The periphery of nuclear speckles defines a spatially and temporally regulated compartment of long-lived intron-retained RNAs that resolves during mitosis

Abstract

RNA localization adds a fundamental layer to gene expression by determining when and where translation-ready mRNAs become available, yet how this timing is coordinated with nuclear architecture and cell-cycle progression remains unclear. Here we identify a subnuclear RNA niche at the nuclear speckle periphery that couples intron retention to cell-cycle-timed RNA release. Using compartment-resolved transcriptional inhibition, sequence-based deep learning and single-molecule and super-resolution RNA imaging in human pluripotent stem cells, we define a class of nuclear RNAs with long-lived retained introns that persist for hours and are enriched in transcripts encoding regulators of genome maintenance and mitosis, including centromere and kinetochore assembly, DNA repair and telomere maintenance. Long-lived retained introns exhibit elevated GC content, predicted structural stability and enrichment for nuclear speckle-associated RNA-binding proteins. In interphase, these RNAs localize to a distinct nuclear speckle-peripheral RNA niche in a spatial arrangement conserved across cell types. During mitotic remodelling, they undergo coordinated, kinase-dependent splicing and are released into the cytoplasm of early G1 daughter cells. Together, these findings link cis-encoded intronic features, subnuclear organization and mitotic remodelling to temporal control of RNA fate. Biayna, Baranovskii and colleagues report that intron-retained RNAs derived from cell cycle- and genome maintenance-related genes are pooled at the periphery of nuclear speckles and undergo synchronous splicing at mitosis, thereby contributing to their temporal regulation.