Mouse Enhancers Database/ Mouse Enhancer annotation

Question

[lucatucciarone]

Hello guys, new to the club.

I'm interested in intersecting my AcH3k27 peaks with some enhancers signature (or known enhancers) in mouse fibroblasts.

I have a couple of questions in this regard:

1) How much are enhancers signatures "Stable" across cell lines? I can understand AcH3k27 changing (Because is relative to enhancer activation) but I cannot see why Enhancers signatures should actually change between different cell lines. I am not talking about signal magnitude but the mere presence of the signature.

2) Other than H3K4me1, how can one identify and annotate enhancers? Have they been annotated? I do have a good ChIP-seq for AcH3k27 and a NA-seq for this primary mouse cells and I'm very curious to have a look at Enhancers role in my experimental settings. If you would have only this 2 dataset at hand, how would you take enhancers into consideration?

Thanks a lot;

Luca

[lucatucciarone]

Thank you very much! This resource will be super helpful for sure. Just a curiosity, would you think H3K27Ac is enough to describe an enhancer? Or Have it to be coupled with H3K4me1?

Thank you a lot again!

[jomo018]

According to this reference: http://www.statehub.org, H3K4me1 is related to the regulatory function whereas H3K27ac is related to level of activity.

Answer 1

[jomo018]

For enhancer list, consider http://www.enhanceratlas.org/download2.php. Click download enhancers and scroll to mouse tissue for Fibroblast.

On page http://www.enhanceratlas.org/index2.php you can find a short description of their method along with a reference.