Fig. 3.
The loop and lower stem domains confer specificity to the association of hY RNAs with euchromatin. (A) Domain structure of hY1 RNA. The nucleotide sequence and the most stable secondary structure of hY1 RNA is shown as determined by the Mfold algorithm. The evolutionarily conserved four domains present in all vertebrate Y RNAs are indicated. (B) Synthesis of Alexa-Fluor-conjugated hY1 RNA mutants. The three mutant hY1 RNAs were synthesised and analysed as detailed for Fig. 1. M indicates the 100-nucleotide RNA ladder, M+ contains an additional 46-nucleotide RNA nucleotide. (C) Alexa-Fluor-conjugated mutant hY1 RNAs support DNA replication in vitro. The indicated RNA molecules were analysed as detailed for Fig. 1. (D) Dynamic association of Alexa-Fluor-conjugated mutant hY1 RNAs with late G1 phase nuclei in vitro. Mutant hY1 RNAs were incubated for 1 and 15 minutes with late G1 phase nuclei in the presence of fractions QA and ArFT. Data were analysed as detailed for Fig. 1. (E) Alexa-Fluor-594-conjugated wild-type hY1 RNA and Alexa-Fluor-488-conjugated mutant ΔLS/ΔLP RNA were co-incubated with late G1 phase nuclei in the presence of fractions QA and ArFT for 1 minute and 15 minutes, as indicated. RNAs were directly visualised as detailed for Fig. 2. Scale bars: 10 μm.