Help with an ATAC-seq cartoon

Question

[Chris]

Hi all,

Would you please explain why we don't observe peaks in open chromatin region in this cartoon (The blue ATAC line in the bottom)? I mean the region between chromosomes. Meanwhile the regions have DNA wrap around chromosome have peaks. Thank you so much!

Answer 1

[rfran010]

I think what they are trying to depict is a situation where the distance between nucleosomes is only big enough for one transposition event, so you recover the nucleosome protected fragments because you would cut to the left and right of the nucleosome. If you piled up the fragment ends you would get peaks in between the nucleosomes instead. Also, I think with real data you would likely get coverage of fragments over these sites as well.