An evolutionarily conserved function of the pre-mRNA splicing regulator TNPO3 for T cell development
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ABSTRACT:
PROVIDER: PRJNA309534 | ENA |
REPOSITORIES: ENA
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Project description:All vertebrates possess lymphocytes, enabling the functional interrogation of this evolutionarily conserved organizing principle of adaptive immunity in non-mammalian species. A forward genetic screen in zebrafish indicated that a mutation of tnpo3, encoding a regulator of alternative splicing of pre-mRNAs, specifically impaired intrathymic T cell development. In mouse T cells, Tnpo3 deficiency predominantly disrupted the splicing of genes encoding RNA-binding motifs, and it specifically blocked the splicing of Va11, associated with reduced numbers of peripheral T cells and the complete loss of iNKT cells. Our results reveal an evolutionarily conserved function of a pre-mRNA processing factor for T cell development, uncovering a previously unappreciated checkpoint during the formation of mature mRNAs of the Tcra gene.
2019-01-23 | GSE77137 | GEO
Project description:Background: Alternative splicing (AS), which generates multiple mRNA isoforms from single genes, is crucial for the regulation of eukaryotic gene expression. The flux through competing AS pathways cannot be determined by traditional RNA-Seq, however, because different mRNA isoforms can have widely differing decay rates. Indeed, some mRNA isoforms with extremely short half-lives, such as those subject to translation-dependent nonsense-mediated decay (AS-NMD), may be completely overlooked in even the most extensive RNA-Seq analyses. Results: RNA immunoprecipitation in tandem (RIPiT) of exon junction complex (EJC) components allows for purification of post-splicing mRNA-protein particles (mRNPs) not yet subject to translation (pre-translational mRNPs) and, therefore, translation-dependent mRNA decay. Here we compared EJC RIPiT-Seq to whole cell RNA-Seq data from HEK293 cells. Consistent with expectation, the flux through known AS-NMD pathways is substantially higher than that captured by RNA-Seq. Our EJC RIPiT-Seq also definitively demonstrates that the splicing machinery itself has no ability to detect reading frame. We identified thousands of previously unannotated splicing events; while many can be attributed to “splicing noise”, others are evolutionarily-conserved events that produce new AS-NMD isoforms likely involved in maintenance of protein homeostasis. Several of these occur in genes whose overexpression has been linked to poor cancer prognosis. Conclusions: Deep sequencing of RNAs in post-splicing, pre-translational mRNPs provides a means to identify and quantify splicing events without the confounding influence of differential mRNA decay. For many known AS-NMD targets, the NMD-linked AS pathway predominates. EJC RIPiT-Seq also enabled identification of numerous conserved but previously unknown AS-NMD events.
2021-02-19 | GSE150228 | GEO
Project description:Evolutionarily Conserved Regulation of Immunity by the Splicing Factor RNP-6/PUF60
| PRJNA592073 | ENA
Project description:Splicing is a vital cellular process that modulates important aspects of animal physiology, including metabolism and lifespan. From a cold stress screen, we identified a novel mutant of the splicing factor RNP-6/PUF60, which evokes resistance to various abiotic stresses, yet is highly sensitive to pathogenic bacterial challenge. Molecular and genetic experiments reveal that RNP-6 suppresses immunity, but promotes animal longevity, suggesting a tradeoff between these processes. Pathogen exposure affects gene expression and splicing in a rnp-6 dependent manner. Another longevity promoting splicing factor, SFA-1, similarly exerts an immuno-suppressive effect, working downstream or parallel to RNP-6. Genetic epistasis and biochemical experiments reveal that RNP-6 acts through PMK-1 MAPK signaling to modulate immunity. The mammalian homolog, PUF60, also displays anti-inflammatory properties, and its levels swiftly decrease after bacterial infection in mammalian cells. Our findings demonstrate an evolutionarily conserved modulation of immunity by specific components of the splicing machinery.
