Fig. 1: LRF BS disruption and KLF1 BS creation in the HBG1/2 promoters in K562 cells.

a Schematic representation of the β-globin locus on chromosome 11, depicting the 5’ hypersensitive sites of the locus control region (5’ LCR HSs; gray boxes), HBE1, HBG2, HBG1, HBD, and HBB genes (colored boxes), the HBG2 and HBG1 promoters (white boxes) and the 3’ hypersensitive to DNase I site (3’HS). The sequence of the HBG2 and HBG1 identical promoters, from –212 to –179 nucleotides upstream of the HBG transcription start sites, is shown below. Red and green ovals indicate LRF repressor and KLF1 activator. HPFH mutations identified in the HBG1 and/or HBG2 promoters are highlighted by black arrows, and HPFH mutations that can be reproduced by ABEs or CBEs are highlighted in green and red, respectively. The percentage of HbF expression in heterozygous HPFH carriers and carriers of SCD (*) or β-thalassemia (**) is indicated in brackets. The sequence of LRF BS upon generation of the LRF 4C, LRF 8C, LRF 2T, and KLF1 profiles is presented, and modified bases are highlighted in red and green. b ChIP–qPCR analysis of LRF at HBG1/2 promoters in edited and control (mock-transfected) K562 cells. ChIP was performed using an antibody against LRF. HBG prom pair of primers was used to amplify the HBG1/2 promoters. DEFB122 served as a negative control. Data were normalized to the values observed at the KLF1 locus (positive control). Data are expressed as mean ± SEM (n = 3 biologically independent experiments) (left panel). C-G to T-A or A-T to G-C base-editing efficiency of the input and the LRF immunoprecipitated fractions was calculated by the EditR software in samples subjected to Sanger sequencing. Data are expressed as mean ± SEM (n = 3 biologically independent experiments) (right panel). *P = 0.0140; **P = 0.0040 (two-way ANOVA with Dunnett correction for multiple comparisons). Source data are provided as a Source Data file.