I have deleted 58bp from a gene in a breast cancer cell line using CRISPR. At a transcript level, I have approximately 99% knockdown but I still detect equal amounts of protein in both the parental and knockout cell line. How is this possible?
58bp deletion should change the entire reading frame, so there is some problem if you still see your protein.
Here some points to consider: 1) Which region of the gene was deleted (exon/intron)? Alternative splicing could be a problem, if the deletion took place in the spliced exon.
2) 99% transkript knockdown. How was it determined ? May be there are still transkript, which escaped your detection but permitting translation of your protein.
3) Protein detection issue: Are your sure to detect your protein and not something else? If it is antibody-based detection (like WB) do you know the epitop of the antibody? If your deletion takes place in c-terminal part of the gene but the antibody recognize the N-terminal epitop, you may still get signal with it, but the detected protein should differ in size.
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