Figure 4.

Structure-seq2 demonstrates the presence of two hidden breaks in chloroplast rRNA. At the two locations known to harbor hidden breaks in chloroplast rRNA, the –DMS RT stop count data spike. The spike at the first hidden break (A) differs by one nucleotide from the published break site in spinach and Arabidopsis (21,28), which could be due to the slight sequence variation between species (Arabidopsis: 5′-GGGAGUGAAA*UAGAACA-3′, Rice: 5′-GGGUAGUGAAAU*AGAACG-3′, where * indicates the proposed break site). The spike at the second hidden break (B) occurs precisely at the published cleavage site for spinach and Arabidopsis (21,28).