Biogenesis and Function of Ago-Associated RNAs

Numerous sophisticated high-throughput sequencing technologies have been developed over the past decade, and these have enabled the discovery of a diverse catalog of small non-coding (nc)RNA molecules that function as regulatory entities by associating with Argonaute (Ago) proteins. MicroRNAs (miRNAs) are currently the best-described class of post-transcriptional regulators that follow a specific biogenesis pathway characterized by Drosha/DGCR8 and Dicer processing. However, more exotic miRNA-like species that bypass particular steps of the canonical miRNA biogenesis pathway continue to emerge, with one of the most recent additions being the agotrons, which escape both Drosha/DGCR8- and Dicer-processing. We review here the current knowledge and most recent discoveries relating to alternative functions and biogenesis strategies for Ago-associated RNAs in mammals. Numerous sophisticated high-throughput sequencing technologies have been developed over the past decade, and these have enabled the discovery of a diverse catalog of small non-coding (nc)RNA molecules that function as regulatory entities by associating with Argonaute (Ago) proteins. MicroRNAs (miRNAs) are currently the best-described class of post-transcriptional regulators that follow a specific biogenesis pathway characterized by Drosha/DGCR8 and Dicer processing. However, more exotic miRNA-like species that bypass particular steps of the canonical miRNA biogenesis pathway continue to emerge, with one of the most recent additions being the agotrons, which escape both Drosha/DGCR8- and Dicer-processing. We review here the current knowledge and most recent discoveries relating to alternative functions and biogenesis strategies for Ago-associated RNAs in mammals. miRNAs are a class of small (∼22 nt) ncRNAs that arise through a series of enzymatic maturation steps mediated by Drosha/DGCR8 in the nucleus and Dicer in the cytoplasm. Mature miRNAs associate with Ago proteins, thereby generating active regulatory complexes that function as post-transcriptional regulators of gene expression. Several miRNA-like species that follow alternative biogenesis pathways have been shown to associate with Ago proteins in a functional manner. The agotrons constitute the most recently discovered class of Ago-associated RNAs that employ a novel biogenesis strategy independent of both Drosha/DGCR8 and Dicer processing. Similarly to conventional miRNAs, agotrons have been shown to be capable of functioning as post-transcriptional regulators of gene expression, but their full potential and biological relevance have yet to be determined. miRNAs are a class of small (∼22 nt) ncRNAs that arise through a series of enzymatic maturation steps mediated by Drosha/DGCR8 in the nucleus and Dicer in the cytoplasm. Mature miRNAs associate with Ago proteins, thereby generating active regulatory complexes that function as post-transcriptional regulators of gene expression. Several miRNA-like species that follow alternative biogenesis pathways have been shown to associate with Ago proteins in a functional manner. The agotrons constitute the most recently discovered class of Ago-associated RNAs that employ a novel biogenesis strategy independent of both Drosha/DGCR8 and Dicer processing. Similarly to conventional miRNAs, agotrons have been shown to be capable of functioning as post-transcriptional regulators of gene expression, but their full potential and biological relevance have yet to be determined. Ago1–4 proteins associate with small regulatory RNAs and are the essential effector proteins in the RISC. recently discovered class of regulatory Ago-associated RNA molecules that employ a novel Drosha/DGCR8- and Dicer-independent biogenesis pathway. the RNase III enzyme that is responsible for the miRNA maturation process that takes place in the cytoplasm. Dicer recognizes the 2 nt 3′ overhang of the pre-miRNA hairpin and cleaves off the loop structure approximately ∼22 nt from the 3′ end, thereby generating a ∼22 nt miRNA duplex. microprocessor subunit; see Drosha the microprocessor complex (Drosha/DGCR8) is responsible for the miRNA maturation process that takes place in the nucleus and comprises one RNase III enzyme, Drosha, and two DGCR8 proteins with RNA-binding domains. The microprocessor complex cleaves the pri-miRNA stem at a specific position, leaving a ∼‏60 nt pre-miRNA hairpin with a 2 nt 3′ overhang. a genome-wide approach to map RNA:protein or RNA:RNA interactions through UV crosslinking and next-generation sequencing. HITS-CLIP can for example be used to identify the direct mRNA targets of a given miRNA through immunoprecipitation of crosslinked Ago proteins. a class of small (∼22 nt) ncRNAs that associate with Ago proteins and function as post-transcriptional regulators of gene expression. a class of functional RNA molecules without protein-coding features. the functional entity that mediates post-transcriptional regulation; consists of a guide RNA, an Ago protein, and several auxiliary factors. nucleotides 2–7 from the 5′ end of the miRNA are known as the seed region and this part of the miRNA is particularly crucial for target recognition. the untranslated region at the 3′ end of an mRNA molecule located between the translation stop codon and the poly-A tail.