2020-07-02 | GSE141097 | GEO
Project description:Intron-containing gene expression in eukaryotes proceeds through the process of RNA splicing to generate protein-coding messenger RNAs (mRNAs). Herein a large and dynamic ribonucleoprotein complex — the spliceosome — removes non-coding introns from pre-mRNAs and joins exons. Spliceosomes must also ensure accurate and timely removal of diverse and highly prevalent introns. Here we show that Sde2 is a conserved splicing regulator, contains a ubiquitin fold, and supports splicing of a subset of pre-mRNAs in an intron-specific manner in Schizosaccharomyces pombe. Its orthologs in S. pombe and humans are synthesized as precursors harboring a ubiquitin fold, followed by an invariant GGKGG motif and an uncharacterized C-terminal domain (referred to as Sde2-C). The precursor must be cleaved at GG^K by the ubiquitin specific proteases Ubp5 and Ubp15 to produce the Sde2-C protein containing a lysine residue at its C-terminus, and is a substrate of the N-end rule pathway of proteasomal degradation. The truncated Sde2-C functions as a component of the spliceosome, and loss of Sde2-C results in inefficient splicing of selected introns from target genes having functions in DNA replication, transcription and telomeric silencing. Thus, the ubiquitin-like processing of Sde2 — associated with its regulation by the N-end rule pathway — contributes to genomic stability in S. pombe through specific pre-mRNA splicing events.
2017-09-22 | GSE97097 | GEO
Project description:Deep sequencing of pre-translational mRNPs reveals hidden flux through evolutionarily conserved AS-NMD pathways
| PRJNA631548 | ENA
Project description:To identify evolutionarily conserved Beta-catenin protein interactions, Beta-catenin mRNA from various metazoans was injected into Xenopus embryos and immunopurified at gastrula stage. Beta-catenin complexes were then separated on an SDS-PAGE gel and subjected mass spectrometric analysis
2023-07-08 | PXD035167 | JPOST Repository
Project description:An evolutionarily conserved ribosome-rescue pathway maintains epidermal homeostasis
| PRJNA415988 | ENA
Project description:How the relatively evolutionarily conserved spliceosome is able to manage the enormously expanded number of splicing events that occur in humans (~200,000 vs. ~400 reported for yeast) is not well understood. Here, we show deposition of one RNA modification-N2-methylguanosine (m2G)-on the G72 nucleoside of U6 snRNA (known to function as the catalytic center of the spliceosome) results in profoundly increased pre-mRNA splicing activity in human cells. This U6 m2G72 modification is conserved among vertebrates. Further, we demonstrate that THUMPD2 is the methyltransferase responsible for U6 m2G72 and show that it interacts with an auxiliary protein (TRMT112) to specifically recognize both sequence and structural elements of U6. THUMPD2 KO blocks U6 m2G72 and down-regulates the pre-mRNA splicing activity of major spliceosome, yielding thousands of changed alternative splicing events of endogenous pre-mRNAs. Notably, the aberrantly spliced pre-mRNA population of the THUMPD2 KO cells elicits the nonsense-mediated mRNA decay (NMD) pathway and restricts cell proliferation. We also show that THUMPD2-mediated control of the U6 m2G72 modification is associated with age-related macular degeneration and retinal function. Our study thus demonstrates how an RNA epigenetic modification of the major spliceosome differentially regulates global mRNA splicing and impacts physiology and disease.
2024-01-02 | GSE236689 | GEO
Project description: In sexually reproducing organisms, sperm contribute half the genomic material required for creation of offspring and natural fertility relies on males producing millions by way of spermatogenesis. This process is essential for continuity and diversity of a species, yet evolutionarily conserved core molecular regulators are undefined. Here we used single cell RNA-sequencing of testicular tissue from mice, pigs, and cattle to generate a multispecies integrated transcriptome database. Through bioinformatic analysis, the gene arrestin-domain containing 5 (Arrdc5) which encodes for an α-arrestin molecule was identified as a potential evolutionarily conserved regulator of spermatogenesis. Expression of Arrdc5 is testis specific in mice, pigs, cattle, and humans. Knockout of Arrdc5 in mice leads to male specific sterility due to production of low numbers of sperm that are immotile and malformed, resembling oligoasthenoteratospermia (OAT) which is a common diagnosis of infertility in men. Spermiogenesis, the final phase of spermatogenesis when round spermatids morphologically transform to spermatozoa, is defective in testes of Arrdc5 deficient mice. Also, epididymal sperm in Arrdc5 knockouts are unable to capacitate and fertilize oocytes. These findings establish Arrdc5 as a core regulator of mammalian spermatogenesis. Considering the role of arrestin molecules as modulators of G-protein coupled signaling and ubiquitination, Arrdc5 is a potential male contraceptive target.
2023-03-06 | GSE206156 | GEO