Nuclear compartmentalization of TERT mRNA and TUG1 lncRNA is driven by intron retention

Gabrijela Dumbović,John L Rinn,Thomas R Cech,Marvin H Caruthers,Evan P Hass,Michael Smallegan,Ulrich Braunschweig,Benjamin Blencowe,Josep Biayna,Heera K Langner,Katarzyna Jastrzebska

doi:10.1038/s41467-021-23221-w

Abstract

The spatial partitioning of the transcriptome in the cell is an important form of gene-expression regulation. Here, we address how intron retention influences the spatio-temporal dynamics of transcripts from two clinically relevant genes: TERT (Telomerase Reverse Transcriptase) pre-mRNA and TUG1 (Taurine-Upregulated Gene 1) lncRNA. Single molecule RNA FISH reveals that nuclear TERT transcripts uniformly and robustly retain specific introns. Our data suggest that the splicing of TERT retained introns occurs during mitosis. In contrast, TUG1 has a bimodal distribution of fully spliced cytoplasmic and intron-retained nuclear transcripts. We further test the functionality of intron-retention events using RNA-targeting thiomorpholino antisense oligonucleotides to block intron excision. We show that intron retention is the driving force for the nuclear compartmentalization of these RNAs. For both RNAs, altering this splicing-driven subcellular distribution has significant effects on cell viability. Together, these findings show that stable retention of specific introns can orchestrate spatial compartmentalization of these RNAs within the cell. This process reveals that modulating RNA localization via targeted intron retention can be utilized for RNA-based therapies.

Highlights

The spatial partitioning of the transcriptome in the cell is an important form of geneexpression regulation
We show that retention of specific introns drives the nuclear retention of both telomerase reverse transcriptase (TERT) pre-mRNA and taurine-upregulated gene 1 (TUG1) long noncoding RNAs (lncRNAs) transcripts
SmRNA FISH revealed that the TUG1 lncRNA is evenly distributed between the nucleus and cytoplasm (Fig. 1)[31,51]

Summary

Introduction

The spatial partitioning of the transcriptome in the cell is an important form of geneexpression regulation. For both RNAs, altering this splicing-driven subcellular distribution has significant effects on cell viability Together, these findings show that stable retention of specific introns can orchestrate spatial compartmentalization of these RNAs within the cell. TERT and TUG1 transcripts represent an opportunity to elucidate when and where splicing occurs, which introns are retained, and how this in turn affects the cellular state. These RNAs provide an opportunity to test if unspliced introns are sufficient to cause nuclear retention, instead of being associated with nuclear retention

Methods

Results

Conclusion