A well-documented, logical role for structured ncRNAs of the RNP Renaissance is to act as versatile platforms for protein assembly (). This role capitalizes on the prior evolution of a large inventory of protein folds and an enormous structural diversity of protein-RNA interactions. Transcription can support synthesis of extremely long RNA polymers in vivo, and yet only short motifs are required for highly specific protein interactions. These features make RNA well suited for gain of function as a protein-bridging platform of macromolecular assembly. Indeed, the functions of most structured ncRNAs are likely to depend at least in part on their protein-scaffolding abilities.
Figure 2 Non-coding RNA function as a scaffold of macromolecular assembly. The ability of even small RNA motifs (of less than 20 nucleotides) to fold uniquely and with high thermodynamic stability is one of several features that suggest ncRNA would be well suited (more ...)
RNA scaffolds have distinct, unique structural properties. Constraints on the relative positioning of proteins bridged by RNA can be tight (if the scaffold is rigid), rotationally flexible (if the otherwise rigid scaffold has hinges), or variable over great distance (if the scaffold harbors segments of duplex RNA with many hinges, has extended single-stranded as well as duplex regions, or undergoes conformational dynamics on a biological time scale). Proteins may exchange from the scaffold with different kinetics, through mutually exclusive, independent, or coordinate interactions. While bridging of several different proteins may be the most common function served by RNA scaffolds, structured ncRNAs can also bridge or nucleate the assembly of multiple subunits of the same protein. For example, heat shock RNA 1 appears to function by trimerizing the heat shock transcription factor HSF1 [10
], which stimulates HSF1 function as a transcriptional activator.
The use of RNA-scaffolded assemblies for chromatin specialization has evolved independently in numerous biological contexts. The Drosophila roX1
RNAs are notable examples of this ncRNA function. RNPs assembled on functionally redundant roX1
accomplish dosage compensation in males by increasing gene expression from the singleton X chromosome. The roX
RNAs bind and bridge numerous proteins (), including chromatin-modifying enzymes [11
]. These RNPs are preferentially recruited to specific chromosome loci and then spread to flanking binding sites, eventually generating a RNP-coated chromosome with a characteristic banding pattern. In addition to their scaffolding role, the roX
RNAs either directly or indirectly serve as allosteric activators of RNP enzyme activity in chromatin modification [12
]. Although chromatin surrounding a roX
RNA expression site preferentially recruits roX
RNPs, this feature is not a fundamental requirement for ncRNA function: sites of roX
RNA expression and function can be physically unlinked [13
]. Mammalian X-chromosome inactivation also involves spreading of ncRNA on chromatin, albeit in a manner more strictly cis
-linked to the ncRNA expression locus [2
]. These and other examples highlight the theme of ncRNA function in chromatin specification and raise the prospect that long, partially structured ncRNAs are particularly well suited to mediate protein spreading along the length of a chromosome.
The scaffolding function of ncRNAs can be exploited to regulate protein activities in response to changing cellular conditions, as demonstrated by the human 7SK RNA. This abundant nuclear ncRNA forms distinct RNP assemblies that are in dynamic, stress-regulated exchange (). In one RNP form, 7SK RNA negatively regulates the transcription elongation factor P-TEFb by sequestering it in a multisubunit RNP complex [14
]. In alternate RNP(s), 7SK RNA interacts with a distinct set of proteins to form complexes predicted to have reciprocally related function [16
]. 7SK RNA has long been thought to be vertebrate-specific, but recent evidence suggests that it has a wider evolutionary distribution [19
]. This finding presents an opportunity to investigate the phylogenetic diversification of 7SK RNP composition and biological regulation as a model for understanding structured ncRNA gain of function in the RNP Renaissance.