Exon skipping for non-sense mutations? Can it work?
Ok i was under the impression that exon skipping would work for nonsense mutations, but I was told that it could require multiple skips to get the desired result.
Why is this so?
I thought that removing the exon with the stop codon in it would basically maintain the reading frame but without the offending exon. Arent all exons in reading frame on their own?
I do know that nonsense mutations can cause exon skipping on their own, of which these can be in reading frame or out of reading frame.
Can someone help me out with some information on why it would ever need mutiple exon skips.
Thanks
Why is this so?
I thought that removing the exon with the stop codon in it would basically maintain the reading frame but without the offending exon. Arent all exons in reading frame on their own?
I do know that nonsense mutations can cause exon skipping on their own, of which these can be in reading frame or out of reading frame.
Can someone help me out with some information on why it would ever need mutiple exon skips.
Thanks
Replies to This Discussion
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Permalink Reply by Julie Gilmore on
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You are looking at exons as individual subunits of the dystrophin gene - and whilst they are all distinct, they each have a specific splicing site motif that must match the adjoining exon in order for a functional protein to be formed during post translational modification.
It's basically like looking at a row in a jigsaw puzzle some pieces you could remove as an individual piece, and it would fit together with the next .... others do not have compatible ends unless you remove one or more pieces. This can be better shown if we look at the splicing site motifs of the first 14 exons of dystrophin:
| 1 > >23456| |7> >891011| |121314br />
If you remove exon 3, exon 4 can still bind to exon 2, as their splice sites are compatible ..... | 1 > >24< this mutation will result in an inframe mutation.
However if you remove exon 2, exon 1 can not bind to exon 3 ...... | 1 > <34< this mutation will result in an out of frame mutation.
On a larger scale you can lose exons 3 to 13, and still have an inframe mutation ....... | 1 > >214< Again the reading frame has not been lost. (This is why multiple exons can be lost, and still result in a BMD phenotype.)
Hope that helps.
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Permalink Reply by Jonathan on
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Ahh now it makes sense. Do you know the connections for the rest of the exons/ or where I can find them? Im interested in exon 23.
Julie Gilmore said:You are looking at exons as individual subunits of the dystrophin gene - and whilst they are all distinct, they each have a specific splicing site motif that must match the adjoining exon in order for a functional protein to be formed during post translational modification.
It's basically like looking at a row in a jigsaw puzzle some pieces you could remove as an individual piece, and it would fit together with the next .... others do not have compatible ends unless you remove one or more pieces. This can be better shown if we look at the splicing site motifs of the first 14 exons of dystrophin:
| 1 > >23456| |7> >891011| |121314br />
If you remove exon 3, exon 4 can still bind to exon 2, as their splice sites are compatible ..... | 1 > >24< this mutation will result in an inframe mutation.
However if you remove exon 2, exon 1 can not bind to exon 3 ...... | 1 > <34< this mutation will result in an out of frame mutation.
On a larger scale you can lose exons 3 to 13, and still have an inframe mutation ....... | 1 > >214< Again the reading frame has not been lost. (This is why multiple exons can be lost, and still result in a BMD phenotype.)
Hope that helps.
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OK so the rest of the exon splice site map is as follows:
<151617| |1819> >2021> >222324252627br /> <28293031323334353637383940br /> <414243| |4445| |4647484950> >5152> >53br /> <54| |5556| |5758> >596061> >62| |63> >64> >65| |66> >67br /> <68| |6970| |71| |72| |73| |74| |75> >76| |77| |78> >79<
So yes you can knock out 23 without disrupting the reading frame. And as far as genetic architecture goes, this is quite a stable region of the gene, as you are within the rod domain, just downstream of the second hinge. There are no promotors or intitiating codons in 23 either :D Hope that helps
Jonathan said:Ahh now it makes sense. Do you know the connections for the rest of the exons/ or where I can find them? Im interested in exon 23.
