Histone Peak Profiles for ChIP

Histone marks have unique distributions across the genome, and are often have different functions in gene regulation. Therefore, their distribution profiles affects how peak callers should be used to identify peaks.

Here we summarize the distribution profiles of some common histone marks, many of which are adapted from the ENCODE project.

In addition, RNA polymerase often has different post-translational modifications on its tail to regulate RNA polymerase activity. These modifications can be used to identify active transcription sites. Phosphorylation of RNA polymerase II at serine 5 (Pol2S5P) is a common mark for active transcription initiation, while phosphorylation at serine 2 (Pol2S2P) is a common mark for active transcription elongation. We also include structural proteins that has stable binding sites across the genome.

Here we summarize the distribution profiles of some common histone marks and RNA polymerase marks:

Broad peak	Narrow peak	Exception
H3F3A	H2AFZ	H3K9me3
H3K27me3	H3ac
H3K36me3	H3K27ac
H3K4me1	H3K4me2
H3K79me2	H3K4me3
H3K79me3	H3K9ac
H3K9me1	H2AUb119
H3K9me2	CTCF
H4K20me1	RNAP-pSer5
RNAP-pSer2

Although H3K9me3 is an exception due to the fact that most of these peaks reside in repetitive regions, it can be called as a broad peak.