Fig. 7. Dynamics of altered ER-bound 3D chromatin interactions on gene transcription.
a, Differential expression of genes involved in gained interactions in day-7 decitabine-treated TAMRs. Genes included in representative examples are labeled. b, Differential expression of genes involved in gained interactions in decitabine recovery TAMRs. Genes included in representative examples are labeled. c, Browser snapshots showing promoter-anchored interactions at the SPATA18 ER target gene. Gar15-13 PDX vehicle-treated and decitabine-treated data tracks are overlayed with ER ChIP-seq for TAMR and MCF7 cell lines3, EPIC methylation for TAMRs, ChromHMM track and PCHi-C for TAMR cell line data. Merged replicate data are shown (n = 4 biological replicates each for Gar15-13 and n = 2 technical replicates for TAMRs). In decitabine-treated PDXs and TAMRs (day-7 decitabine), the SPATA18 promoter displays an increased number of interactions with an upstream enhancer region, which gains ER binding with decitabine-treatment in PDXs, concomitant with loss of DNA methylation in both PDXs and TAMRs. These ectopic chromatin interactions are lost after 28 days of decitabine recovery with partial recovery of DNA methylation at that locus. SPATA18 gene expression was significantly upregulated in decitabine-treated versus vehicle-treated PDXs (bottom right, RNA-seq transcripts per million, TPM) and in day-7 decitabine-treated TAMRs and suppressed in decitabine recovery TAMRs (bottom left, RNA-seq TPM). d, Browser snapshots showing promoter-anchored interactions at the B4GALT1 ER target gene. Gar15-13 PDX vehicle-treated and decitabine-treated data tracks are overlayed with ER ChIP-seq for TAMR and MCF7 cell lines3, EPIC methylation for TAMRs, ChromHMM track and PCHi-C for TAMR cell line data. Merged replicate data are shown (n = 4 biological replicates each for Gar15-13 and n = 2 technical replicates for TAMRs). In decitabine-treated PDXs and TAMRs (day-7 decitabine), the B4GALT1 promoter displays an increased number of long-range interactions with a distal enhancer region, which gains ER binding with decitabine treatment in PDXs, concomitant with loss of DNA methylation in both PDXs and TAMRs. These ectopic chromatin interactions are partially reversed after 28 days of recovery with recovery of DNA methylation at that enhancer locus. B4GALT1 expression increased decitabine-treated versus vehicle-treated PDXs (bottom right, RNA-seq TPM) and in day-7 decitabine-treated TAMRs compared to control early samples and was restored in decitabine recovery TAMRs (bottom left, RNA-seq TPM).