Is it possible for a TF to bind to closed chromatin without opening it? I mean, is it possible for chip-seq peaks of non-pioneer TFs to exist in closed chromatin?
If it is, can we assume that TF does not affect the gene expression of the corresponding gene?
Chromatin activation marks contributing to change in gene expression, like H3K4me3, show up in the sequence of the gene or are they in the TF binding site?
Do chromatin activation marks correspond to gene expression activation or does it just mean chromatin is available to bind TFs and depending if the TF is repressor or activator, gene expression decreases or increases?
Thanks in advance :)