Chromatin state
About chromatin state:

We collected 20 Malus domestica epigenomic datasets, including ChIP-seq, DNase-seq and DNA methylation datasets. A hidden Markov model was applied to aggregate or collapse the multi-dimensional matrices into a small number of chromatin states. We identified 24 chromatin states located in 620,122 segments across the whole genome, and different chromatin states contained different epigenetic features.

All of 24 states:


StatePreferential epigenetics marksPreferential location
State 1weak accessible DNAintergenic,promoter,TE
State 2accessible DNApromoter,intergenic
State 3accessible DNApromoter,intergenic
State 4accessible DNA,H3K4me3,weak H3K27me3promoter,5'UTR,exon,intergenic
State 5accessible DNA,H3K27me3,weak H3K4me3,weak H3K36me2intergenic,promoter
State 6accessible DNAintergenic,promoter
State 7accessible DNAintergenic,promoter
State 8H3K36me2,accessible DNA3'UTR,exon,intergenic,promoter
State 9H3K36me2intron,exon,3'UTR
State 10weak H3K36me2intron
State 11H3K4me3,H3K36me2,weak H3K27me3intron,exon
State 12H3K4me3,weak H3K27me3,weak accessible DNAintron
State 13H3K4me3,H3K27me3,weak accessible DNAexon
State 14H3K4me3,H3K27me3,weak accessible DNAexon
State 15H3K27me3,weak H3K36me2,weak H3K4me3intron,exon
State 16H3K27me3exon,intergenic,promoter,intron
State 17H3K27me3，weak accessible DNAintergenic,promoter,intron,exon
State 18H3K27me3intergenic,TE,promoter
State 19H3K27me3，accessible DNAintergenic,promoter,TE
State 20weak H3K27me3intergenic,TE,promoter
State 21H3K27me3intergenic,TE
State 22H3K27me3TE,intergenic
State 23weak H3K27me3TE,intergenic
State 24rare signalintergenic,TE

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