Active enhancers for mm39

Question

[Marco Pannone]

Hey!

Does any of you know where it is possible to find the coordinates for all active enhancers in mm39? I need to download them as .bed file for ChIP-seq analysis.

I found some resources online as this one, but unfortunately there are no data based on mm39, only older versions of the mouse genome.

Thanks in advance!

[Matthias Zepper]

Wouldn't liftOver be an option to remap the coordinates to the new assembly? E.g. the mm10 to mm39 chain?

[seidel]

Just curious what you mean by "active" enhancers. Enhancers are active in a given context (e.g. cell type developmental state, etc.), and most are inactive at any given time. Do you mean "known" enhancers? Or do you really mean two kinds of information, enhancers and under what conditions they're known to be active?

[Marco Pannone]

Well yes, I meant enhancers which are known to be transcribed.

[Matthias Zepper]

Then using the enhancers called using by the FANTOM5 project is likely the most promising approach. Since they are defined by CAGE-seq, you can be sure, that they are bivalently transcribed. Unfortunately, the data is not available from their repository until end of March due to maintenance works and would need to be lifted over to mm39 from mm10.

[Marco Pannone]

Thanks a lot for your answer, I will check it out!

Answer 1

[LChart]

Ensembl has a regulatory build for GRCm39:

https://ftp.ensembl.org/pub/current_regulation/mus_musculus/

Note that the elements are defined in the gff3; and activities need to be looked up on a per-sample basis.

At the same time, you can take the (ENCODE-SCREEN) cCRE database from mm10 and lift it over to mm39.