3D chromatin structure of the PU.1 locus. (A) Genome browser representation showing the Hi-C interaction profile in 72-hour PMA-differentiated THP-1 cells²³  within a 220-kb TAD (chromosome 11: 47 280 000-47 500 000, hg19) containing the PU.1 locus in 10 kb resolution and at the indicated intensity range (top). Visible is the SubTAD structure (dark red triangles). Narrow peak representation of CTCF ChIP-seq data from 72-hour PMA-treated THP-1 cells (GSM2544246) (upper middle). The UCSC gene track is shown below. Interpolated 4C-seq near-cis interaction profile of the PU.1 promoter (VP) in human monocytes (gray dashed line), normalized to reads per million (lower middle). The PU.1 SubTAD is white, and other SubTADs are gray. The plot is representative of 2 biological repeats. UCSC browser view of H3K27ac ChIP-seq track from human monocytes (Gene Expression Omnibus sample accession number GSM1003559) (bottom). Green arrowheads represent position of the PU.1 promoter and the −17-kb URE. Red dashed lines mark the boundaries of the PU.1 SubTAD (chromosome 11: 47 375 000-47 450 000, hg19). (B) Real-time PCR showing PU.1 mRNA expression in healthy monocytes and blast cells isolated from 5 different FAB M5 AML patients. All values are relative to those of GAPDH used as internal control. *P < .05; **P < .01; ***P < .0002 (significantly different variances calculated by the F test, shown in reference to monocytes). Mean and standard error of mean are represented. (C) PU.1 promoter VP 4C-seq profiles within the PU.1 SubTAD boundaries of blast cells from the AML patients indicated in panel B using the same color coding. In all 4C-seq profiles of (A,C), black dots represent running medians of fragment reads, normalized to reads per million, interpolated with a locally estimated scatterplot smoothing (LOESS)–smoothed blue line and gray shading of 20 and 80% quantiles. (D) Running mean near-cis 4C-seq profile overlay visualization with the PU.1 promoter VP (gray dashed line) of the same AML patients shown in panel C with the same color coding. The shown trend lines represent LOESS-smoothed unmasked fragment reads. Red dashed lines mark the boundaries of the PU.1 SubTAD (white area). Green arrowheads at the bottom represent the position of the PU.1 proximal promoter and the URE. chr, chromosome; PP, proximal promoter; RPM, reads per million.