Dars2 is involved in mRNA splicing in mouse bone marrow hematopoietic stem and progenitor cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE213952 | GEO | 2023/09/25
REPOSITORIES: GEO
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Project description:Aspartyl-tRNA synthetase 2 (Dars2) is involved in the regulation of mitochondrial protein synthesis and tissue-specific mitochondrial unfolded protein response (UPRmt). The role of Dars2 in the self-renewal and differentiation of hematopoietic stem cells (HSCs) is unknown. Here we show that knockout (KO) of Dars2 significantly impairs the maintenance of HSCs and progenitor cells (HSPCs) without involving its tRNA synthetase activity. Dars2 KO results in significantly reduced expression of Srsf2/3/6 and impairs multiple events of mRNA alternative splicing (AS). Dars2 directly localizes to Srsf3 labeled spliceosomes in HSPCs and regulates the stability of Srsf3. Dars2-deficient HSPCs exhibit aberrant AS of mTOR and Slc22a17. Dars2 KO greatly suppresses the levels of labile ferrous iron and iron-sulfur cluster containing proteins, which dampens mitochondrial metabolic activity and DNA damage repair pathway in HSPCs. Our study reveals that Dars2 plays an unprecedented role in the iron-sulfur metabolism and maintenance of HSPCs by modulating RNA splicing.
2023-09-26 | PXD045562 | Pride
Project description:Alternative splicing generates functional diversity in higher organisms through alternative first and last exons, skipped and included exons, intron retentions and alternative donor and acceptor sites. In large-scale microarray studies in human and mouse, emphasis so far has been placed on exon-skip events, leaving the prevalence and importance of other splice types largely unexplored. Using a new human splice variant database and a genome-wide microarray to probes thousands of splice events of each type, we measured differential expression of splice types across 6 pairs of diverse cell lines and validated the database annotation process. Results suggest that splicing in human is more complex than simple exon skip events, which account for a minority of splicing differences. The relative frequency of differential expression of the splice types correlates with what is found by our annotation efforts. In conclusion, alternative splicing in human cells is considerably more complex than the canonical example of the exon-skip. The complementary approaches of genome-wide annotation of alternative splicing in human and design of genome-wide splicing microarrays to measure differential splicing in biological samples provide a powerful high-throughput tool to study the role of alternative splicing in human biology. Keywords: alternative splicing
2007-12-08 | GSE9734 | GEO
Project description:We explored alternative splicing events upon hsa-miR-139-5p/HNRNPF axis regulation in our cell system using the Multivariate Analysis of Transcript Splicing (rMATS) computational tool (https://doi.org/10.1073/pnas.1419161111). Differential analysis of major splicing outcomes (skipped exon, alternative 5’/3’ splice, mutually exclusive exons and retained intron) revealed a total of 174 events significantly activated or repressed (FDR<0.05) upon HNRNPF regulation.
2019-08-26 | GSE123680 | GEO
Project description:Celf6 is an RNA binding protein expressed in a subset of neurons in the brain. We conducted an analysis of splicing in RNAseq data derived from Celf6 knockout mice, compared to wildtype littermates. We profiled both total tissue RNAseq from a hindbrain dissection, as well as Translated Ribosome Affinity Purified (TRAP)seq specifically from serotonergic neurons – a population of cells we previously characterized as expressing Celf6. We used MISO for the splicing analysis (PMID: 21057496). MISO uses read evidence found in a sample in a Bayesian model in order to assign a percent spliced in (PSI) value, defining the expected frequency of an alternate event. In the total RNA sample, the number of measurable PSI events was 1817. The most annotated events found were the Skipped Exons (35.5%) , Retained Introns (25 %), and Tandem 3’UTR (alternative poly-adenylation, 17.2%) categories. In general, the Skipped Exons category has the largest number of annotated events in MISO (Figure 1C). Out of 1817 assignable events, 95 showed nominal ANOVA p<0.05 between WT and Celf6 KO with 0 meeting Benjamini-Hochberg FDR <0.05. Alternative event categories had roughly the same distribution in nominally significant differentially abundant alternative events as to the data as a whole. 