Trends in Biochemical Sciences
ReviewParaspeckles: Where Long Noncoding RNA Meets Phase Separation
Section snippets
New Insights into Paraspeckles Have Helped Us Understand Both Long Noncoding RNA Structure/Function and Membraneless Organelle Formation
Dynamic cellular organelles that form without a membrane boundary have long fascinated scientists. What triggers such structures to form? How do a whole variety of specific molecules get targeted there? How are such structures maintained in steady state, yet also rapidly broken down when triggered to do so? The nucleoplasm is rich in such membraneless organelles, often termed ‘nuclear bodies’. These bodies regulate gene expression, albeit with mechanisms that have been hard to pin down. Another
Setting the Scene – What Are Paraspeckles?
Paraspeckles are mammal-specific RNA–protein nuclear bodies that regulate gene expression. First described in 2002 as nuclear foci enriched in the marker protein paraspeckle component protein 1 (PSPC1) [1], paraspeckles are now known to contain over 40 different proteins (generally ubiquitously expressed RNA-binding proteins) and one architectural lncRNA, nuclear paraspeckle assembly transcript 1 (NEAT1; see Table 1). Some component proteins mediate critical RNA–protein or protein–protein
The Longer Isoform of NEAT1 Is the Structural Backbone of Paraspeckles
The lncRNA, NEAT1, is an essential structural component of paraspeckles, forming a scaffold for protein binding 2, 4, 6, 7. The requirement of NEAT1 for paraspeckle formation was one of the first concrete examples of a functional lncRNA at a time when controversy over their functionality was still raging. As such, paraspeckles have now become one of the most well-studied lncRNA–protein complexes in the cell.
Two transcripts are generated by RNA polymerase II from the NEAT1 gene: NEAT1_1 and
Paraspeckles Are Chains of Spheroids, Each with a Core and Shell Structure
Paraspeckles are readily labeled with specific marker proteins and RNAs using fluorescent microscopy, and under the electron microscope (EM) are also distinguishable as electron-dense structures in the interchromatin space. Despite initially being observed as punctate foci, EM and super-resolution microscopy have revealed paraspeckles as actually elongated prolate structures with a uniform width of approximately 360 nm in human cells and slightly less in murine cells, but with length varying up
How Do Paraspeckles Form?
Paraspeckle biogenesis starts with transcription of NEAT1_2, with paraspeckles forming close to the NEAT1 gene and often appearing clustered near this locus [6]. Once NEAT1_2 is made, the essential paraspeckle proteins NONO and SFPQ rapidly bind to form and stabilize a minimal NEAT1_2 ribonucleoprotein particle (RNP) that is an intermediate in paraspeckle formation ([13], Figure 1). It is not yet known precisely which RNA sequence or structure in NEAT1_2 is responsible for NONO/SFPQ binding,
Liquid–Liquid Phase Separation Is Critical for Paraspeckle Formation
Paraspeckles actually share many features with cytoplasmic stress granules, another type of membraneless organelle. Paraspeckles and stress granules both contain common component proteins [25], become more abundant with stress, seem to function through molecular sequestration (more on this below), and both have distinct subsets of molecules found either within the core or shell regions 13, 26. Our understanding of the type of molecular interactions driving formation of such membraneless
What Is the Molecular Mechanism of Paraspeckle Function?
Once paraspeckles form, what is their role in the cell? As yet, no distinct catalytic activity has been demonstrated to occur within the paraspeckle. The main molecular mechanisms identified for paraspeckle function relate to sequestration of molecules, be it RNA or proteins (summarized in Figure 3).
Paraspeckles Play a Role in a Variety of Developmental and Disease Scenarios
In which biological settings might paraspeckles play a role in regulating gene expression? The paraspeckle proteins can be found both inside and outside paraspeckles, therefore study of paraspeckle protein function cannot be seen as akin to paraspeckle function. By contrast, NEAT1_2 is strictly only found within paraspeckles, and NEAT1_2 levels can be considered a proxy for paraspeckle appearance. Thus, observation and manipulation of NEAT1_2 is a route to functional studies of paraspeckles.
Concluding Remarks and Future Perspectives
In the 15 years since their discovery, paraspeckles have flourished from obscure nuclear body to important lncRNA–protein model system with novel roles in gene regulation in different disease contexts. By studying how paraspeckles form, we are learning more about how nuclear proteins use their RNA binding and protein–protein aggregation propensity to form such membraneless organelles. With many questions remaining about paraspeckle biology (see Outstanding Questions) we are confident that the
Acknowledgments
We are grateful to the members of our laboratories for helpful reading of this manuscript and apologize to those whose work we could not cite due to space limitations. This work was supported by the Australian Research Council grant DP160102435 to A.H.F. and C.S.B.
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