Figure 1
Characterization of 5hmC patterns in undifferentiated and retinoic acid differentiated NCCIT embryonic carcinoma cells. (A) Promoters, CGIs, and genes with peaks of 5hmC in UD NCCIT human ECCs (hECC) and H1 human ESCs (hESC) were compared. Numbers represent features common between or exclusive to UD hECCs and H1 hESCs. Overlapping sets in all three features were statistically significant (P < 0.0001). (B) Log2 tag density of 5hmC- and 5mC-sequencing in UD and DF cells from -5 to +5 kb across promoters, across gene bodies (represented as a percentage from 25% to 75%) and -5 to +5 kb across the TSS. Dotted lines represent TSS, +5 kb from TSS/25% of gene body, 75% of gene body/-5 kb from transcription termination site (TTS), and TTS. (C) 5hmC tag density across exons with high (HCP), intermediate (ICP), and low (LCP) CpG density promoters and (D) across CGIs in promoters, gene bodies, and intergenic regions. (E) Number of gene promoters and gene bodies with differential 5hmC upon RA differentiation of NCCIT cells. (F) Promoters and gene bodies with elevated 5hmC in DF cells were compared to genes whose expression increased upon differentiation. Blue and yellow bars represent overlapping genes with differential 5hmC and increased expression (shown as a percentage of upregulated genes); the grey bar represents the percentage of all differentiation-upregulated genes in the genome. Transcriptionally upregulated genes with gain of 5hmC are significantly overrepresented (*P < 0.0001). (G) Ontology analysis of upregulated genes with increased 5hmC enrichment. (H) Examples of the three types of 5hmC changes observed in DF cells: (i) increased 5hmC; (ii) partial loss and redistribution of 5hmC; and (iii) total or near complete loss of 5hmC.