Dear Rongrong

Since super-enhancers are clusters of (more) active enhancers you can indeed define them from the normal enhancer marks - and it is actually via H3K27 some of the first super-enhancers were described.

Take a look at the introduction to the SuperDB paper - they have a nice introduction with many relevant references: https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkv1002

Do however note that transcription based methods are, compared to chromatin based methods, are better at detecting active enhancers. For more info on this see: http://www.nature.com/nature/journal/v507/n7493/full/nature12787.html and https://www.ncbi.nlm.nih.gov/pubmed/25450156 .

Hope this helps

Kristoffer

Dear Rongrong

Super-enhancers can be defined by basically all enhancer marks (Histone marks (activating), openness (ATAC-seq, DHS-seq), co-activators (especially MED1, EP300 and BRD4 have previously been used). You can also define them by transcription factor profiles (especially cell-type definingTFs).

Take a look at http://genome.cshlp.org/content/early/2015/08/04/gr.188300.114 and https://www.ncbi.nlm.nih.gov/pubmed/2727373 and the original publications where they were first charachterized https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3816444/ and http://younglab.wi.mit.edu/publications.htm (several publications)

There are a lot of tools out there to define them, if you do not want to do it yourself but the most widely used is probably ROSE made by the Young lab (http://younglab.wi.mit.edu/super_enhancer_code.html)

Hope you found it helpful

Best 

Bjørk

Dear Rongrong,

what I usually do for defining the super-enhancers is first to delineate a set of active enhancers based on H3K4me1 and K3K27ac ChIP-seq. I then use this set of enriched regions to compute the H3K27ac signal using ROSE (https://bitbucket.org/young_computation/rose) as said above and it give reproducible results which are in accordance with the literature. Good luck!