I'd like to generate a reference-dataset of coordinates for the -1, NFR, +1 nucleosome region surrounding the TSS of genes. I've seen that several papers use datasets such as MNase to do this sort of mapping, but I have not been able to find MNase-seq data in the HCT116 cell line unfortunately.
- I'd like to know if there is another way to create this dataset?
- Are NFR regions conserved enough that I could possibly use several MNase-seq datasets from other cell lines to identify these regions in mine?
- Could I use DHS to identify these regions instead? I've read that not all TSS will have DHS sites because they are known to mark transcriptionally active regions of the genome so I've been hesitant to spend the time hunting down datasets for my cell line.