MENε/β noncoding RNAs are essential for structural integrity of nuclear paraspeckles

TLDR

Thousands of noncoding RNAs are transcribed in mammals, many of which are retained in the nucleus to coordinate gene expression, yet the RNA components and structural roles of subnuclear organelles such as paraspeckles remain largely unknown. The study proposes a model in which specific ncRNAs and RNA‑binding proteins cooperate to maintain and establish nuclear paraspeckle structure. The authors model paraspeckle organization as a cooperative interaction between MENε/β ncRNAs and the RNA‑binding proteins p54/nrb and PSF, with PSP1 excluded from this stabilization. MENε/β ncRNAs localize to paraspeckles, and their depletion causes paraspeckle disintegration and prevents reassembly, with p54/nrb and PSF selectively binding MENβ to stabilize the structure, whereas PSP1 plays no role.

Abstract

Recent transcriptome analyses have shown that thousands of noncoding RNAs (ncRNAs) are transcribed from mammalian genomes. Although the number of functionally annotated ncRNAs is still limited, they are known to be frequently retained in the nucleus, where they coordinate regulatory networks of gene expression. Some subnuclear organelles or nuclear bodies include RNA species whose identity and structural roles are largely unknown. We identified 2 abundant overlapping ncRNAs, MENepsilon and MENbeta (MENepsilon/beta), which are transcribed from the corresponding site in the multiple endocrine neoplasia (MEN) I locus and which localize to nuclear paraspeckles. This finding raises the intriguing possibility that MENepsilon/beta are involved in paraspeckle organization, because paraspeckles are, reportedly, RNase-sensitive structures. Successful removal of MENepsilon/beta by a refined knockdown method resulted in paraspeckle disintegration. Furthermore, the reassembly of paraspeckles disassembled by transcriptional arrest appeared to be unsuccessful in the absence of MENepsilon/beta. RNA interference and immunoprecipitation further revealed that the paraspeckle proteins p54/nrb and PSF selectively associate with and stabilize the longer MENbeta, thereby contributing to the organization of the paraspeckle structure. The paraspeckle protein PSP1 is not directly involved in either MENepsilon/beta stabilization or paraspeckle organization. We postulate a model for nuclear paraspeckle body organization where specific ncRNAs and RNA-binding proteins cooperate to maintain and, presumably, establish the structure.