Dear all,
From this page in ENCODE
https://www.encodeproject.org/search/?type=Experiment&status=released&assay_slims=DNA+binding&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&award.project=Roadmap&biosample_term_name=IMR-90
I can get the Chip-Seq of different histone modifications, but how can I get Chip-Seq of unmodified H3 to get the Incative domains? I want to follow the method described in this nature paper to know the active, inactive and repressed domains..
https://www.nature.com/articles/nature16496
for active and repressed, they can know them based on histone modifications, while for inactive domains, they know it with the dominance of unmodified H3.
Thank you
Hi Ahmed,
In the Nature paper you refer to, the inactive domain is mostly defined as regions where four marks are absent: H3K4me2, H3K79me3, H3K27me3 and H3K9me2. This they determine by calculating absence of enrichment of these marks over a ChIP-seq data set that covers most of the genome (i.e. H3)
See the supplementary information for more information:
https://images-nature-com.insb.bib.cnrs.fr/original/nature-assets/nature/journal/v529/n7586/extref/nature16496-s1.pdf
The ENCODE consortium apparently didn't include H3 for IMR90 cells. But they also didn't include H3K79me3 or H3K9me2. You will therefore need to redefine your markers for active and repressed chromatin first.
To calculate enrichments, you next need to find a data source that covers most of the genome. You have 2 options here:
1. In our hands, the Input (or 'control' on the Encode page) is very similar to H3. You can therefore use this instead. This is prefered, because the chromatin was treated in the same way.
2. Another option is to take published H3 data in IMR90 from another study. For instance this one: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1418957
Here you will not know though, if the material was treated very different between experiments.
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