Ribozyme-Mediated Knockdown of lncRNA Gene Expression in <em>Drosophila</em>

Long noncoding RNAs (lncRNAs) are increasingly understood to play important roles in cell biology, development, and disease, though the vast majority of annotated lncRNAs have yet to be functionally characterized. Disrupting lncRNAs is often challenging owing to their tolerance for mutations (e.g., single-nucleotide polymorphisms and short indels) along with the limitations of other genetic knockdown strategies such as RNA interference (RNAi). Here, we describe a protocol to achieve robust knockdown of lncRNAs in the fruit fly <i>Drosophila</i> using a self-cleaving ribozyme. The 111-bp ribozyme cassette, which consists of the N79 hammerhead ribozyme flanked by flexible linker sequences, is inserted into transcript regions of lncRNA genes using CRISPR/Cas9-mediated homology-directed repair (HDR). The fluorescent eye transformation marker is then removed using a piggyBac transposase, leaving no other modifications at the lncRNA locus save the ribozyme cassette insertion. When transcribed as part of the lncRNA, the ribozyme folds and catalyzes its own self-cleavage, resulting in two RNA cleavage fragments. The efficacy of lncRNA knockdown is then evaluated using reverse transcription quantitative PCR (RT-qPCR) and single-molecule RNA fluorescence in situ hybridization (smFISH). This approach has resulted in efficient knockdown of both nuclear and cytoplasmic lncRNAs in <i>Drosophila</i>, with knockdown of steady-state RNA levels in 3' cleavage fragments typically exceeding 90% and no evidence of off-target effects. The method can also be applied to protein-coding genes in order to knock down specific mRNA isoforms. Thus, self-cleaving ribozymes are a valuable addition to the genetic toolkit in <i>Drosophila</i>. Key features • The ribozyme has the potential to knock down any RNA but is particularly useful for long noncoding RNAs, which can be resistant to mutations. • The ribozyme is useful for the knockdown of nuclear-localized RNAs as well as RNAs that overlap with other genes in the genome. • Ribozyme knockdown is typically stronger than RNAi and occurs in every cell. • Insertion of the ribozyme cassette in the 5' region of a transcript ensures that most of the transcript is degraded.