Comparison of Chromatin Modifications and Transcription Factor Binding in Responsive vs. Non-responsive Genes

Jan 25, 2026

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This study analyzes the differences in chromatin modifications (H3K4me3, H3K27me3, etc.) and transcription factor binding (e.g., Cdx2, Pou5f1, Sox2) between responsive and non-responsive genes lacking CpG islands. Data was carefully examined to highlight the proportion of genes with various histone marks, transcription factor binding motifs, and their respective gene expression responses. The findings contribute to understanding gene regulation and the role of chromatin dynamics in embryonic stem cell pluripotency and differentiation.

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Comparison of Chromatin Modifications and Transcription Factor Binding in Responsive vs. Non-responsive Genes

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Genes: Responsive Non-responsive H3K4me3 H3K27me3 H3K36me3 H3K9me3 Cdx2 Pou5f1 Sox2 Nanog Stat3 Smad1 Klf4 Zfx E2f1 Myc Mycn Esrrb Tcfcp2l1 Ctcf Cdx2 Pou5f1 Sox2 Nanog Stat3 Smad1 Klf4 Zfx E2f1 Myc Mycn Esrrb Tcfcp2l1 Ctcf Brg1 GABP NRF1 YY1 MIT004 MIT008 TATA 1 TF binding motifs Binding of TFs Chromatin 0.8 0.6 Proportion of genes 0.4 n/s n/s n/s n/s 0.2 n/s n/s n/s n/s n/s n/s n/s n/s n/s n/s 0 <1 Kb <0.3 Kb from TSS 0.3 to 15 Kb from TSS Additional File 13.Comparison of chromatin modifications [7], binding of transcription factors [9, 16, 17], and binding motifs among responsive and non-responsive genes with no CpG islands; “n/s” = non-significant.