Fig. 2
Isolated genetic variants within GATA1 peaks co-occur with dramatic changes in GATA1 binding and nearby transcription. a Summary of discSNP pairs in GATA1 peaks (200 bp, n = 35,166). b GATA1 ChIP-seq intensity tracks (input and library-size-normalized, identical y-axis scales) reveal dramatic changes in GATA1 binding associated with single-nucleotide variants adjacent to (chr3: 66,455,298 - 66,457,298) or within (chr19: 46,129,935 - 46,131,935) a GATA1 motif (no other discSNPs within 1 kb). Dotted vertical line indicates discSNP position. c GATA1 ChIP-qPCR at native (N) loci in either G1E-ER4 or MEL cells where one cell line contains an intact (I) GATA1 motif and the other cell line has a disrupted (D) motif. A 200-bp region centered on these intact/disrupted motifs was barcoded and cloned into ectopic (E) locations in G1E-ER4 cells and GATA1 ChIP-qPCR was performed at these sites. Mean ± SEM, n = 3. d GATA1 ChIP-qPCR and e RT-qPCR in 5 MEL clones edited at a control locus (WT) or at the Bola1-proximal GATA1 peak. For d–e, mean ± SEM, n = 3. f For discSNPs found in TSS-proximal GATA1 peaks, Pearson's correlation coefficients between delta GATA1 binding and delta transcription at a range of FDR cutoffs for differential binding. g Scatterplot of delta GATA1 binding vs. delta transcription at an FDR cutoff of 1e−4, PCC = 0.43. h Pearson's correlation coefficients between delta GATA1 binding and delta transcription at a range of cutoffs for distance between the GATA1 peak and nearby TSS. For f–h, error bars are 95% confidence intervals, *p = 0.03, **p < 0.001 (Fisher’s Z-transform)
