Small RNA-directed DNA elimination

Small RNA-mediated transcriptional gene silencing is a fundamental process that has been observed in many different eukaryotes including fungi, plants, flies, worms and mammals. One of its main tasks is to neutralize the activity of transposable elements (TEs), which otherwise destabilize our genome and potentially cause diseases. Small RNAs use their base complementarities to TEs to specifically silence them. However, how cells ensure TE-silencing without disturbing expressions of normal genes is not fully understood.

The ciliated protozoan Tetrahymena identifies TE-derived sequences by a germline-some genome comparison mechanism using small RNAs during programmed DNA elimination, which provides fascinating examples of epigenetic genome regulations and important insights into the interaction between TEs and host genomes. Because programmed DNA elimination can be synchronously induced in laboratory in a large scale, it serves as a useful laboratory model for genetically and biochemically investigating small RNA-mediated chromatin regulation.

Using this tiny-hairy eukaryotic model, we aim to understand: how cells accumulate small RNAs specifically from TE-related sequences; how cells use those small RNAs to identify TE-related sequences; and how a small RNA pathway establishes silent chromatin environment (heterochromatin) on TE-related sequences.