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Thread: introns

  1. #1 introns 
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    do RNA introns have any connection to 'junk' DNA? and if not, why do they exist? what would cause a segment of RNA to be such that it would be excised before translation?


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    I like this question!

    You have to make sure you get the terminology right.
    pre-mRNA would be before it is spliced and mRNA is after.

    It is actually really neat, depending on how the pre-mRNA is spliced it can lead to a different protein being produced. This can lead to another, finer, control of gene expression.

    It is interesting that you ask WHY. Well, there are a lot of cases where there is no introns! For example organisms with extremely compact genomes, such as S. cerevisea, have very few introns (there still have some at the 5'-end of some of their genes though).


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    About the "junk DNA" ... if it is transcribed it does not qualify as "junk DNA".
    (from all the definitions i've ever heard, but i'm sure you could debate that point).
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    Quote Originally Posted by sigmafactor
    I like this question!

    You have to make sure you get the terminology right.
    pre-mRNA would be before it is spliced and mRNA is after.

    It is actually really neat, depending on how the pre-mRNA is spliced it can lead to a different protein being produced. This can lead to another, finer, control of gene expression.

    It is interesting that you ask WHY. Well, there are a lot of cases where there is no introns! For example organisms with extremely compact genomes, such as S. cerevisea, have very few introns (there still have some at the 5'-end of some of their genes though).
    Yeah, i know that about the pre mRNA and the mRNA... so, the pre has the introns. that's interesting about some species not having many introns, which makes me wonder more how some species did end up with them. and (for confirmation), you're saying the introns are not related to junk DNA?
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    Quote Originally Posted by sigmafactor
    About the "junk DNA" ... if it is transcribed it does not qualify as "junk DNA".
    (from all the definitions i've ever heard, but i'm sure you could debate that point).
    makes sense.
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    Quote Originally Posted by Chemboy
    Yeah, i know that about the pre mRNA and the mRNA... so, the pre has the introns. that's interesting about some species not having many introns, which makes me wonder more how some species did end up with them. and (for confirmation), you're saying the introns are not related to junk DNA?
    The only example I am really familiar is budding yeast. (only about ~4% of its genes have introns) Most of their genes are just processed pseudogenes. So that means that after the mRNA has had all of the introns removed it is reverse transcribed and the processed cDNA recombines (via homologous recombination) back into its 'original place' on the genome, and is under the control of its natural promoter.

    It is suggested that there is selective pressure for the budding yeast to have more compact genomes, so that is why the yeast are 'losing' them.

    Original source:
    Fink, G. 1987. Pseudogenes in yeast? Cell 49:5-6.

    Another thing I find interesting:
    Most of the introns that do remain are at the 5'end of the gene. It is proposed that this is because the reverse transcriptase is not very processive and simply falls off before it can make the cDNA of that end.
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    According to wiki
    In molecular biology, "junk" DNA is a collective label for the portions of the DNA sequence of a chromosome or a genome for which no function has yet been identified. About 97% of the human genome has been designated as "junk", including most sequences within introns and most intergenic DNA.
    So yes, some junk DNA gets transcribed, but is spliced out before translated.
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    But it is really just a semantics argument. The "function" could be to be spliced out.

    ALSO, since there is cases where whether or not introns are spliced changes the outcome of the protein (depending on physiological conditions) that is being produced.

    I am uncomfortable labelling introns as "junk" DNA because they ~kind of~ do something... but really, it is just a matter of how you define the words.
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    Quote Originally Posted by sigmafactor
    I am uncomfortable labelling introns as "junk" DNA because they ~kind of~ do something... but really, it is just a matter of how you define the words.
    I agree, I find the definition also to broad.
    To argument, the introns can have their influence on the stability of the mRNA and thus on the level of protein and thus on the function. Hence I also wouldn't can them junk.

    The definition is bad! but is it the definition commenly used? iIf so I vote it should be changed.
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