siRNA and miRNA processing: new functions for Cajal bodies

Abstract

In diverse eukaryotes, micro-RNAs (miRNAs) and small interfering RNAs (siRNAs) regulate important processes that include mRNA inactivation, viral defense, chromatin modification, and transposon silencing. Recently, nucleolus-associated Cajal bodies in plants have been implicated as sites of siRNA and miRNA biogenesis, whereas in animals siRNA and miRNA dicing occurs in the cytoplasm. The plant nucleolus also contains proteins of the nonsense-mediated mRNA decay pathway that in animals are found associated with cytoplasmic processing bodies (P-bodies). P-bodies also function in the degradation of mRNAs subjected to miRNA and siRNA targeting. Collectively, these observations suggest interesting variations in the way siRNAs and miRNAs can accomplish their similar functions in plants and animals.

Figure 1

Compartments of the interphase cell nucleus. The nuclear envelope is a double membrane punctuated by nuclear pores through which molecules traffic to and from the cytoplasm. The nuclear lamina is a meshwork of proteins mediating nuclear envelope structure and chromatin attachment. In the nucleus, chromosomes occupy non-random positions known as chromosome territories [52]. Genes transcribed simultaneously tend to cluster in "transcription factories” [53]. In the vicinity of transcription factories for Pol II-transcribed protein-coding genes, speckles serve as storage, recycling or assembly sites for snRNPs and other splicing proteins. The nucleolus is the site of ribosome biogenesis and numerous RNA-related functions. Cajal bodies are spherical structures involved in the biogenesis of ribonucleoprotein complexes including siRNA and miRNA RISC complexes in plants. PML bodies are linked to various aspects of transcriptional regulation, virus accumulation, tumor suppression and DNA repair.

Figure 2

Roles of P-bodies (processing bodies) in miRNA and siRNA functions and post-transcriptional regulation in animals. Pol II transcription gives rise to imperfectly base-paired double-stranded pri-miRNAs as well as pre-mRNAs, both of which undergo processing in the nucleus followed by export to the cytoplasm. Pre-miRNAs processed by Drosha in the nucleus undergo further cleavage by Dicer in the cytoplasm and one strand is loaded into an Argonaute-containing RNA-induced silencing complex (RISC; denoted miRISC in the figure). Similarly, perfectly base-paired double-stranded siRNA precursors are diced and one strand is loaded into a RISC complex (denoted siRISC). The miRNA or siRNA strands within the RISC complexes target homologous mRNAs for translational arrest or destruction in P-bodies (GW bodies) that are enriched for activities including the AGO-interacting GW182 protein, decapping (DCP) and exonuclease (XRN1) enzymes and proteins of the nonsense-mediated decay (NMD) pathway. mRNAs targeted to P-bodies can also be stored and released to the cytoplasm for translation.

Figure 3

The role of Cajal bodies in miRNA and siRNA biogenesis and function in plants. In Arabidopsis, miRNA processing by DCL1 and 24 nt siRNA production by DCL3 occur within processing centers located in nucleolus-associated Cajal bodies rather than in the cytoplasm, as in animals. Multiple proteins of the nonsense-mediated decay pathway also localize within the nucleolus, suggesting that aberrant mRNAs or non-coding RNAs may be sensed and degraded in the nucleus, possibly feeding into the siRNA-directed DNA methylation pathway in order to silence the offending loci. It is possible that AGO1-mediated miRNA targeting of mRNAs or pre-mRNAs may take place primarily in the nucleus. However, the involvement of the Exportin 5 homolog, HASTY in some miRNA-mediated developmental phenomena suggests that at least some miRNAs function in the cytoplasm, presumably in the context of P-bodies, as in animals.