Supplementary Figure 3: A complex is formed between 26 proteins and the 5′ ETS in the presence of the MS2 tag, which does not inhibit ribosome assembly in vivo.

(a) SDS PAGE analysis of tandem affinity purified RNA-protein complexes with RNA and protein baits as indicated on the top. GFP-tagged UtpA (via Utp10), UtpB (via Utp1) and U3 snoRNP (via Rrp9) were used as baits to purify the 5´ ETS particle. Lanes 2 and 3 contain Utp10 with 3´ or 5´ tagged 5´ ETS sequences. Positions of protein baits, and proteins that are part of the purification scheme are indicated on the right. Corresponding mass spectrometry analysis is listed in Supplementary Table 1. (b) Northern blot analysis for 5´ MS2-tagged 5´ ETS transcripts shown in (a) using probes specific for the 5´ ETS (left) and the MS2 aptamer (right). Native 35S and 23S pre-rRNA intermediates are highlighted. (c) Growth phenotypes of yeast strains expressing a single copy of untagged (L-1496) or MS2-tagged (YSK145) rDNA. YPD plates were incubated for 1 day at 30 °C. (d) Schematic representations of the 35S pre-rRNA transcripts that are generated from pRDN4 (top) and pMS2x5-RDN4 (bottom). Boxes indicate positions of probes. (e) Northern blot analysis of pre-rRNAs from strains L-1496 and YSK145 using probes specific to the 5’ ETS (left) and the MS2 aptamer (right).