MCC reveals patient-specific enhancer-promoter interactions in primary patient cells. (A) A schematic for the MCC protocol. (B) MCC at the MEIS1 locus using the promoter (blue highlight) as the viewpoint (triangle) for SEM cells (blue) or chALL1 cells (red), or from the chALL1-unique enhancer region (enhancer 27; red highlight), together with TOPmentation for H3K27ac and KMT2A-N. (C) MCC at the RUNX2 locus in chALL1 cells using either the promoter (blue highlight) or open chromatin regions (enhancers 36-47) within the identified enhancer region (red highlight) as the viewpoint (triangle) together with TOPmentation for H3K27ac and KMT2A-N in SEM and chALL1 cells. (D) MCC at the CD69 locus in chALL1 cells using either the promoter (blue highlight) or open chromatin regions (enhancers 14-19) within the identified enhancer regions (red highlight) as the viewpoint (triangle) together with TOPmentation for H3K27ac and KMT2A-N in SEM and chALL1 cells. (E) Expression of CD69 in patients-derived KMT2A::AFF1 blast samples. (F) MCC for the ARID1B viewpoint (triangle) together with ChIP-seq for H3K27ac and KMT2A-N at the ARID1B locus. The SEM-specific intragenic enhancer is highlighted in blue. (G) Expression of ARID1B in patient-derived KMT2A::AFF1 blast samples. (H) Expression of genes linked to chALL1-unique enhancer regions between KMT2A::AFF1 single-cell blast samples.
Figure 6.

MCC reveals patient-specific enhancer-promoter interactions in primary patient cells. (A) A schematic for the MCC protocol. (B) MCC at the MEIS1 locus using the promoter (blue highlight) as the viewpoint (triangle) for SEM cells (blue) or chALL1 cells (red), or from the chALL1-unique enhancer region (enhancer 27; red highlight), together with TOPmentation for H3K27ac and KMT2A-N. (C) MCC at the RUNX2 locus in chALL1 cells using either the promoter (blue highlight) or open chromatin regions (enhancers 36-47) within the identified enhancer region (red highlight) as the viewpoint (triangle) together with TOPmentation for H3K27ac and KMT2A-N in SEM and chALL1 cells. (D) MCC at the CD69 locus in chALL1 cells using either the promoter (blue highlight) or open chromatin regions (enhancers 14-19) within the identified enhancer regions (red highlight) as the viewpoint (triangle) together with TOPmentation for H3K27ac and KMT2A-N in SEM and chALL1 cells. (E) Expression of CD69 in patients-derived KMT2A::AFF1 blast samples. (F) MCC for the ARID1B viewpoint (triangle) together with ChIP-seq for H3K27ac and KMT2A-N at the ARID1B locus. The SEM-specific intragenic enhancer is highlighted in blue. (G) Expression of ARID1B in patient-derived KMT2A::AFF1 blast samples. (H) Expression of genes linked to chALL1-unique enhancer regions between KMT2A::AFF1 single-cell blast samples.

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