Fig. 1
AI treatment induces KRT80 expression via epigenetic reprogramming. a Hi-C 3D interactions in GM12878 cells were analyzed using http://promoter.bx.psu.edu/hi-c/view.php. Data to derive individual TAD were downloaded from http://chromosome.sdsc.edu/mouse/hi-c/download.html. Bars represent the normalized median change in H3K27ac within the Type II-Keratin TAD compared to the overall change in H3K27ac between parental MCF7 cells (green) and drug-resistant non-invasive (gray) and drug-resistant invasive (orange) counterparts. The bottom heatmap shows the normalized expression of RNA-seq data for protein coding genes within the Type II-Keratin in all breast cancer cell lines. b Bird-eye view of the H3K27ac profile of the Type II-Keratins locus. ChIP-seq signal profiles from7 are shown across the entire TAD. c Targeted ChIP-qPCR for the E1 enhancer locus using H3K4me1, H3K4me2 and H3K27ac antibodies. Individual biological replicates, mean and SD are shown. Asterisks represent significance at the p < 0.001 level. d Live-imaging cell counts of mate-labeled MCF7 cells grown in presence or absence of estrogen for 48 h. Dotted line represents an ideal stalling dynamic in cell number during the time of the assay. Mean and SD of three independent counts are shown. e Population level single-cell RNA-seq data for KRT80 expression are shown. KRT80 was identified in 10.8% of MCF7 cultured in estrogen rich media and in 39.9% of MCF7 deprived of estrogen for 48 h. The distribution of the two set of data was compared using a Fisher exact test. Experiments were run comparing cells within 48 h in absence of major cell division/apoptosis. f Representative single-molecule, single cell RNA-FISH for SREBP1 (red) and KRT80 (green) in MCF7 and LTED cells. g KRT80 protein levels in MCF7 and additional independent models of invasive drug-resistant breast cancer cell lines. The asterisk represents an unspecific band. Acronyms: LTED cells: MCF7 that were long term estrogen deprived; and double resistant; MCF7T, MCF7F, LTEDT, and LTEDF: MCF7 and LTED cells resistant to Tamoxifen or to Fulvestrant respectively; ETR: endocrine treatment resistant; E2: estrogen; TAD: topological associated domain; RPKM: reads per kilobase million; KRT: keratin; SREBP1: sterol regulatory element binding protein 1
