Table 1 Histone modifications and transcription factor binding sites used in our experiments
From: ProbC: joint modeling of epigenome and transcriptome effects in 3D genome
Species & cell type | Histone modifications | Transcription factor binding sites |
|---|---|---|
Human ES | H3K4me1, H3K4me3, H3K9me3, H3K27ac, H3K79me2, H3K36me3, H4K20me1, H3K27me3, H3K56ac, H3K23ac, H2AK5ac, H2A.Z, H3K9ac, H3K4me2, H4K8ac, H3K18ac | CTCF, SMC3, MAFK, CHD1, POLR2A, Dnase I, RAD21, CEBPB, MAZ, FOS, USF2, RCOR1, RFX5, ELK1, MXI1, NFE2L2 |
Human IMR90 | H3K4me1, H3K4me3, H3K9me3, H3K27ac, H3K79me2, H3K36me3, H4K20me1, H3K27me3, H3K56ac, H3K23ac, H2AK5ac, H2A.Z, H3K9ac, H3K4me2, H4K8ac, H3K18ac | CTCF, SMC3, MAFK, CHD1, POLR2A, Dnase I, RAD21, CEBPB, MAZ, FOS, USF2, RCOR1, RFX5, ELK1, MXI1, NFE2L2 |
Mouse ES | H3K4me3, H3K27ac, H3K36me3, H3K4me1, H3K9me3, H3K27me3, H3K9ac | CTCF, POLR2A, EP300, MAFK, CHD2, HCFC1, ZC3H11A, ZNF384 |