Input ChIP-seq coverage changes at centromere/telomeres

Question

[Carlo Yague]

Hi guys,

I'm looking at ChIP-seq input DNA (sonicated chromatin) and I see big differences in mapped reads coverage between conditions (WT vs mutant of S.pombe ) at centromeres and sub-telomeric regions.

input DNA : test vs ctl (image generated with the CNV-seq package)

How can I interpret such differences ?

1. Is it copy number variation ? That would make sense at telomeres because there is a two-fold increase in coverage. But what about the centromeres ?

2. Could it be differences in chromatin accessibility impacting the sonication process ?

3. In general, how do you make a difference between chromatin accessibility changes or copy number variation ?

Any suggestion is welcome !

Thanks,

Carlo