I have ChIP-seq for H3K79me2 and H3K36me3 and RNA-seq data for treated and untreated samples. Those two histones mark active genes. Lets say, hypothetically, a peak caller finds differential sites at gene A for both of those histone modifications. However, when I run RNA-seq analysis tools (like edgeR or DESeq2) this gene is not marked as differentially expressed (well it has a FDR value of >0.05).
There might be several technical reasons for RNA-seq analysis methods not to find this gene as differentially expressed because
- it is really not differentially expressed
- or it is not differentially expressed enough for the tools to detect it
However, I am more interested in the biological aspect. If two histones mark gene A as active in treated samples, one would expect that it would be expressed in RNA-seq. What mechanism could lead to the result that however the genes is marked as active by histones, it will not be differentially expressed in RNA-seq?