Exon often targeted by mobile element insertions?

Question

[German.M.Demidov]

Dear community members,

not exactly bioinformatic question, but as a bioinformatician I simply don't have accounts at purely biological boards,

I see that a long exon of one particular human disease causing gene is often targeted by mobile elements of different families (LINE1 and ALU) at different positions - so seems that the whole exon is vulnerable.

It happens at a rate certainly higher than random. The question: why?

As a bioinformatician, of course the first thing I thought is "there should be some specific motif" - but how to find such a motif + the insertions happen at different positions.

Which epigenetic data could help to establish the vulnerability of this exon?

Answer 1

[benformatics]

I think that that is a possible explanation you can't necessarily make that assumption.

You can use DNA-methylation or histone methylation to check if the region is "silenced" another alternative would be ATAC-seq to find open chromatin.

Other explanations:

Your disease in question is caused by mutations of this gene in the same specific region and so as expected there is an enrichment of disruptions (e.g. transpositions) in the gene.

The gene in question provides a major fitness benefit when the specific exon is disrupted allowing for cells harboring that mutation to out compete all others (i.e. cancer-like).