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Expression of fission yeast Pho1 acid phosphatase is repressed during growth in phosphate-rich medium. Repression is mediated by transcription of the  prt  locus upstream of  pho1  to produce a long noncoding (lnc)  prt  RNA. Repression is also governed by RNA polymerase II CTD phosphorylation status, whereby inability to place a Ser7-PO 4  mark (as in  S7A ) derepresses Pho1 expression, and inability to place a Thr4-PO 4  mark (as in  T4A ) hyper-represses Pho1 in phosphate replete cells. Here we find that basal  pho1  expression from the  prt–pho1  locus is inversely correlated with the activity of the  prt  promoter, which resides in a 110-nucleotide DNA segment preceding the  prt  transcription start site. CTD mutations  S7A  and  T4A  had no effect on the activity of the  prt  promoter or the  pho1  promoter, suggesting that  S7A  and  T4A  affect post-initiation events in  prt  lncRNA synthesis that make it less and more repressive of  pho1 , respectively.  prt  lncRNA contains clusters of DSR (determinant of selective removal) sequences recognized by the YTH-domain-containing protein Mmi1. Altering the nucleobase sequence of two DSR clusters in the  prt  lncRNA caused hyper-repression of  pho1  in phosphate replete cells, concomitant with increased levels of the  prt  transcript. The isolated Mmi1 YTH domain binds to RNAs with single or tandem DSR elements, to the latter in a noncooperative fashion. We report the 1.75 Å crystal structure of the Mmi1 YTH domain and provide evidence that Mmi1 recognizes DSR RNA via a binding mode distinct from that of structurally homologous YTH proteins that recognize m 6 A-modified RNA.

Transcription of lncRNA prt, clustered prt RNA sites for Mmi1 binding, and RNA polymerase II CTD phospho-sites govern the repression of pho1 gene expression under phosphate-replete conditions in fission yeast