3C was done essentially as described previously (51) with some modifications. Specifically, mouse Lp30 leukemic GMP cells (Lin cKit+ Sca1 CD150 CD41 FcgRII/III+) were isolated by FACS, while cKit+ WT BM cells were isolated by magnetic-activated cell sorting (MACS) (CD117 magnetic microbeads, Miltenyi Biotech) for comparison. Approximately 2 million cells were used per reaction, fixed in 1.5% formaldehyde in 10 ml of cold PBS/RPMI medium 50%/50% rotating at room temperature for 10 min, and quenched for 2 min in 187 mM of added glycine. Lysis was done by douncing (glass) 10 strokes on ice after 15 min of incubation on ice. Cell fragments/nuclei were recovered by centrifugation at 2200g for 5 min at 4°C and washed once in ice-cold restriction buffer and resuspended in 0.5 ml of restriction buffer. Chromatin was exposed for digestion by a 1-hour incubation with 0.1% of SDS at 37°C, followed by a 1-hour incubation with 1% Triton X-100 at 37°C. Overnight digestion with 200 U of Xba I (R0145T, NEB) with the addition of 100 U of enzyme for the last 4 hours was followed by 30 min of heat inactivation at 65°C. Ligation was performed with 20,000 U of T4 ligase (M0202T, NEB) for 3 hours at 20°C. DNA was isolated by RNase A (19101, QIAGEN) exposure for 30 min, followed by addition of 1 mg of proteinase K (P6556, Sigma-Aldrich) and incubation in 0.4% SDS for 2 hours and phenol-chloroform extraction using phase-lock tubes (713-2536, 5-prime). RT-qPCR was performed as described above, with quadruplicates for each data point and a high-stringency, 50-cycle program. All primers are listed in data file S7.

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