) responsible and the associated alleles can be considered dominant. The simplest case is if an allele results in the loss or reduced function of the protein it codes for. Let's call the allele a and the phenotype p-. If an individual has two of this allele (aa) the individual has not functioning protein and the phenotype is p-. However, if he is heterozygote and carries a functional version (b) in addition to a, the functional one may be sufficient to cover the deficit, hence ab would be p+. Then there may be a third allele, c, which is functional, but not quite as efficient as b. If you have got cc, you have phenotype somewhere between p+ and p-, let's call it p+/-. So if you got bc, you got p+, as the more efficient b covers c. Thus b is dominant over a and c. But if you have ac, the somewhat functional c covers the deficit of a and you may have p+/-.

 

Often, it is not that straightforward as in the given example, though (especially if loci in question play regulatory roles). 

 

However, OP seems to be confused about the definition of dominance as it does not have anything to do with RNA binding, nor does it have anything to do with fitness.


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#5 Itoero

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Posted 7 October 2016 - 04:19 PM

A Kermode bear is an american black bear with a white coat.
The white coat is due to a double recessive gene.
When something causes bears with a white coat to be the fittest and bears with a black coat to be in disadvantage then the recessive gene must become dominant so the population would not diminish to much.
Recessive genes that become dominant and vice versa enables evolution of DNA-based organisms.

There must be something which causes this 'switch'.
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#6 CharonY

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Posted 7 October 2016 - 07:18 PM

Nope, that is not how it works. At all. The only thing that is correct is homo and heterozygotes face different selective pressures.


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#7 Itoero

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Posted 8 October 2016 - 11:48 AM

Nope, that is not how it works. At all. The only thing that is correct is homo and heterozygotes face different selective pressures.

ok,then what would happen if a recessive gene causes the fittest phenotype?
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#8 Itoero

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Posted 9 October 2016 - 03:21 PM

However, OP seems to be confused about the definition of dominance as it does not have anything to do with RNA binding, nor does it have anything to do with fitness.

Dominance and recessiveness of alleles is only observable because of the interaction with RNA/ribosomes. RNA copies an allele and carries it to a ribosome where the allele is decoded into a protein which can cause a phenotype. The alleles which are copied (by RNA) and possible cause a phenotype are either dominant or recessive.(or something in between)
This process allows you to study the functionality of alleles and this process determines the functionality of alleles.
RNA is probably the only thing that interacts with DNA and decides what is dominant or recessive.
So if a recessive allele has to become dominant then imo only the interaction with RNA can cause this.

If you don't agree with this, then plz tell me why.
This idea is in my head for quite some time now and I can't find any real explanations on google.

Edited by Itoero, 9 October 2016 - 08:31 PM.

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#9 CharonY

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Posted 10 October 2016 - 03:24 AM

You have a very weird way to describe transcription and translation. Yet the main mechanism underlying cases that are not regulatory in nature are based on protein functions. Have you read  and tried to understand String's and my earlier post? 

The mRNA is just a transcript based on the DNA sequence and (again outside of regulation) the interaction is always the same, regardless of whether you got a recessive or dominant allele. The issue is that you are mixing up various levels of mechanisms (molecular, phenotype, selection) without seemingly having a clear view how the elements work or interact with each other. 


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#10 Itoero

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Posted 10 October 2016 - 10:36 AM

You have a very weird way to describe transcription and translation. Yet the main mechanism underlying cases that are not regulatory in nature are based on protein functions. Have you read  and tried to understand String's and my earlier post? 
The mRNA is just a transcript based on the DNA sequence and (again outside of regulation) the interaction is always the same, regardless of whether you got a recessive or dominant allele. The issue is that you are mixing up various levels of mechanisms (molecular, phenotype, selection) without seemingly having a clear view how the elements work or interact with each other.

I did read it but it does not explain what causes dominance or how it can change.
Your post gave an explanation on how alleles can behave dominant or recessive.
The mRNA is a transcript based on the DNA sequence but RNA still has to bind to the correct allele to form mRNA.
A dominant allele can block transcription of a recessive allele (this is a very important property) so there is something which causes RNA to bind to the correct alleles.
DNA is useless on its own, the interactions with RNA give DNA a purpose.
It's like our brain that can't survive without our body and vice versa.

Edited by Itoero, 10 October 2016 - 10:39 AM.

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#11 StringJunky

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Posted 10 October 2016 - 06:24 PM

I did read it but it does not explain what causes dominance or how it can change.

I don't think you want to read what CharonY and I presented because you have your own pet theory... I suspect.

 

Read:

 

 

The simplest situation of dominant and recessive alleles is if one allele makes a broken protein. When this happens, the working protein is usually dominant. The broken protein doesn't do anything, so the working protein wins out.


Edited by StringJunky, 10 October 2016 - 06:25 PM.

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#12 CharonY

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Posted 10 October 2016 - 07:30 PM

I did read it but it does not explain what causes dominance or how it can change.Your post gave an explanation on how alleles can behave dominant or recessive.The mRNA is a transcript based on the DNA sequence but RNA still has to bind to the correct allele to form mRNA.A dominant allele can block transcription of a recessive allele (this is a very important property) so there is something which causes RNA to bind to the correct alleles.DNA is useless on its own, the interactions with RNA give DNA a purpose.It's like our brain that can't survive without our body and vice versa.