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Permalink Reply by Melanie Sunny on
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Julie, here is my son's Gene Test Result and he has a non-sense mutation.
DMD deln/dupln --- NO Deletion/Duplication
DMD Sequencing --- * Sequence Alteration --- Predicted Positive
DNA variant 1: Transversion G> T
Nucleotide position: 2299
Codon position: 767
Amino acid change: Glutamic acid > Amber
DNA variant type: Predicted disease-associated mutation (hemizygous)
No other abnormal DNA sequence variants were identified in the remainder of the coding sequence or intron/exon junctions of this gene.
Please could you let me know which Exon skipping might help my son?
Thank you very so much for your help.
-Melanie
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Hi Melanie,
If my memory serves me correct (and it has been a long time since I looked at nucleotide positions within the DMD gene) your son has a premature stop codon in either exon 17 or exon 18. (I am leaning towards exon 18, as ex17 contains the entire second hinge, and that finishes at the 717 codon). Either way you will require a double skip of both 17 and 18 to restore the reading frame.
Hope that helps :)
Jules
Melanie Sunny said:Julie, here is my son's Gene Test Result and he has a non-sense mutation.
DMD deln/dupln --- NO Deletion/Duplication
DMD Sequencing --- * Sequence position: 767
Amino acid change: Glutamic acid > Amber
DNA variant type: Predicted disease-associated mutation (hemizygous)
No other abnormal DNA sequence variants were identified in the remainder of the coding sequence or intron/exon junctions of this gene.
Please could you let me know which Exon skipping might help my son?
Thank you very so much for your help.
-Melanie
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Thank you very much Julie. - Melanie
Julie Gilmore said:Hi Melanie,
If my memory serves me correct (and it has been a long time since I looked at nucleotide positions within the DMD gene) your son has a premature stop codon in either exon 17 or exon 18. (I am leaning towards exon 18, as ex17 contains the entire second hinge, and that finishes at the 717 codon). Either way you will require a double skip of both 17 and 18 to restore the reading frame.
Hope that helps :)
Jules
Melanie Sunny said:Julie, here is my son's Gene Test Result and he has a non-sense mutation.
DMD deln/dupln --- NO Deletion/Duplication
DMD Sequencing --- * Sequence position: 767
Amino acid change: Glutamic acid > Amber
DNA variant type: Predicted disease-associated mutation (hemizygous)
No other abnormal DNA sequence variants were identified in the remainder of the coding sequence or intron/exon junctions of this gene.
Please could you let me know which Exon skipping might help my son?
Thank you very so much for your help.
-Melanie
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Permalink Reply by Tracey Hartz on
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Julie, you are so good with this! I was wondering about this myself. My son has a stop codon on exon 6-so he'd need a skip of 7 and 8?
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Hi Tracey, as stop codon in 6 would require a triple skip - 6,7 and 8.
:)
Tracey Hartz said:Julie, you are so good with this! I was wondering about this myself. My son has a stop codon on exon 6-so he'd need a skip of 7 and 8?
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Permalink Reply by Deb Robins on
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http://www.dmdregistry.org/reports/predictor/ is a tool you can use to roughly predict candidacy for exon skipping.
Although Jules has more detailed explanations than the tool, Steve Wilton spoke about his exon skipping work at our sydney conference in February & Pat has featured the link to "informative video" from Aussie TV last week in the RSS widget - left hand sidebar here.
Check out our webpage http://www.parentproject.org.au/html/s02_article/article_view.asp?i...
to contact Annemieka Aartsma -Rus who runs the Leiden laypersons website & it is she who also responds to the recent immune response question in the widget too.
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Thanks Julie. I figured that out like an hour after I posted it. :)
Julie Gilmore said:Hi Tracey, as stop codon in 6 would require a triple skip - 6,7 and 8.
:)
Tracey Hartz said:Julie, you are so good with this! I was wondering about this myself. My son has a stop codon on exon 6-so he'd need a skip of 7 and 8?
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