The Nowacki lab wrote a review on “Functions and mechanisms of eukaryotic RNA-guided programmed DNA elimination” published in Biochemical Society Transactions. A focus is the elimination of DNA guided by complementary small RNAs, for which the knowledge about the mechanism and major open questions are discussed, as well as how these systems given their mechanistic understanding could be used as genome editing tools.
Abstract:
Many eukaryotic organisms, from ciliates to mammals, employ programmed DNA elimination during their postmeiotic reproduction. The process removes specific regions from the somatic DNA and has broad functions, including the irreversible silencing of genes, sex determination, and genome protection from transposable elements or integrating viruses. Multiple mechanisms have evolved that explain the sequence selectivity of the process. In some cases, the eliminated sequences lack centromeres and are flanked by conserved sequence motifs that are specifically recognized and cleaved by designated nucleases. Upon cleavage, all DNA fragments that lack centromeres are lost during the following mitosis. Alternatively, specific sequences can be destined for elimination by complementary small RNAs (sRNAs) as in some ciliates. These sRNAs enable a PIWI-mediated recruitment of chromatin remodelers, followed up by the precise positioning of a cleavage complex formed from a transposase like PiggyBac or Tc1. Here, we review the known molecular interplay of the cellular machinery that is involved in precise sRNA-guided DNA excision, and additionally, we highlight prominent knowledge gaps. We focus on the modes through which sRNAs enable the precise localization of the cleavage complex, and how the nuclease activity is controlled to prevent off-target cleavage. A mechanistic understanding of this process could enable the development of novel eukaryotic genome editing tools.
Read the Review in Biochemical Society Transactions (Open Access)
Abstract and figure from Stefanov and Nowacki (2025) Biochem Soc Trans published under a CC BY 4.0 license.