Does H3K27ac generate narrow or broad peaks?
2
0
Entering edit mode
4.6 years ago
jklopp • 0

Hi,

I have been trying to find out whether the H3K27ac Histone modification generates sharp or broad peaks during a ChiP-Seq experiment and therefore to either use the "--broad"-flag in macs2 or not.

Several studies I found (http://www.nature.com/nrg/journal/v12/n1/full/nrg2905.html for example) mentioned that H3K27me3 "and other" histone modifications generate broad peaks but H3K27ac was never explicitly addressed.

In contrast some studies (https://www.researchgate.net/publication/299653522_Identification_of_Epigenetic_Biomarkers_of_Lung_Adenocarcinoma_through_Multi-Omics_Data_Analysis) even treat H3K27ac as narrow peak creating but unfortunately lack suitable sources.

I really appreciate your help!

ChIP-Seq macs2 broad peak H3K27ac • 4.9k views
ADD COMMENT
4
Entering edit mode
4.6 years ago

H3K27ac is a sharpish mark, so you can start with the defaults.

@kennethcondon2007: Some marks (e.g., H3K4Me3) are known to produces sharp distinct peaks. Other marks (e.g., H3K9me3) produce wide >10kb regions of enrichment. ChIPseq itself isn't any noisier than ATACseq or anything else, the noise is due to the underlying biology.

ADD COMMENT
0
Entering edit mode

Clarification always help, thank you :)

ADD REPLY
0
Entering edit mode
4.6 years ago
YaGalbi ★ 1.5k

All the broad flag does is combine narrow peaks that are very close together into 1 peak. Run MACS2 with 1) broad, 2) narrow and 3) gapped options and then view the 3 results in IGV and you'll see it clearly.

Not so sure about the next bit but my 2 cents is...:

I dont think the mark itself produces the "broad" they are referring to. I think the use of the word "broad" is referring to resolution or noise of Chip-seq data, for example ATAC-seq data would be expected to produce narrower peaks than Chip-seq data.

ADD COMMENT

Login before adding your answer.

Traffic: 2135 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6