Fig. 4

2C-ChIP analysis of a differentiation time course identifies a HOXA cluster region resistant to H3K27me3 demethylation. a Time points of RA-induced NT2-D1 differentiation examined in this study. b Steady state transcript levels of HOXA and lncRNA genes as measured by RT-qPCR during RA treatment. RNA levels relative to actin are shown on the y-axis. Dashed lines indicate values below which measurements are unreliable. Oligonucleotide sequences used for quantification are shown in Additional file 1: Table S1. All RNA measurements are from at least three PCRs. c-h 2C-ChIP analysis of H3K4me3 and H3K27me3 levels, and of the chromatin-binding proteins Ash2L, SUZ12, CTCF, and UTX during the RA induction time course. 2C-ChIP tracks are presented as described in Fig. 2f and Additional file 7: Figure S1. The dashed black box identifies a HOXA cluster region slow to lose H3K27me3 signal. 2C-ChIP BED files including surrounding negative controls are in Additional file 6: BED file 7–30