Beckground: Specific long noncoding RNAs (lncRNAs) act as skeleton of subcellular structures, therefore, termed “architectural lncRNAs”. Paraspeckle is a nuclear body formed on the specific architectural NEAT1 lncRNA. We have identified ~40 novel paraspeckle proteins (PSPs): seven PSPs are essential for paraspeckle assembly. Here, we identified SWI/SNF chromatin remodeling complexes as novel paraspeckle components. RNAi knockdown revealed that it was required for paraspeckle formation.

Aim: We asked how SWI/SNF complexes contribute to formation of paraspeckle and other nuclear RNA granules. We attempted to detect alteration of the process of paraspeckle formation in the SWI/SNF-depleted cells.

Method: The expression, localization and interaction of the known essential paraspeckle components were examined by RPA, FISH-IF, ChIP and coIP. Electron-microscopic study was employed for observation of the detail localization of SWI/SNF complexes within paraspeckle (collaboration with G. Pierron). Effects of SWI/SNF depletion in formation of other RNA-dependent nuclear bodies were examined.

Results: Two distinct roles of SWI/SNF complexes in paraspeckle formation were identified. First, SWI/SNF complexes facilitate the protein-protein interactions between the essential PSPs. CoIP revealed that SWI/SNF complexes themselves interact with these PSPs, suggesting that SWI/SNF complexes act as the hub for the formation of the PSP network within paraspeckles. The electron-microscopic observation revealed that SWI/SNF complexes prominently enriched in the interior part of paraspeckles where chromatin was poorly detected, suggesting that the appeared function of SWI/SNF complexes is independent of their canonical function on the chromosome. Second, SWI/SNF complexes attenuate transcriptional elongation of RNA polymerase II (RNAPII) on the NEAT1 locus. SWI/SNF depletion resulted in marked increase of binding of the elongating RNAPII, resulted in up-regulation of NEAT1 isoform. Unlike the canonical pattern, SWI/SNF complexes are broadly distributed throughout the NEAT1 locus and this distribution depends on RNAPII elongation. It suggests that the SWI/SNF complexes co-migrate with RNAPII on the NEAT1 locus to attenuate the RNAPII elongation. Other than paraspeckles, formation of the lncRNA-dependent nuclear stress bodies (nSBs) also requires SWI/SNF complexes. SWI/SNF complexes are likely involved in the assembly step of nSBs rather than expression of StaIII lncRNA.

Conclusion: SWI/SNF complexes function as essential factors for lncRNA-dependent paraspeckle assembly by integrating plural steps for paraspeckle assembly. SWI/SNF complexes possibly conduct a common molecular pathway in architecture of at least two distinct lncRNA-dependent nuclear bodies.