>>11716294They didn't do ChIP-seq though, they did ChIP-qPCR which is a little different. Basically, they use an antibody that binds to their protein of choice which is known to bind to a DNA sequence of interest, they isolate the DNA bound to that Ab (or bound to the protein bound to the Ab), wash away all the protein, and then do qPCR, which is like PCR except they can quantify the amounts of DNA. Then they can determine relative amounts of DNA produced from PCR depending on the Ab used, and indirectly determine, relatively, how frequently a protein of interest is binding to a DNA sequence of interest. In figure 1E, they use an Ab against acetylated H3K27 histones to determine histone acetylation before and after mutating position 197. Histone acetylation is typically associated with gene upregulation, and you can see that more HBG promoter DNA was produced from PCR after mutation than before, indicating that that specific mutation causes increased histone H3K27 acetylation. Not too sure what the point of HBB is.
LRF is a transcriptional repressor, and figure F basically just shows that LRF isn't really involved in the mechanism by which mutation 197 causes increased HBG acetylation, although I guess it's still possible.
And an antibody that binds to IgG, another antibody, shouldn't bind to much DNA at all, so it's a good control that should give a negative qPCR result.
