RNA was extracted from cell pellets using TRI reagent (Sigma-Aldrich) and analyzed by glyoxal-agarose gel or urea-PAGE and transferred to nylon membrane. For Northern blot analysis, oligonucleotides (Table S4 ) were 5′ labeled with γ-[32P]ATP using T4 polynucleotide kinase and used as probes. Random prime-labeled probes hybridizing immediately upstream and downstream of the A’ cleavage in the 5′ETS (ETS1 and ETS2, respectively) were produced from PCR products (Turner et al., 2009 (link)). Random prime-labeled probes against the full-length RNase MRP RNA and the S domain of 7SL were also generated.
For metabolic labeling experiments using 3H methyl-methionine, the cells were incubated in methionine-free media (15 min) and then in methionine-free media containing 50 µCi/ml 3H-labeled methyl-methionine (30 min). The cells were then incubated in normal media containing 10× the normal concentration of methionine and harvested at the required time points (0, 15, 30, 60, 120, and 240 min). For metabolic labeling experiments using 32P orthophosphate, cells were grown in phosphate-free media (1 h) followed by phosphate-free media containing 15 µCi/ml 32P-labeled inorganic phosphate (1 h). Cells were then incubated in normal media and harvested at the required time points (0, 30, 60, 120, and 240 min). RNA was extracted using TRI reagent and analyzed by agarose-glyoxal or urea-PAGE as appropriate. Results were visualized using a phosphorimager (Typhoon FLA9000; GE Healthcare). All quantitation was normalized to the levels of mature 18S or 28S rRNA, as appropriate.
For metabolic labeling experiments using 3H methyl-methionine, the cells were incubated in methionine-free media (15 min) and then in methionine-free media containing 50 µCi/ml 3H-labeled methyl-methionine (30 min). The cells were then incubated in normal media containing 10× the normal concentration of methionine and harvested at the required time points (0, 15, 30, 60, 120, and 240 min). For metabolic labeling experiments using 32P orthophosphate, cells were grown in phosphate-free media (1 h) followed by phosphate-free media containing 15 µCi/ml 32P-labeled inorganic phosphate (1 h). Cells were then incubated in normal media and harvested at the required time points (0, 30, 60, 120, and 240 min). RNA was extracted using TRI reagent and analyzed by agarose-glyoxal or urea-PAGE as appropriate. Results were visualized using a phosphorimager (Typhoon FLA9000; GE Healthcare). All quantitation was normalized to the levels of mature 18S or 28S rRNA, as appropriate.