Clearly formed IgG Peaks in CLIP-Seq

Question

[IV]

Hello Biostars,

I saw recently a CLIP-Seq control dataset using IgG as controls and there were few but clearly shaped peaks.

Shape (clear columns, reads stacked ontop of the other, no scattering), size (30-50bp, which was legit for the experiment) and numbers of reads (strong enrichment) looked like the peaks that you originally get from the non-control samples.

I wanted to ask how often have you seen really clearly shaped peaks (not noise with variable levels of read counts) in a relevant setting.

Thanks a lot,

IV

Answer 1

[bede.portz]

While I don't have CLIP-seq experience, I have ChIP-seq experience specifically using a protocol with inherently low background relative to other methodologies. In the absence of of any IgG, or with a pre-immune serum control, it is possible to see peaks. This is in essence the point of the no-IgG, or non-specific IgG control. Certainly with ChIP-seq, there are regions of the genome where peaks can be found with any IgG or no IgG control, so called "blacklist" regions. Given the myriad conformations RNA can adopt (the very phenomena enabling experiments like SELEX that generate RNA aptamers) I guess I am not surprised that specific RNA can be enriched in a CLIP-seq control experiment.