scholarly journals Nuclear compartmentalization of TERT mRNA and TUG1 lncRNA transcripts is driven by intron retention: implications for RNA-directed therapies

2020 ◽  
Author(s):  
Gabrijela Dumbović ◽  
Ulrich Braunschweig ◽  
Heera K. Langner ◽  
Katarzyna Jastrzebska ◽  
Michael Smallegan ◽  
...  
Keyword(s):  
Single Molecule ◽  
Temporal Dynamics ◽  
Intron Retention ◽  
Single Cells ◽  
Bimodal Distribution ◽  
Protein Coding ◽  
Rna Molecules ◽  
Global Connections ◽  
Spatio Temporal ◽  
Nuclear Compartmentalization

AbstractNumerous global connections have been made between splicing and other layers of gene regulation, including the spatial partitioning of the transcriptome in the cell. Yet, there has been surprisingly little analysis of the spatio-temporal regulation of individual protein-coding and non-coding RNA molecules in single cells. 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 revealed that nuclear TERT transcripts uniformly and robustly retain two specific introns whose splicing 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 had significant effects on cell growth. Together, these findings show that stable retention of specific introns can orchestrate spatial compartmentalization of RNAs within the cell; this process reveals new targets for RNA-based therapies.

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

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Gabrijela Dumbović ◽  
Ulrich Braunschweig ◽  
Heera K. Langner ◽  
Michael Smallegan ◽  
Josep Biayna ◽  
...  
Keyword(s):  
Single Molecule ◽  
Gene Expression Regulation ◽  
Temporal Dynamics ◽  
Intron Retention ◽  
Bimodal Distribution ◽  
Spatial Partitioning ◽  
Rna Targeting ◽  
Spatio Temporal ◽  
Retained Introns ◽  
Nuclear Compartmentalization

AbstractThe 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.

scholarly journals Shaping development by stochasticity and dynamics in gene regulation

Open Biology ◽  
2017 ◽  
Vol 7 (5) ◽  
pp. 170030 ◽  
Author(s):  
Peng Dong ◽  
Zhe Liu
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Single Cell ◽  
Cell Fate ◽  
Single Molecule ◽  
Large Scale ◽  
Single Cells ◽  
Individual Gene ◽  
Functional Specification ◽  
Spatio Temporal

Animal development is orchestrated by spatio-temporal gene expression programmes that drive precise lineage commitment, proliferation and migration events at the single-cell level, collectively leading to large-scale morphological change and functional specification in the whole organism. Efforts over decades have uncovered two ‘seemingly contradictory’ mechanisms in gene regulation governing these intricate processes: (i) stochasticity at individual gene regulatory steps in single cells and (ii) highly coordinated gene expression dynamics in the embryo. Here we discuss how these two layers of regulation arise from the molecular and the systems level, and how they might interplay to determine cell fate and to control the complex body plan. We also review recent technological advancements that enable quantitative analysis of gene regulation dynamics at single-cell, single-molecule resolution. These approaches outline next-generation experiments to decipher general principles bridging gaps between molecular dynamics in single cells and robust gene regulations in the embryo.

scholarly journals Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting

2018 ◽  
Author(s):  
Orsolya Symmons ◽  
Marcello Chang ◽  
Ian A. Mellis ◽  
Jennifer M. Kalish ◽  
Marisa S. Bartolomei ◽  
...  
Keyword(s):  
Single Molecule ◽  
Single Cells ◽  
Gene Copy ◽  
Specific Expression ◽  
Rna Molecules ◽  
Gene Copies ◽  
Extensive Cell ◽  
Allele Specific ◽  
Transcriptional Bursting ◽  
Diploid Cells

AbstractExtensive cell-to-cell variation exists even among putatively identical cells, and there is great interest in understanding how the properties of transcription relate to this heterogeneity. Differential expression from the two gene copies in diploid cells could potentially contribute, yet our ability to measure from which gene copy individual RNAs originated remains limited, particularly in the context of tissues. Here, we demonstrate quantitative, single molecule allele-specific RNA FISH adapted for use on tissue sections, allowing us to determine the chromosome of origin of individual RNA molecules in formaldehyde-fixed tissues. We used this method to visualize the allele-specific expression of Xist and multiple autosomal genes in mouse kidney. By combining these data with mathematical modeling, we evaluated models for allele-specific heterogeneity, in particular demonstrating that apparent expression from only one of the alleles in single cells can arise as a consequence of low-level mRNA abundance and transcriptional bursting.

scholarly journals Single molecule tracking reveals spatio-temporal dynamics of bacterial DNA repair centres

