ELAVL1 coordinately regulates IPA isoforms in the nucleus and cytosol in response to Doxo. (A) Intersection of the three main categories of Doxo-regulated IPAs (Cyto IPA:LE up, Cyto IPA:LE down, and Nuc IPA:LE down, as identified by 3′-seq in Fig. 2A) with nuclear and cytosolic Doxo-regulated ELAVL1 binding sites located in IPA and LE regions (as indicated at the bottom). Plotted is the percentage of Doxo-regulated IPAs of each category that have a Doxo-regulated ELAVL1 binding site in the indicated region. (B) Identification of abundant IPA isoforms for which the IPA:LE ratio is regulated by siELAVL1 when compared to siCTRL, by 3′-seq analysis on cytosol of MCF-7 cells grown either without or with Doxo. (C) Intersection of the three main categories of Doxo-regulated IPAs (Cyto IPA:LE up, Cyto IPA:LE down, and Nuc IPA:LE down) with siELAVL1-regulated IPAs. (D) RT-qPCR analysis of the effects of Doxo and siELAVL1 on the cytosolic IPA:LE isoform ratio in the indicated genes. (*) P = 0.06; (**) P < 0.01.
