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Is it typical to find a ~30 bp motif enriched in promoters of ~20 related genes?
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20 months ago
biostart • 290
Germany

Hello,

I am observing an enrichment of a ~30 bp motif in promoters of a group of ~20 genes of my interest. I guess, it is too large for a single TF binding site. Just wonder, is a typical thing to find such a large motif or rather not typical?

Thanks!

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It also depends on the target proteins. If the data is from histone modification study, you may find long motifs as histones spans a large part of DNA. Hence, reads generated from those regions gives you long motifs.

What is the target protein of your experiment/data ?

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23 days ago
RamRS 21k
Houston, TX

30 bp is indeed too large for a single motif. My guess is that the region might be a set of motifs along with smaller, less conserved regions to bind a TF complex. Did you try comparing your motif with the consensus of common motifs or looking up the genomic location on TF databases?

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Yes, I did compared with the consensus of common motifs - it is recognized by a bunch of different TFs. This by itself is not surprising, since the genes I am looking at are co-regulated, and it is expected that they have some common TFs binding at the promoter. What I did not expect was to find such a large motif, which indeed looks like an assembly place for a larger TF complex. Still, my question remains: is it typical to find such a large common region in so many gene promoters?

PS. The motif was initially identified using MEME with standard parameters

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I've never seen TF motifs longer than 8, but my experience is not extensive. My mentor did state that the majority are either 6-mers or 8-mers.

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