Fig. 4

The transcription of 17q23 amplification-associated transcription coupling (ATC) loci is concordantly regulated through long-range interactions with an ERα hub on 20q13. a. 17q23 region with Hi-C interaction frequencies overlaid on ChIP-seq peaks and RNA-seq (top) from human mammary epithelial cells (HMECs), and DNA methylation landscapes (bottom) of primary breast tumors and normal controls. The dotted triangles indicate identified topologically associating domains (TADs). A total of seven TADs (four active/open and three repressive/closed) at the 17q23 region flanked by enrichment of boundary-associated CTCF peaks. b. Expression profile of the 12 genes in this region of tumors and normal controls. c. Normalized expression of the 12 genes on 17q23 by PAM50 subtypes. d. Inter-chromosomal rearrangement between 17q23 and 20q13. Breakpoint junctions used for Nanopore sequencing (see also Additional file 1: Figure S3). e. Abrogation of estrogen-mediated transcriptional activation of 17q23 genes by CRISPR/Cas9 targeted deletion of an ERα hub at 20q13. Blue dots indicate previously identified ERα sites located within a 1-kb region on 20q13. Arrowheads denote the targeting sites by the single guide RNAs (sgRNAs) and PCR primers used for validation of the deletion are shown by horizontal arrows. f. Quantitative RT-PCR carried out upon estrogen (E2) stimulation over a time course. Data shown are mean ± SD of three independent experiments