What makes a transcription factor bind and another not? Let's say a certain promoter has binding sites for TF A and B, and those TF are freely available. What can be the reason for the binding of A and not B? It's just a timing issue? Or it could be that these binding sites are separated by different nucleosomes and, as such, in one the histone tails are acetylated (and one binds) and in the other nucleosome histone tails are not (and the other doesn't bind)? Or even if all binding sites are around the same nucleosome, can histone acetylation be different between one binding site and the other? Let's say a difference of about 100bp from one to the other?
In ChIP analysis, if I IP for Ac-H3 and then ampliffy two different sequences on the same promoter, one for the binding site of A and another for B, can it be that the Ac-H3 is bigger in one of these sequences and in the other remains unchanged? (mRNA increases overall)
Thank you all for your input!
If a stretch of DNA is wrapped around a histone, then it probably doesn't have a transcription factor functionally bound to it...
So it's a question of at that point whether the binding site is in the linker DNA or part of the nucleosome?
Yes, or more generally whether the DNA is accessible, since if the histones are packed together it doesn't much matter whether a binding site is in a linker region or not.
And this difference in histone packing in theory can happen even in a very short distance, let's say 200bp?
Presumably, since ~140 bases of DNA will wrap around a single histone and that's the unit at which compaction will be occurring.