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

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.

Aging-regulated TUG1 is dispensable for endothelial cell function

“…MALAT1 is exclusively associated to chromatin (40), whereas DANCR is a well characterized transcript known to be mainly cytoplasmic (41), where it is also translated (26). Consistent with previous results obtained within other cell types (42–44), TUG1 was equally distributed across the nucleoplasm, the chromatin, and cytoplasm within ECs, suggesting that TUG1 might incorporate different functions in ECs.…”

“…The high levels of TUG1 transcript might serve as a backup for certain stress responses. This was further supported by the findings of Dumbovic et al (44): Intron retention in the TUG1 transcript drives nuclear compartmentalization and the authors hypothesize that this might indeed serve as a system for buffering the TUG1 transcript in particular stress conditions. In addition, TUG1 is involved in diabetic retinopathy in mice (6) and many types of cancer via a nuclear or cytoplasmic function (21, 51, 30, 52, 53).…”

“…The high levels of TUG1 transcript might serve as a backup for certain stress responses. This was further supported by the findings of Dumbovic et al(44): Intron retention in the TUG1 transcript…”

Identification and targeting of G-quadruplex structures in MALAT1 long non-coding RNA

“…As described early in the result section, we have re-analyzed and identified more than 350 rG4 in about 200 ncRNAs using our published rG4-seq dataset. In this list ( Supplementary Table S1 ), we also found rG4s in other biologically relevant lncRNAs such as TUG1 (taurine upregulated gene 1) , HCG11 (HLA Complex Group 11) , DGCR5 (DiGeorge Syndrome Critical Region Gene 5) , HOTAIRM1 (HOXA Transcript Antisense RNA, Myeloid-Specific 1), which have been functionally characterized in other studies recently ( 98–105 ). Our view is that this list is likely an underestimation of the rG4s in ncRNAs as the rG4-seq was polyA-enriched ( 5 ), and that many ncRNAs do not have polyA tail or polyA region in their sequences.…”

Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads

“…We identified 4 such studies [17, 49–51] that validated a total of 9 RIs in our sets of target genes as defined above (5 and 7 in HX1 and iPSC respectively) (Table S3). (The above four plus an additional ten studies [9, 30, 68–75] experimentally validated RIs in an additional 6 and 9 genes that were found in our target gene sets for in HX1 and iPSC respectively, but without evidence of IR in our samples, and 41 and 36 genes, respectively, that did not pass our sample coverage thresholds for inclusion in this study.) The validated intron coordinates (Table S3) were extracted either from the published intron number [17, 49, 50], assuming a count from the gene’s 5’ to 3’ end, or via BLAT queries of the target sequence [51].…”