Fig. 2

Emerging strategies for investigating biological functions of lncRNAs. Reverse-genetics methods differ as to their abilities to target transcripts and cause off-target/non-specific effects. As such, unambiguous phenotype-lncRNA assignment, especially using methods that do not exclusively target RNA, requires RNA rescue experiments and combination of multiple approaches. Considering the highly specialized patterns of expression for most lncRNAs, in vivo phenotypes are expected to occur only in the cell types expressing the targeted transcript. In contrast, abnormalities happening in the cells that do not express the lncRNA likely indicate transcript-independent effects. On the other hand, cell-based assays have a number of attractive features and remain the only option for lncRNAs whose in vivo expression is not known or with no known homologs in animal models. In cultured cell systems, a phenotypic analysis can be performed either for a single lncRNA (middle) or in a large-scale high-throughput screen (right). More details are in the text