Fig. 4
From: Sparse conserved under-methylated CpGs are associated with high-order chromatin structure
Cell lineage scUMCs are associated with the dynamic regulation of chromatin loops. a Processes and functions enriched for cell lineage-specific scUMCs. Functional significance of scUMCs differentially methylated between ESCs and blood cell lineages were predicted by GREAT 2.0. Y-axis represents the log-transformed, FDR-corrected hypergeometric p value. Ontology sources are color-coded: Gene Ontology Biological Process (BP), Cellular Component (CC), Molecular Function (MF), and Mouse Genome Informatics Phenotype (MP). Associations in GREAT based on gene-regulatory domain basal (±3 kb TSS) plus up to 500-kb extension. b Dynamic occupancy of chromatin-looping factors (Rad21, Znf143, and CTCF) in GM12878 (coral) and H1 (green) cells at regions centered on scUMCs: blood-specific, ESC-specific, or control. c Distribution of Rad21 chromatin-looping interaction intensities in GM12878 cells [14] for anchor regions overlapping scUMCs: blood-specific, ESC-specific, or control. *P value < 0.05, Wilcoxon signed-rank test, one-tail. d Representative genomic region of a blood-specific scUMCs. Top, ChIP-seq signal densities of Rad21, Znf143, CTCF in GM12878 and H1 cells. Bottom, CpG methylation ratios in ESCs or blood-lineage cells