It's a little bit general, but I think there is no reference protocol, so I thought to ask here if someone has an idea.
So, if I have few different histone methylation and TF chip-seq around certain gene. By the way, all of them are coming from different studies. How can I say that this epigenetic change in the histone mark would affect the transcription?
Reference protocols, experiences and papers are highly appreciated
Histone deacetylase (HDAC) is a major class of deacetylation enzymes. Many HDACs exist in large protein complexes in cells and their functions strongly depend on the complex composition. The identification of HDAC‐associated proteins is highly important in understanding their molecular mechanisms. Although affinity probes have been developed to study HDACs, they were mostly targeting the direct binder HDAC, while other proteins in the complex remain under‐explored. We report a DNA‐based affinity labeling method capable of presenting different probe configurations without the need for preparing multiple probes. Using one binding probe, 9 probe configurations were created to profile HDAC complexes. Notably, this method identified indirect HDAC binders that may be inaccessible to traditional affinity probes, and it also revealed new biological implications for HDAC‐associated proteins. This study provided a simple and broadly applicable method for characterizing protein‐protein interactions.
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