Hi, I am applying the technique ATAC seq for naive T cells in mouse. I am currently in process to analyze my data but i have a difficulty how to know the localization of enhancer in the genome to see its impact at chromatin level and gene expression later. I read some paper that it is related to histone modifications and EP300. Does anyone has any information to help me and thank you.
Achouak
Hi Achouak,
I use H3K27ac mark in T-cells to mark enhancers. In my experience it has worked better than H3K4me1 and H3K9ac marks in this cell type. EP300 chip-seq is already available in Th1 and Th2 cells here.
https://www.ncbi.nlm.nih.gov/pubmed/23178119
Hi I agree with Satyajeet, H3K27Ac is a good mark. But I would consider it in combination with H3K4me1/EP300 and RNA-seq profiles. All tese info may help you to discriminate between actice or poised enhancers and super enhancers. Have a look at this paper: http://www.nature.com/nrg/journal/v15/n4/full/nrg3682.html
Hope this helps and best of luck!
a
Hi, I also agree, combining ATAC-seq data with ChIP-seq H3K27ac and H3K4me1 is a good approach. Let me know if I can help. we have ChIP-seq grade validated antibodies and kits to perform your ChIP-seq experiment.
https://www.diagenode.com/en/index.php
Best,
Geoffrey
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