What is the possible effects of a homozygous deletion in the 5' end of a gene on gene expression at the level of RNA?
Hi Mahmoud,
assuming the gene is expressed, it is likely that the 3' part of the gene is still expressed also after deletion of the 5' end. So if analyzing for example RNAseq, you'd still detect reads of the first few exons.
We have observed this for example for SMAD4 deletions in some cell lines we charaterized: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4924731/
Figure 3 shows the DNA and RNA signal for 2 cell lines with partial deletions of SMAD4. The probes which are in deleted exons (lower signal in the copy number panel) also show extremely low signal in the expression array. The probes in exons that are not deleted, show normal expression level.
Dear Arnoud,
Thanks a lot of r your reply. I have identified homozygous deletion in the 5' of the deletion in a patient when I assessed the expression by qPCR with primers i the 5' part. I got the upper chart which is consistent with the CNV. The expression in the patient is nearly nothing, and the mother Carrier has expression level half the level of the normal control. With primers in the 3' part of the gene, there are doubling the expression level of the patient compared to the mother and control??? I don't know how we can justify this??
Hi Mahmoud,
I don't have a solid explanation for this, but one option would be a feedback loop?
(the cell notices it doesn't have enough of your gene of interest, and tries to upregulate?)
Well, I have the same explanation of feedback loop but is it true? The problem is that the antibody against that protein is towards the c-Terminus and I am expecting to see more protein in the patient compared to the control. I will try the WB and see!!
Thanks a lot
I think it's not very easy to prove, one would have to make such a deletion themselves in a cell line, and compare expression before and after deletion? (or inhibit the feedback loop somehow, like overexpressing your protein, and seeing whether the expression of your target gene lowers again?)
how informative will protein levels be? as you have a huge deletion, it's possible that the protein stability will be affected?
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