Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution

Abstract

Nuclear speckles are self-assembled organelles composed of RNAs and proteins. They are proposed to act as structural domains that control distinct steps in gene expression, including transcription, splicing, and mRNA export. Earlier studies identified differential localization of a few components within the speckles. It was speculated that the spatial organization of speckle components might contribute directly to the order of operations that coordinate distinct processes. By performing multi-color structured illumination microscopy, we characterized the multilayer organization of speckles at a higher resolution. SON and SC35 localize to the central region of the speckle, whereas MALAT1 and snRNAs are enriched towards the speckle periphery. Coarse-grained simulations indicate that the non-random organization arises due to the interplay between favorable, sequence-encoded intermolecular interactions of speckle-resident proteins and RNAs. Finally, we observe positive correlation between the total amount of RNA present within a speckle and the speckle size. These results imply that speckle size may be regulated to accommodate RNA accumulation and processing. Accumulation of RNA from various actively transcribed, speckle-associated genes could contribute to the observed speckle size variations within a single cell.