H3K4me3 in promoter regions, which are free of nucleosomes

Question

[panacotaforcota]

Hello!

I'm trying to deal with histone mark and their localization on the genome. I read that marks H3K4me3 are localized in the promoter regions. But I know that promoters are free of nucleosomes. How is this possible? Do I understand correctly that the presence of histone marks from an experiment Chip-seq means the presence of a nucleosome in this region? I read several articles, but did not find the answer.

I will be glad to any answer, especially useful articles on this topic.

Answer 1

[ATpoint]

Promoters are not free of nucleosomes but there is a nucleosome-free stretch of DNA at which the DNA-binding machinery assembles. This is flanked by histones that undergo modifications at, e.g. their lysin tails (K4).

[panacotaforcota]

Thank you very much! It becomes clearer. So, is it true that the data from the Chip-seq experiment correspond to the active state? Or is it an inactive state, but with histone marks that are there all the time?

[colin.kern]

There is some research that has found H3K4me3 is generally found in all high CpG promoters (the majority in human) regardless of transcriptional activity, but are only present at low CpG promoters when the gene is actively transcribed (https://www.nature.com/articles/nature06008 ). H3K27ac may be more predictive of active transcription at promoters/TSS than H3K4me3 (see https://www.pnas.org/content/107/7/2926 ).

[panacotaforcota]

Thank you for these articles! Exactly what is needed!

[ATpoint]

From what I understand H3K4me3 is often referred to as a "promoter mark", even though it boils down to an indication for active transcription.