Not to mention that you even got the basics wrong and try to fill gaps with speculation. RNA does not bind to the "correct" allele. It is simply formed as the complementary sequence along the respective locus. The polymerase actually binds and elongates base by base.

Edited by CharonY, 10 October 2016 - 07:33 PM.

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#13 Delta1212

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Posted 10 October 2016 - 08:45 PM

ok,then what would happen if a recessive gene causes the fittest phenotype?


Then the dominant gene would likely be quickly weeded out of the gene pool because every carrier of it would be made less fit. Constrasted a recessive phenotype that is less fit, where someone with a single copy of the gene generally does not negatively impact the fitness of the carrier and as such those genes tend to persist in populations in low levels because there isn't a strong enough selection pressure against them to weed them out entirely.

At no point will a recessive gene switch to being a dominant one or vice versa just because it is selectively advantageous or disadvantageous. That will affect the rate at which the genes appear in the gene pool, but not whether they are dominant or recessive.
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#14 Itoero

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Posted 11 October 2016 - 04:07 PM

The simplest situation of dominant and recessive alleles is if one allele makes a broken protein. When this happens, the working protein is usually dominant. The broken protein doesn't do anything, so the working protein wins out.

This is just an explanation of a dominant relationship between alleles...that does not say anything about the cause for the relationship.

Then the dominant gene would likely be quickly weeded out of the gene pool because every carrier of it would be made less fit. Constrasted a recessive phenotype that is less fit, where someone with a single copy of the gene generally does not negatively impact the fitness of the carrier and as such those genes tend to persist in populations in low levels because there isn't a strong enough selection pressure against them to weed them out entirely.

At no point will a recessive gene switch to being a dominant one or vice versa just because it is selectively advantageous or disadvantageous. That will affect the rate at which the genes appear in the gene pool, but not whether they are dominant or recessive.

That's true but what makes a dominant gene to be weeded out?
There must be a system that makes it more likely for unnecessary alleles or genes to be deleted from the gene pool.
Genes can become dominant/recessive, dominance and recessiveness can change.

I just found how it's possible.
The way an allele becomes dominant over another allele is simple: a small RNA encoded by the first allele recognises a specific sequence on the second allele and blocks its expression.
It's a RNA-target mechanism.
"There are two possible models to explain how dominant and recessive relationships are controlled with the small RNA-target mechanism in a multi-allelic system. In Model 1, the dominant gene has several small RNAs that each act on a different allele (target). In Model 2, recessive genes have several targets, each recognised by a small RNA from the dominant gene."
http://www.inra.fr/e...olution/(key)/2

Double recessive alleles which cause the fittest phenotype are not blocked because there is no dominant allele present and have many interactions with mRNA which imo causes RNA targets to become encoded RNA.
This process is controlled, otherwise all double recessive alleles which cause a livable phenotype would become dominant.
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#15 Delta1212

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Posted 11 October 2016 - 04:20 PM

The method by which deleterious dominant traits get weeded out of the gene pool is the death of everyone that carries them because they're always expressed and the trait is deleterious.
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#16 CharonY

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Posted 11 October 2016 - 07:10 PM

They do not even have to be expressed. Sometimes a phenotype (on which selection works) is there because a gene is not expressed. Also note that sRNA regulation is a special case and using that to understand the general mechanisms of dominance is a bit like trying to understand extrapolate energy metabolism by looking at phosphorylation of glucose.


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#17 Itoero

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Posted 11 October 2016 - 07:43 PM

They do not even have to be expressed. Sometimes a phenotype (on which selection works) is there because a gene is not expressed. Also note that sRNA regulation is a special case and using that to understand the general mechanisms of dominance is a bit like trying to understand extrapolate energy metabolism by looking at phosphorylation of glucose.

Why do you think that's a special case? What else can block a recessive gene?
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#18 CharonY

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Posted 11 October 2016 - 09:26 PM

Sigh. Really? A recessive gene does not need to be prevented from expression. In fact, some better known examples work on the protein level. For example due to different level of functionality. 


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#19 Itoero

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Posted 13 October 2016 - 03:17 PM

Sigh. Really? A recessive gene does not need to be prevented from expression. In fact, some better known examples work on the protein level. For example due to different level of functionality.

I meant to ask: 'What else can block a recessive allele?'
I suppose you mean something like a modifier gene?
There is a dominance-based relationship between the alleles of a modifier gene.
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#20 CharonY

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Posted 13 October 2016 - 05:48 PM

Why should a recessive allele be blocked in the first place? You are aware that in almost all the posts before we discussed how it is in a non-regulatory situation? If you still think that dominance is specifically a mechanisms that prevents expression of a recessive allele by the dominant one, then your model is flawed. The description is based on phenotype and the interaction can be simple. Examples were given above example (i.e. protein activity, did you understand that part or was that unclear) or due to regulatory influences, that may involve interactions with other gene products. These includes often transcription factors, though the role of small RNAs is getting more and more attention.

 

If you are really confused how gene regulation works, I would first look into transcription factors, which is a more canonical view as basis. Then expand into regulatory RNAs. I do feel that you may have quite some ground to cover in order to understand the elements and their interaction.


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