Why does "Input" sample give a sharp peak around TSS?

[lee_sh]

Hi. I found this forum by google and this is my first time posting thread here. Now I meet a problem in ChIP-seq. There is a sharp peak around TSS region in my Input samples. Although I have heard that the TSS region might be more sensitivity to sonication, my Input sample give so sharp peak around TSS region. Have anyone met this problem too? Why?

[ETHANol]

You should post this in the epigenetics forum but the answer is open chromatin sonicates more efficiently. Check out FAIRE-seq

http://www.ncbi.nlm.nih.gov/pubmed/17179217

The question is how to minimize this effect.

[simonandrews]

Are you sure that it's a peak at the TSS, rather than a trough before? We saw this in a number of different samples and it turned out that the major cause (although there may be others) was a loss of mappability in promoters containing CpG islands. If we separated out our transcripts into those whose promoter contained CpG islands, and those which didn't then we saw very different shaped profiles.

[lee_sh]

You should post this in the epigenetics forum but the answer is open chromatin sonicates more efficiently. Check out FAIRE-seq

http://www.ncbi.nlm.nih.gov/pubmed/17179217

The question is how to minimize this effect.

Thank you for your answer and literature. It seems that sonication quality is important for ChIP-seq and the natural enrichment around TSS is hard to avoid.

[lee_sh]

Senior Member: In my samples, it is a peak/enrichment around TSS and a trough around TES. I did twice ChIP-seq: one is not so sharp, but another one is very sharp and affect my decision on the ChIP lane.

Yeah, I also saw trough aroudn TSS in "Input" of other people's samples. Your explanation for trough around TSS seems to be a good answer for such phenomenon. Thanks a lot!