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Significance While RNAs are known to misfold, the causes of this remain unknown, especially for large RNAs. Similarly, how RNA chaperones promote native folding remains unclear. By studying 18S rRNA folding in yeast, we show that three-helix junctions are prone to misfolding. Furthermore, the data also show that assembly factors function as folding chaperones by isolating helical junctions, thereby allowing them to fold to the native state without interference from kinetic traps. Moreover, chaperones bind interaction partners, not the junctions themselves, thus acting indirectly. This local activity of chaperones contrasts with the role of protein chaperones which unfold the protein. These data provide insight into the folding of complex RNAs and show how chaperones function in RNA folding.

Assembly factors chaperone ribosomal RNA folding by isolating helical junctions that are prone to misfolding