Characterization of S. pombe box C/D snoRNAs. Northern blot detection (A) and reverse transcription analyses (B) for selected box C/D snoRNAs: Lane M shows molecular weight markers. (C) Determination of selected rRNA methylation sites by primer extension; lanes T, G, C, and A show the rDNA sequence ladder; lane 1 is the control reaction at 1.5 mM dNTP; lane 2 is the primer extension at 4 µM dNTP. Arrows and solid boxed coordinates indicate potential methylation sites predicted by the novel snoRNAs. Arrows and dashed boxed coordinates indicate methylation sites modified by the previously known snoRNAs. Arrows without box refer to the modification sites with unknown molecules. (D) A schematic of snoRNA gene clusters (from transcription start site [TSS] to the last transcription terminating site [TTS] of each cluster). The exons (gray-filled rectangle), snoRNAs (black-filled rectangle), and introns (straight line) were drawn using the same scale. snR90* is a box H/ACA snoRNA reported previously (Li et al. 2005). snR57 and snR55 are within two introns in juxtaposition without intercalating exon, and this special genomic organization has been reported previously (Mitrovich et al. 2010).