33/95 nominally significant events were in genes that were putative CELF6 targets, however only two (C1d, Rit2) were in genes matching both CLIP stringency criteria (significant enrichment in both CLIP input & antibody non-specific binding controls). As PSI describes the probability of being either in alternative form A (PSI = 0) or B (PSI = 1), large changes in PSI between one sample to another might indicate a splicing switch between predominant forms. Among the nominally significant events, the majority (88/95, 92.6%) were between -0.2 to 0.2 indicating only slight changes in splice form abundance. There were a few events with larger changes in PSI, with differences between KO and WT greater that 0.2, 5 in alternative polyadenylation, 1 in a Mutually Exclusive Exon event, and 1 in Alternative 5’ Splice Site usage. The largest change of these was in Acox1 (not a putative CELF6 target), peroxisomal straight-chain acyl-CoA oxidase, with a change of -0.62 in the KO (p = 0.037) which may indicate evidence of a switch in usage of a 897 nucleotide 3’UTR in the WT (WT median PSI = 0.89) to a 1660 nucleotide 3’UTR in the KO (KO median PSI = 0.26). However, none of these survive FRD correction. In serotonergic cell mRNA accessed by TRAP, the total measurable events was 2,201 with a distribution of effect sizes similar to that found in total RNA. 112 of these events showed nominal p values < 0.05, with 2 events meeting Benjamini-Hochberg FDR < 0.05, which showed a similar distribution to the data as a whole. 40 nominally significant events were found in putative CELF6 CLIP targets, 5 genes meeting the most stringent criteria (Snap25, Tpm1, Rnf14, Shroom2, App). As with total RNA, most events showed small differences in PSI between WT and KO (-0.2 to 0.2, median ~.01), with only 4 events outside this range. The largest such difference was found in Nmnat2, nicotinamide nucleotide adenylyltransferase 2 (not a putative CELF6 target), again in an alternative 3’ UTR. The WT median PSI of 0.55 indicates two isoforms are similarly abundant: a 3.6 kb 3’UTR and a 400 bp UTR. In the KO, this is shifted towards the shorter UTR (KO median PSI 0.98).
2021-01-11 | GSE160293 | GEO
Project description:The latest version of microarrays released by Affymetrix, the GeneChip Gene 1.0 ST Arrays (gene arrays), are designed in a similar fashion as exon arrays, which enables to identify differentially expressed exons, rather than only the expression level of whole transcripts. Here, we propose an extension, Gene Array Analyzer (GAA), to our previously published Exon Array Analyzer (EAA). GAA enables to analyse gene arrays on exon level and therefore supports to identify alternative splicing with gene arrays. To show the applicability of GAA, we used gene arrays to profile alternative splice events during the development of the heart. Further re-analysis of published gene arrays could show, that some of these splice events reoccur under pathological conditions. The web interface of GAA is user friendly, functional without set up and freely available at http://GAA.mpi-bn.mpg.de. Alternative splicing and gene expression analysis during development of the heart and cardiomyoyte differentiation.
2011-11-28 | E-GEOD-30429 | biostudies-arrayexpress
Project description:The latest version of microarrays released by Affymetrix, the GeneChip Gene 1.0 ST Arrays (gene arrays), are designed in a similar fashion as exon arrays, which enables to identify differentially expressed exons, rather than only the expression level of whole transcripts. Here, we propose an extension, Gene Array Analyzer (GAA), to our previously published Exon Array Analyzer (EAA). GAA enables to analyse gene arrays on exon level and therefore supports to identify alternative splicing with gene arrays. To show the applicability of GAA, we used gene arrays to profile alternative splice events during the development of the heart. Further re-analysis of published gene arrays could show, that some of these splice events reoccur under pathological conditions. The web interface of GAA is user friendly, functional without set up and freely available at http://GAA.mpi-bn.mpg.de. Alternative splicing and gene expression analysis during development of the heart and cardiomyoyte differentiation.
