Rationale of gene location on chromosome

[Quickless]

Is there any rationale for the genes that are located on a particular chromosome, i.e. are the genes that are located on a particular chromosome related in some functional way? Another way to approach this is does it make a difference if a gene is located on chromosome 1 or 2 or 3…?

 

[Vesalius]

Try this link..(it is the only one I could comprehend )

http://www.nature.com/ng/journal/v31/n2/abs/ng887.html

Kindly post the link if you find something more substantial..

 

[mishrashubham]

As far as I know, the only effect of any hypothetical gene transfer from one chromosome to another will be to make the gene inaccessible to cis-acting elements on the previous chromosome and thus disrupting its normal expression. This may or may not have significant phenotypical effects depending on the gene.

Like the above link says, housekeeping genes are generally found in clusters. This happens due to a process called Gene duplication.

Let us take a certain gene A on some particular chromosome P, which performs some function X that is essential to the survival of the organism. If A mutates then it will no longer be able to perform the essential function X. Thus the organism will die. Let us suppose, during the course of replication, A accidentally gets duplicated. In such a case, there is an extra copy of the gene A which is free from selective pressure i.e. it is free to accumulate harmless mutations.This is because even if the extra copy changes and becomes a slightly different gene B, the organism would live since it still has a copy of A. So the now changed copy of A which has become B can perform some other function Y. This explains why related genes are found together on a chromosome.

 

[Quickless]

Thanks for the link. Even the conclusion to this article is a little confusing and I had to read it a few times

"We examined Serial Analysis of Gene Expression (SAGE)4 data for 14 tissues and found significant clustering, in each tissue, that persists even after the removal of tandem duplicates. We confirmed clustering by analysis of independent expressed-sequence tag (EST) data. We then tested the possibility that the human genome is organized into subregions, each specializing in genes needed in a given tissue. By comparing genes expressed in different tissues, we show that this is not the case: those genes that seem to be tissue-specific in their expression do not, as a rule, cluster. We report that genes that are expressed in most tissues (housekeeping genes) show strong clustering. In addition, we show that the apparent clustering of genes with high expression rates3 is a consequence of the clustering of housekeeping genes."

Although it does not directly address the issue of function and location, I found this article to be of general interest - http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation

Thanks

 

[Quickless]

I think the gist of function and location can be stated as follows – a gene codes for a sequence of amino acids, collective termed a protein. Whether a gene is located on chromosome A or B, the protein is still coded for. Therefore the position of the gene, chromosome A or B, does not influence the functioning of the whole.

As an aside, I found this article of Thomas Hunt Morgan to be first rate - http://www.columbia.edu/cu/alumni/Magazine/Morgan/morgan.html

 

[mishrashubham]

I think the gist of function and location can be stated as follows – a gene codes for a sequence of amino acids, collective termed a protein. Whether a gene is located on chromosome A or B, the protein is still coded for. Therefore the position of the gene, chromosome A or B, does not influence the functioning of the whole.

Actually all genes in a cell are not activated. Their expression is regulated. In different parts of your body, different regions of your DNA are activated and others silenced. This way you can have different types of cells (brain cells, skin cells, muscle cells etc). Some genes are promoted while others are suppressed. Some are only activated at certain times and some keep working all our lives. That is to say, if a gene exists, it simply does not mean that it ultimately will make the protein it codes for. There are many mechanisms to regulate gene expression. Check http://en.wikipedia.org/wiki/Regulation_of_gene_expression

In fact, not all of our DNA even codes for any protein. Many of them have the sole function of regulating some other gene. Such regions of DNA are called cis-acting elements. They regulate the expression of genes present in the same chromosome as they are.

And like I said earlier, it does matter if a gene is on chromosome A or B, since only then will it be accessible to those cis-acting elements whose function is to modify its expression.

Check http://en.wikipedia.org/wiki/Cis-regulatory_element

 

[Vesalius]

I think the gist of function and location can be stated as follows – a gene codes for a sequence of amino acids, collective termed a protein. Whether a gene is located on chromosome A or B, the protein is still coded for. Therefore the position of the gene, chromosome A or B, does not influence the functioning of the whole.

As an aside, I found this article of Thomas Hunt Morgan to be first rate - http://www.columbia.edu/cu/alumni/Magazine/Morgan/morgan.html

Though it may not have significant implications on the function of the gene, its location on a particular chromosome and absence on an other is certainly interesting as it may offer clues as to how the human genome was shaped during evolution...(DNA assimilation and so forth.) and it certainly assumes importance in case of abnormalities (trans locations, deletions of arms or chromosomes..) Your thoughts on that?

 

[mishrashubham]

Though it may not have significant implications on the function of the gene...

It does have consequences. Check previous posts about regulatory elements.

 

[Vesalius]

What I meant is that if a particular gene has to be expressed for certain essential functions of the organism, it is of little consequence whether it is located on chromosome A or chromosome B. Ultimately, all the housekeeper genes are not located only on a few particular chromosomes, they are distributed throughout the genome.

 

[That Neuron]

It may be a possibility (along with the regulatory structure of a chromosome as a whole fitting together to express some genes as discussed above) chromosomes may have evolved with their structure due to telomere placing, and its impact on which genes degrade over time... and which don't, since there is only enough room for some genes that remain intact (i.e. the center of the chromosome, away from areas near telomeres) genes important to the well-being of the cell may be placed in this portion of the chromosome, whereas other less important genes may be put near these fraying ends of the chromosomes... Although, I doubt such a complex scenario is present.

 

[mishrashubham]

...chromosomes may have evolved with their structure due to telomere placing, and its impact on which genes degrade over time... and which don't, since there is only enough room for some genes that remain intact (i.e. the center of the chromosome, away from areas near telomeres) genes important to the well-being of the cell may be placed in this portion of the chromosome, whereas other less important genes may be put near these fraying ends of the chromosomes...

Where did you read this; or why do you think that genes may have evolved to accumulate in the center of chromosomes due to telomere shortening? If a gene has some function then its loss would definitely affect the organism. Nature's solution is not to put the more important genes near the centre but to maintain a certain length of telomere (gene location does seem to have an effect on variation although that is more due to genetic linkage as demostrated by this article). Telomere shortening is one of the important processes which contributes to apoptosis and it is increased telomerase activity in some tumourous cells that causes some types of cancer. Also the telomere length remains the same in every new generation since telomerase is active in germ cells and hence non-heritable. I mention only "a certain length" because natural selection is almost entirely based on reproductive success and the lifespan of individual organism is usually of little importance after it has reached a stage where it cannot reproduce.

 

[That Neuron]

Where did you read this; or why do you think that genes may have evolved to accumulate in the center of chromosomes due to telomere shortening? If a gene has some function then its loss would definitely affect the organism. Nature's solution is not to put the more important genes near the centre but to maintain a certain length of telomere (gene location does seem to have an effect on variation although that is more due to genetic linkage as demostrated by this article).

After reading it, it makes more sense, I was under the impression that genes near the degraded telomeres had a higher rate of mutation/degredation... I have no idea why lol, After delving into it more It seems that a shortened telomere causes the cell to completely stop dividing, so all genes would be equally impacted before end genes could be lost. I suppose that's the end of my assumption Hahahah... Thanks for helping me 'see the light'