Skip to main content
. Author manuscript; available in PMC: 2022 Dec 28.
Published in final edited form as: Nat Genet. 2022 Feb 3;54(2):170–179. doi: 10.1038/s41588-021-00993-x

Figure. 2. The rs3824662 A allele increases GATA3 expression and induces global expression changes in GM12878 cells and ALL PDX samples.

Figure. 2

a, Effects of rs3824662 on gene expression within the local topologically associating domain (TAD). Gene expression was quantified by qPCR in wildtype (C/C) and engineered GM12878 cells (A/A), normalized to ACTB (n=3). TAD was defined using the GM12878 wildtype Hi-C data. Bottom panel shows results of ALL PDX samples (n=2, 3, and 2 for those with AA, AC, and CC genotype). Data are presented as mean values +/− SEM. b, Chromatin interactions between the rs3824662 (yellow bar) and GATA3 promoter (red bar) as determined by Capture-C. c, Heatmap of GATA3 ChIP-seq and ATAC-seq in GM12878 (WT) and engineered GM12878 (A/A) cells. Each row represents a 6kb genomic region flanking a GATA3 binding site that is specific in engineered GM12878 (A/A) cells. d, Luciferase reporter assay showed that rs3824662 enhancer activity increased with co-expression of NFIC, particularly with the enhancer element harboring the A allele (n = 8), two-sided unpaired T test, pGL4.23 rs3824662 A vs. pGL4.23 rs3824662 C, p-value = 0.0003997. e, shRNA-mediated knockdown of NFIC in GM12878 (A/A) cells resulted in significant reduction of GATA3 expression, n = 3 for each bar, two-sided unpaired T test, In the NFIC group, Parental vs. NFIC shRNA1 p-value = 0.002738, Parental vs. NFIC shRNA2 p-value = 0.003499, Parental vs. NFIC shRNA3 p-value = 0.003998. For the GATA3 group, Parental vs. NFIC shRNA1 p-value = 0.004096, Parental vs. NFIC shRNA2 p-value = 0.004434, Parental vs. NFIC shRNA3 p-value = 0.009699. Data are presented as mean values +/− SEM. f, 232 Differential gene expression between GM12878 (A/A) and GM12878 (WT) cell lines were also validated in PDX samples with different genotype at rs3824662. g, Gene Set Enrichment Analysis of genes upregulated with the A allele at 3824662 in the Molecular Signatures Database (MSigDB) shows enrichment of microtubule polymerization. h, Genes up-regulated in the GM12878 (A/A) cell line are showed more significant enrichment of GATA3 binding than those not affected or up-regulated in the GM12878 (WT) cells.