Which Are Proteins Not Binding At Promoters [Chip-Seq/Mouse]

Question

[Sukhi Singh]

We are doing promoter centric analysis for the proteins which bind at promoters and regulate the gene expression. Just to use as a negative control, I am looking for a protein, which doesn't bind at promoters like p300 and specifically the ChIP-Sequencing datasets to include in the study. Can someone suggest a few, with or without GEO (I can lookup for them) in Mouse.

Much appreciated!!

Answer 1

[André Rendeiro]

I'd say the best chance would probably be a chromatin modification, since there's a lot of datasets and some are not usually at promoters, but that also depends on what you define as a promoter (I work with more compact genomes that mammals) and what you call 'binding'.

If you're looking for something that does not have a peak like p300 and in general is not in promoters I'd say H3K4me1 could be ok. But if you're looking for something that has the binding-pattern of a TF (peak-like) and not a more spread domain like most chromatin modifications, then H3K4me1 might not be for you.

[André Rendeiro]

I just saw after answering, that this question is 3 months old. Still I'm curious about which protein you ended up using...