Extended Data Fig. 1: Dense perturbation of the β-globin locus.
From: Transcription factor competition at the γ-globin promoters controls hemoglobin switching
a, Flow chart of the dense perturbation experiment design. b, Zoomed in view of the dense perturbation results at HBB and HBD genes. gRNAs that target the exons are enriched in Cas9 experiment. HbF raw score is enrichment of individual gRNAs in HbF-high compared to unsorted population at end of erythroid maturation, plotted as log2 fold change. HbF score shows deconvoluted underlying genomic regulatory signal with corresponding p-values shown on -log10 scale. c, Zoomed in view of the dense perturbation results at HBG1 gene. Not that gRNAs that target the exons are depleted in Cas9 experiment. d, Zoomed in view of the dCas9 dense perturbation result at HS3 of the LCR aligned to PhastCons46way scores. The four regions highlighted in green contain GATA1 or GATA1-TAL1 composite motifs (CTG[N8-9]GATA), with the sequences shown below. e, RT-qPCR showing that dCas9/sgRNA binding at -115 of γ-globin promoters reduced γ-globin expression in HUDEP-2 cells. Note that the γ-globin is only expressed at a basal level in cells expressing AAVS1 control sgRNA. The result is shown as mean (SD) of three technical replicates. Statistical tests of the beta coefficients were performed empirically through bootstrapping and two-tailed tests. Multiple hypothesis testing was accounted for with the Benjamini-Hochberg (BH) procedure.