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Thomas C. Rösch ◽  
Stephan Altenburger ◽  
Luis Oviedo-Bocanegra ◽  
Miriam Pediaditakis ◽  
Nina El Najjar ◽  
...  
Keyword(s):  
Dna Repair ◽  
Single Molecule ◽  
Temporal Dynamics ◽  
Single Molecule Tracking ◽  
Bacterial Dna ◽  
Spatio Temporal

scholarly journals NAD tagSeq reveals that NAD+-capped RNAs are mostly produced from a large number of protein-coding genes in Arabidopsis

2019 ◽  
pp. 201903683 ◽  
Author(s):  
Hailei Zhang ◽  
Huan Zhong ◽  
Shoudong Zhang ◽  
Xiaojian Shao ◽  
Min Ni ◽  
...  
Keyword(s):  
Single Molecule ◽  
Enzymatic Reaction ◽  
Accurate Identification ◽  
Protein Coding ◽  
Rna Molecules ◽  
Rna Transcripts ◽  
Protein Coding Genes ◽  
Oxford Nanopore ◽  
Almost All ◽  
Identification And Quantification

The 5′ end of a eukaryotic mRNA transcript generally has a 7-methylguanosine (m7G) cap that protects mRNA from degradation and mediates almost all other aspects of gene expression. Some RNAs in Escherichia coli, yeast, and mammals were recently found to contain an NAD+ cap. Here, we report the development of the method NAD tagSeq for transcriptome-wide identification and quantification of NAD+-capped RNAs (NAD-RNAs). The method uses an enzymatic reaction and then a click chemistry reaction to label NAD-RNAs with a synthetic RNA tag. The tagged RNA molecules can be enriched and directly sequenced using the Oxford Nanopore sequencing technology. NAD tagSeq can allow more accurate identification and quantification of NAD-RNAs, as well as reveal the sequences of whole NAD-RNA transcripts using single-molecule RNA sequencing. Using NAD tagSeq, we found that NAD-RNAs in Arabidopsis were produced by at least several thousand genes, most of which are protein-coding genes, with the majority of these transcripts coming from <200 genes. For some Arabidopsis genes, over 5% of their transcripts were NAD capped. Gene ontology terms overrepresented in the 2,000 genes that produced the highest numbers of NAD-RNAs are related to photosynthesis, protein synthesis, and responses to cytokinin and stresses. The NAD-RNAs in Arabidopsis generally have the same overall sequence structures as the canonical m7G-capped mRNAs, although most of them appear to have a shorter 5′ untranslated region (5′ UTR). The identification and quantification of NAD-RNAs and revelation of their sequence features can provide essential steps toward understanding the functions of NAD-RNAs.

Spatial and temporal dynamics of Pacific capelin Mallotus catervarius in the Gulf of Alaska: implications for ecosystem-based fisheries management

2020 ◽  
Vol 637 ◽  
pp. 117-140 ◽  
Author(s):  
DW McGowan ◽  
ED Goldstein ◽  
ML Arimitsu ◽  
AL Deary ◽  
O Ormseth ◽  
...  
Keyword(s):  
Temporal Dynamics ◽  
Marine Ecosystem ◽  
Gulf Of Alaska ◽  
Data Series ◽  
Limited Information ◽  
Important Species ◽  
Multiple Data ◽  
Spatial And Temporal Dynamics ◽  
Spawning Areas ◽  
Spatio Temporal

Pacific capelin Mallotus catervarius are planktivorous small pelagic fish that serve an intermediate trophic role in marine food webs. Due to the lack of a directed fishery or monitoring of capelin in the Northeast Pacific, limited information is available on their distribution and abundance, and how spatio-temporal fluctuations in capelin density affect their availability as prey. To provide information on life history, spatial patterns, and population dynamics of capelin in the Gulf of Alaska (GOA), we modeled distributions of spawning habitat and larval dispersal, and synthesized spatially indexed data from multiple independent sources from 1996 to 2016. Potential capelin spawning areas were broadly distributed across the GOA. Models of larval drift show the GOA’s advective circulation patterns disperse capelin larvae over the continental shelf and upper slope, indicating potential connections between spawning areas and observed offshore distributions that are influenced by the location and timing of spawning. Spatial overlap in composite distributions of larval and age-1+ fish was used to identify core areas where capelin consistently occur and concentrate. Capelin primarily occupy shelf waters near the Kodiak Archipelago, and are patchily distributed across the GOA shelf and inshore waters. Interannual variations in abundance along with spatio-temporal differences in density indicate that the availability of capelin to predators and monitoring surveys is highly variable in the GOA. We demonstrate that the limitations of individual data series can be compensated for by integrating multiple data sources to monitor fluctuations in distributions and abundance trends of an ecologically important species across a large marine ecosystem.

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