Alternative promoter usage modulates miRNA-guided translation inhibition of a m6A reader in phosphate starvation

Alternative transcription start sites (TSSs) are widespread in eukaryotes. In plants, light, development and tissue regulate selective usage of several TSSs, producing transcripts with distinct 5'UTR as well as shorter protein isoforms with distinct subcellular localization or activity. However, the function of non-coding transcripts generated by alternative TSSs is still largely unknown. We show that phosphate availability regulates numerous alternative TSSs, including a non-coding alternative TSS (ALTECT4) associated with ECT4, encoding a N6-methyladenosine (m6A) reader. We found that ECT4 harbors a cleavage-resistant miR826b target site at its 3UTR, also present in ALTECT4. In the absence of ALTECT4, miR826b guides translation inhibition of ECT4. Phosphate deficiency triggers specific and robust expression of ALTECT4, counteracting miR826b inhibition of its targets, including ECT4. The role of ALTECT4 as a miR826b antagonist shows that it acts in cis to regulate translation of the m6A reader ECT4, and this function might be shared among other non-coding transcripts generated by alternative TSS.