Fig. 4. CTCF binding is not required to maintain gene expression or chromatin boundaries in the HOXA gene cluster.

a RT-qPCR for HOXA9 in single mutants with heterozygous or homozygous deletions at CBSA6/7, CBSA7/9, or CBSA10. HOXA9 expression from the Kasumi-1 cell line is shown in blue as a no-HOXA9 expressing control. No statistically significant differences were identified between wild-type OCI-AML3 and homozygous mutants (Bonferroni-corrected P > 0.05 using a two-sided unpaired T-test for all comparisons). b RT-qPCR for HOXA9 in double and triple mutants at the CTCF binding sites indicated. Kasumi-1 cells are included in blue as in a. ** denotes a Bonferroni-corrected P < 0.01 between wild-type OCI-AML3 and CBSA7/9-CBSA10 double mutant clones using a two-sided unpaired T-test. c–f RNA-seq expression of all HOXA genes in single mutants (c–e) and triple mutants (d). Expression level is shown in log₂ transcripts per million (TPM), with lines connecting expression values derived from the same mutant clones and/or the same RNA-seq experiment (for wild-type OCI-AML3 cells). g ChIP-seq for H3K4me3 and H3K27me3 in deletion mutants lacking CTCF at site CBSA7/9 (in red; N = 2). Mean ChIP-seq signal from wild-type OCI-AML3 cells (N = 2) is shown in gray. h Mean ChIP-seq for H3K4me3 and H3K27me3 in triple mutants (N = 2), with ChIP-seq from wild-type cells shown in gray, as in g.