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

Mutagenesis of amino acids that contact m⁶A RNA in other YTH proteins. (A) Stereo view of the superimposed YTH domains of Mmi1 (green) and YTHDF with m⁶A nucleoside bound (yellow), highlighting the three aromatic amino acids (Trp432, Trp486, Trp491) that form a cage around the m⁶A nucleobase and make van der Waals contacts to the N6-methyl atoms (indicated by dashed lines). The corresponding Mmi1 amino acids are Trp372, Trp421, and His426. (B) DSR RNA binding by Mmi1 YTH mutants. Reaction mixtures contained 100 nM 5′ ³²P-labeled 14-mer DSR RNA and 250, 500, or 1000 nM wild-type Mmi1(319–488) or the indicated alanine mutants. Mmi1(319–488) was omitted from the control reactions in lanes indicated by (–). The free RNA and RNA•protein complexes were resolved by native PAGE and visualized by autoradiography.