Figure 3

Selected isoform switches affected by the expression of ERβ. The ERβ-dependent differential splicing events that affect most prominently the balance of different isoforms for each gene were identified by using the following parameters: (i) isoform ratio (FPKM_isoform/FPKM_gene %) changing of at least 10% after estradiol stimulation, either in the wt cells or in both the ERβ + cells in at least one of the isoforms of the gene; (ii) at least one isoform of the gene significantly regulated by estradiol (p-value ≤ 0.05; |FC| ≥ 1.3) either in the wt cells or in both the ERβ + cells; (iii) isoform ratio changing in opposite direction in the wt cells compared to the ERβ + cells; (iv) at least one splicing event identified by MATS analysis. Thirty-five genes satisfied all the selection requirements; of these, only 2 to 3 isoforms were selected for presentation, according to the expression levels and the regulation by estradiol. Left panel: heat map of regulation of the selected genes by estradiol in: Ct-ERβ (MCF-7 subclone stably expressing ERβ tagged with the TAP-tag at the C-terminus); Nt-ERβ (MCF-7 subclone stably expressing ERβ tagged with the TAP-tag at the N-terminus); wt (parental MCF-7 cells). Right panel: heat map with the change in isoform ratio (FPKM_isoform/FPKM_gene %) between E2-treated and non-treated cells in the indicated cell lines; for each gene, at least two different isoforms are presented, to show estrogen-induced switch from one isoform to the other.