2011-11-28 | E-GEOD-32998 | biostudies-arrayexpress
Project description:22 Normal adult mouse tissues on custom alternative transcript sensitive Affymetrix microarray used to address differeneces in tissue specific alternative splicing. Abstract: Alternative splicing contributes to both gene regulation and protein diversity. To discover broad relationships between regulation of alternative splicing and sequence conservation, we applied a systems approach, using oligonucleotide microarrays designed to capture splicing information across the mouse genome. In a set of 22 adult tissues, we observe expression of RNA containing at least two alternative splice junctions for about a third of the 3200 alternative events we could detect. Statistical comparisons identify 171 cassette exons whose inclusion or skipping is different in brain relative to other tissues, and another 28 exons whose splicing is different in muscle. A subset of these exons is associated with unusual blocks of intron sequence whose conservation in vertebrates rivals that of protein-coding exons. By focusing on sets of exons with similar regulatory patterns, we have identified new sequence motifs implicated in brain and muscle splicing regulation. Of note is a motif strikingly similar to the branchpoint consensus, but which is located downstream of the 5' splice site of exons included in muscle. Analysis of three paralogous membrane-associated guanylate kinase (MAGUK) genes reveals that each contains a paralogous tissue regulated exon with a similar tissue inclusion pattern. While the intron sequences flanking these exons remain highly conserved among mammalian orthologs, the paralogous flanking intron sequences have diverged considerably, suggesting unusually complex evolution of the regulation of alternative splicing in multigene families. Keywords: Alternative splicing isoform specific, adult mouse tissues
2006-01-19 | GSE3063 | GEO
Project description:Alternative polyadenylation has been implicated as an important regulator of gene expression. In some cases, alternative polyadenylation is known to couple with alternative splicing to influence last intron removal. However, it is unknown whether alternative polyadenylation events influence alternative splicing decisions at upstream exons. Knockdown of the polyadenylation factors CFIm25 or CstF64 was used as an approach in identifying alternative polyadenylation and alternative splicing events on a genome-wide scale. Although hundreds of alternative splicing events were found to be differentially spliced in the knockdown of CstF64, genes associated with alternative polyadenylation did not exhibit an increased incidence of alternative splicing. These results demonstrate that the coupling between alternative polyadenylation and alternative splicing is usually limited to defining the last exon. The striking influence of CstF64 knockdown on alternative splicing can be explained through its effects on UTR selection of known splicing regulators such as hnRNP A2/B1, thereby indirectly influencing splice site selection. We conclude that changes in the expression of the polyadenylation factor CstF64 influences alternative splicing through indirect effects. HeLa cell line was stably transfected with shRNA plasmids targeting CstF64. Total RNA was isolated from CstF64 KD cells and wild-type control cells using Trizol according to manufacturerâs protocols. Samples were deep sequenced in duplicate using the Illumina GAIIx system.
2016-03-14 | E-GEOD-79157 | biostudies-arrayexpress
Project description:Alternative polyadenylation has been implicated as an important regulator of gene expression. In some cases, alternative polyadenylation is known to couple with alternative splicing to influence last intron removal. However, it is unknown whether alternative polyadenylation events influence alternative splicing decisions at upstream exons. Knockdown of the polyadenylation factors CFIm25 or CstF64 was used as an approach in identifying alternative polyadenylation and alternative splicing events on a genome-wide scale. Although hundreds of alternative splicing events were found to be differentially spliced in the knockdown of CstF64, genes associated with alternative polyadenylation did not exhibit an increased incidence of alternative splicing. These results demonstrate that the coupling between alternative polyadenylation and alternative splicing is usually limited to defining the last exon. The striking influence of CstF64 knockdown on alternative splicing can be explained through its effects on UTR selection of known splicing regulators such as hnRNP A2/B1, thereby indirectly influencing splice site selection. We conclude that changes in the expression of the polyadenylation factor CstF64 influences alternative splicing through indirect effects.
2016-03-14 | GSE79157 | GEO
Project description:The latest version of microarrays released by Affymetrix, the GeneChip Gene 1.0 ST Arrays (gene arrays), are designed in a similar fashion as exon arrays, which enables to identify differentially expressed exons, rather than only the expression level of whole transcripts. Here, we propose an extension, Gene Array Analyzer (GAA), to our previously published Exon Array Analyzer (EAA). GAA enables to analyse gene arrays on exon level and therefore supports to identify alternative splicing with gene arrays. To show the applicability of GAA, we used gene arrays to profile alternative splice events during the development of the heart. Further re-analysis of published gene arrays could show, that some of these splice events reoccur under pathological conditions. The web interface of GAA is user friendly, functional without set up and freely available at http://GAA.mpi-bn.mpg.de.
2011-11-28 | GSE30429 | GEO