Deep mutational scanning of CPEB3 ribozyme

Despite the transcription of noncoding RNAs in 75% of the human genome and their associations in many diseases, we know very little about them without structural clues. The centerpiece of structural clues is precise RNA base-pairing structure at the single base-pair level that currently can only be obtained from costly and inefficient 3D structure determination. Here, we performed deep mutational scanning of self-cleaving CPEB3 ribozyme by error-prone PCR and showed that a library of <5 x 10^4 single-to-triple mutants is sufficient to infer its nearly perfect base-pairing structure including non-Watson-Crick base pairs and non-nested (pseudoknot) tertiary contacts.