Tomato chromatin states

We collected 136 Solanum lycopersicum epigenomic datasets, including ChIP-seq, DNase-seq and DNA methylation data. A Hidden Markov Model was applied to aggregate or collapse the multi-dimensional matrices into a small number of chromatin states. We identified 35 chromatin states located in 977,473 segments across the whole genome and different chromatin states contained different epigenetic features.

All of 35 states:

Annotation of chromatin state:

StatePreferential epigenetics marksPreferential location
State 1accessible DNA, H3K36me3(weak signal), DNA methylationintergenic, promoter
State 2accessible DNA, H3K36me3, H3K4me2, H3K27me3, DNA methylation, H3K9me3, H3K4me3promoter，intergenic
State 3accessible DNA, H3K4me3, H3K27acpromoter
State 4accessible DNA, H3K27ac(weak signal)promoter，intergenic
State 5accessible DNA, H3K27ac(weak signal)promoter，intergenic
State 6accessible DNA(weak signal), H3K27ac(weak signal), weak DNA methylationpromoter，intergenic
State 7H3K4me3, H3K27ac(weak signal), accessible DNA(weak signal)exon, promoter
State 8H3K4me3, accessible DNA, H3K27acpromoter, miRNA, 5'UTR
State 9H3K4me3, H3K27ac, accessible DNA, H3K36me3, H3K4me25'UTR, exon, miRNA, promoter
State 10H3K4me3, H3K27ac, H3K36me3, H3K4me2, accessible DNA(weak signal)exon, intron
State 11H3K27ac, H3K4me3, H3K36me3, H3K4me2, accessible DNA(weak signal)exon, miRNA, intron
State 12H3K27ac, accessible DNA, H3K4me3(weak signal)3'UTR, exon
State 13H3K27ac, accessible DNAexon, 3'UTR
State 14accessible DNA(weak signal)exon, intron
State 15H3K36me3, H3K4me3, H3K27ac, accessible DNA(weak signal)exon, intron
State 16H3K36me3, accessible DNA(weak signal), H3K4me3(weak signal)exon, intron
State 17H3K36me3, accessible DNA(weak signal)exon, intron
State 18H3K27me3intergenic
State 19H3K27me3, DNA methylationintergenic, TE
State 20H3K27me3intergenic
State 21H3K27me3intergenic
State 22H3K27me3intergenic
State 23H3K27me3, H3K4me3(weak signal)intergenic, miRNA
State 24H3K27me3, H3K4me3, accessible DNA(weak signal), H3K27ac(weak signal)miRNA, exon
State 25H3K9me3, H3K27ac, H3K27me3, H3K4me2, H3K36me3, accessible DNA, H3K4me3, DNA methylationintergenic, TE, promoter
State 26H3K9me3, H3K4me2, H3K27ac, H3K27me3, H3K36me3, accessible DNA, H3K4me3, DNA methylationintergenic, TE
State 27DNA methylation,H3K27ac, H3K27me3, H3K4me2, H3K4me3，accessible DNA(weak signal) intergenic, TE
State 28DNA methylation, H3K27me3, H3K27ac(weak signal), H3K4me2(weak signal), H3K9me3(weak signal)intergenic, TE
State 29DNA methylation, H3K27me3, H3K9me3(weak signal), H3K27ac(weak signal)intergenic, TE
State 30DNA methylationintergenic, TE
State 31accessible DNA(fruit 47DPA specific), DNA methylationintergenic, TE
State 32H3K27me3(fruit 17DPA specific), DNA methylationintergenic, TE
State 33H3K27me3(fruit 17DPA specific), DNA methylationintergenic, TE
State 34H3K27me3(weak signal), accessible DNA(weak signal)intergenic, TE
State 35rare signalintergenic
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Maintained by Jiajie She in Zhen Su's Lab | China Agricultural University
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