What do you think about ChIP-seq with proteins that are highly mobile in nature? Why is there less data published about using them?
The problem with mobile proteins is not that they are mobile per say but more that they are less likely to be a particular location. By fixing the cells, we are freezing them at a specific moment in time. However, ChIP-seq is designed to use populations of fragments to see where a protein is enriched in a given cell type. If a protein doesn’t have any sites where it is preferentially binding, the ChIP can’t work. However, there are some mobile proteins that are somewhat commonly ChIPed including RNA Pol II and cohesin. – answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde.
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