Fig. 1

Eleanor topologically associating domain (TAD) corresponds to the Eleanor-expressing chromatin domain. a Cells used in this study: MCF7, long-term estrogen deprivation (LTED), and LTED-RES cells. MCF7 cells were cultured in estrogen-deprived medium for >3 months to establish LTED cells, which was then treated with 100 μM resveratrol for 24 h (LTED-RES cells). Cell death occurs early during estrogen deprivation and after resveratrol treatment. b Alignment of TADs and 4C-Seq (chromosome conformation capture combined with high-throughput sequencing) profiles in the region, including the ESR1 gene on human chromosome 6 (6q25.1). Top: Hi-C contact matrix and predicted TAD positions (gray and black bars)²⁹. Middle: 4C-Seq (this study) and RNA-Seq²⁷ profiles of the indicated cells. The arrowhead indicates the position of the 4 C bait, and the dark blue bars indicate the valley regions of the 4C peaks (Supplementary Fig. 2a). Bottom: positions of RefSeq genes and BAC clones (green bars) used as probes for RNA fluorescence in situ hybridization (FISH) in this study. The black bar TAD with yellow highlights delineates the position of the Eleanor TAD. c Quantitative reverse transcription polymerase chain reaction analysis for the expression levels of genes inside and outside the Eleanor TAD. Genes inside the Eleanor TAD were cooperatively activated in LTED cells and were downregulated by resveratrol treatment (LTED-RES). The value of MCF7 expression level was set to 1. Data are representative of three independent experiments (mean ± s.e.m.). P values were calculated using unpaired, two-tailed, Student’s t test (*P < 0.05, **P < 0.01, ***P < 0.001). d RNA FISH analysis along the Eleanor TAD. BAC clones used as probes are indicated above each panel. Eleanor RNA foci were diminished with resveratrol treatment (LTED-RES). Scale bar, 10 µm. e Quantification of RNA FISH. n = 50–100 nuclei per sample. Boxplots shown are center line, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range; points, outliers. P values were calculated using two-tailed, Mann–Whitney U test