ChIP-seq of conventional TFs: what are the peaks w/o the motif?

[apredeus]

Hello all,

I've read several papers estimating the quality of ChIP-seq and most estimate percentage of peaks that include the consensus sequence at about 50%. Having lower FDR does not improve this very dramatically (to 70% maybe).

So what are the high confidence peaks that do not contain the target motif? What causes them? Is there a systematic study of any sort?

I'd be grateful for any pointers.

cheers

[sowmyai]

Here is our GR paper that might have some answers

http://genome.cshlp.org/content/22/9/1798.long

[apredeus]

Thank you, this would certainly help!

[mlodato]

One source would by DNA looping. For example, if a TF binds to an enhancer, which then loops to a promoter, the TF would remain bound and at some frequency be cross-linked during a ChIP experiment to the promoter sequence, where there might not be a binding site.