Uploading piRNAs to the Cloud.

A new paper finds a protein linking piRNA transcription with processing in nuage.

The Piwi/piRNA system is responsible for protecting the germline from the mutagenic effects of transposon mobilisation. As summarised in an earlier post, in Drosophila large arrays of transposon fragments, located in pericentromeric and subtelomeric chromatin domains give rise to long piRNA cluster transcripts. These transcripts are then processed to produce the 23-30 nt piRNAs which, when complexed with Piwi-family argonaute proteins effect the post-transcriptional silencing of transposons. Although a more limited piRNA system functions in the somatic follicle cells surrounding the Drosophila egg chamber, the bulk of germline transposon silencing is performed by the system active in the germline siblings of the oocyte – the nurse cells. Here, dual-strand piRNA cluster transcripts are processed in the nuage, a perinuclear electron-dense cytoplasmic structure, where the ‘ping-pong’ system of reciprocal cutting and complexing between the Piwi proteins Aubergine (Aub) and Ago3 leads to piRNA amplification.

Nuage is a hallmark of germline cytoplasm in animals, and appears to be the site of both piRNA processing and transposon silencing. A hierarchy of proteins responsible for the assembly and function of nuage has been revealed by studies in Drosophila. Vasa, a DEAD-box RNA-dependent helicase protein, is required for the localisation of Tudor and other Tudor-domain-containing (Tdrd) proteins. These serve as a platform for the piRNA system, binding Aub and Ago3. Defects in many of these piRNA biogenesis components do not just lead to uncontrolled transposon activity; rather, they affect the asymmetric localisation of RNAs in the developing oocyte – a process by which developmental prepattern is organised. Zheng et al. discovered that weak mutations in the uap56 gene caused similar defects, suggesting a potential role in piRNA biogenesis.

UAP56 is another DEAD-box containing RNA-binding protein. It is ubiquitously expressed, localised in nuclei and has previously been shown to be involved in mRNA splicing and export. Zheng et al. found that in nurse cells it localises to discrete foci in the periphery of the nucleus. This was a similar pattern to that of Rhino (Rhi), a Heterochromatin Protein 1 variant previously shown to associate with piRNA clusters. Indeed, UAP56 and Rhino co-localised ~99% of the time in nurse cell nuclei.  Mutations in either uap56 or rhi caused a failure in the focal localisation of the other protein, showing their co-dependence.

When Vasa was imaged at the same time, it became apparent that it localised to foci in the nuage directly across the nuclear envelope from UAP-56-Rhi foci. Co-labelling with a nucleoporin showed that in fact UAP56-Rhi foci and Vasa foci directly abut nuclear pores from either side.

In the absence of functional UAP56 the nuage fails to assemble properly; Vasa, Aub and Ago3 all fail to localise. Similar effects are observed in rhi mutants, placing both UAP56 and Rhino upstream of Vasa as extrinsic factors necessary for nuage assembly. The uap56 mutants also fail to produce a large part of the proper complement of piRNAs leading to a consequent mobilisation of transposons. No effects on the level of genic mRNAs were detectable. Due to the failure of nuage assembly, the uap56 mutants also display germline DNA damage and the morphological defects caused by mislocalisation of asymmetric RNAs.

DEAD-box containing proteins act as ATP-dependent RNA clamps. As Rhino is known to associate with dual-strand piRNA clusters, Zhang et al postulated that UAP56 may be binding and stabilising nascent cluster transcripts. Indeed piRNA cluster transcripts could be co-immunoprecipitated with UAP56 and Vasa.

The data therefore suggests an attractive model in which cluster transcripts are passed across the nuclear pore between the two DEAD-box containing proteins, UAP56 and Vasa. The authors term this a nuclear pore spanning piRNA processing compartment. piRNA cluster transcripts must in some way be marked and specifically transported via the trans– nuclear pore compartment.

Running through this work as a consistent undertone are the implicit links to the broader RNA processing systems. The nuage is obviously intricately linked to the differential transportation of RNAs from the nurse cells and around the oocyte. UAP56 has other roles in mRNA splicing and export from the nucleus. What exactly are the links between the germline specific role of UAP56 and the general RNA splicing and export machinery? Zhang et al end with the enticing observation that mutations in two different genes encoding conserved exon junction splicing components also lead to similar asymmetric RNA localisation defects. It appears that the control of piRNA processing and transposon silencing in nuage is intimately linked to broader networks controlling germline specification and the patterning of the oocyte. Although the different strands of these systems are difficult to tease apart, Drosophila oogenesis continues to offer an unparalled paradigm for their investigation. The piRNA system is widely conserved in animals, but there does appear to be quite a lot of plasticity in its specifics. For instance, as discussed at length in this series of posts, in C. elegans, piRNAs are individually transcribed. I’d be very interested to find out whether homologues of Rhino and UAP56 play any role in this system? I’ll riff on the similarities and differences of piRNA systems and their links to development some more in future posts.

Zhang, F., Wang, J., Xu, J., Zhang, Z., Koppetsch, B., Schultz, N., Vreven, T., Meignin, C., Davis, I., Zamore, P., Weng, Z., & Theurkauf, W. (2012). UAP56 Couples piRNA Clusters to the Perinuclear Transposon Silencing Machinery Cell, 151 (4), 871-884 DOI: 10.1016/j.cell.2012.09.040

Lin, H. (2012). Capturing the Cloud: UAP56 in Nuage Assembly and Function Cell, 151 (4), 699-701 DOI: 10.1016/j.cell.2012.10.026

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