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An RNA Splicing System that Excises DNA Transposons from Animal mRNAs [Illlumina]

ABSTRACT: All genomes harbor mobile genetic parasites called transposable elements (TEs). Here we describe a system, which we term SOS splicing, that protects C. elegans and human genes from DNA transposon-mediated disruption by excising these TEs from host mRNAs. SOS splicing, which appears to operate independently of the spliceosome, is a pattern recognition system triggered by base-pairing of inverted terminal repeat elements, which are a defining feature of DNA transposons. We identify three factors required for SOS splicing in both C. elegans and human cells; AKAP17A, which binds TE-containing mRNAs; the RNA ligase RTCB; and CAAP1, which bridges RTCB and AKAP17A, allowing RTCB to ligate mRNA fragments generated by TE excision. We propose that SOS splicing is a novel, conserved, and RNA structure-directed mode of mRNA splicing and that one function of SOS splicing is to genetically buffer animals from the deleterious effects of DNA-transposon-mediated gene perturbation.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE288885 | GEO | 2025/09/17

REPOSITORIES: GEO

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An RNA Splicing System that Excises DNA Transposons from Animal mRNAs [Nanopore]

Project description:All genomes harbor mobile genetic parasites called transposable elements (TEs). Here we describe a system, which we term SOS splicing, that protects C. elegans and human genes from DNA transposon-mediated disruption by excising these TEs from host mRNAs. SOS splicing, which appears to operate independently of the spliceosome, is a pattern recognition system triggered by base-pairing of inverted terminal repeat elements, which are a defining feature of DNA transposons. We identify three factors required for SOS splicing in both C. elegans and human cells; AKAP17A, which binds TE-containing mRNAs; the RNA ligase RTCB; and CAAP1, which bridges RTCB and AKAP17A, allowing RTCB to ligate mRNA fragments generated by TE excision. We propose that SOS splicing is a novel, conserved, and RNA structure-directed mode of mRNA splicing and that one function of SOS splicing is to genetically buffer animals from the deleterious effects of DNA-transposon-mediated gene perturbation.

2025-09-17 | GSE288884 | GEO

Transcriptional activity and epigenetic regulation of transposable element in the symbiotic fungus Rhizophagus irregularis

Project description:Arbuscular mycorrhizal (AM) fungi form mutualistic relationships with most land plant species. AM fungi have long been considered as ancient asexuals. Long-term clonal evolution would be remarkable for a eukaryotic lineage and suggests the importance of alternative mechanisms to promote genetic variability facilitating adaptation. Here, we assessed the potential of transposable elements (TEs) for generating genomic diversity. The dynamic expression of TEs during Rhizophagus irregularis spore development suggests ongoing TE activity. We find Mutator-like elements located near genes belonging to highly expanded gene families. Characterising the epigenomic status of R. irregularis provides evidence of DNA methylation and small RNA production occurring at TE loci. Our results support a potential role for TEs in shaping the genome, and roles for DNA methylation and small RNA-mediated silencing in regulating TEs. A well-controlled balance between TE activity and repression may therefore contribute to genome evolution in AM fungi.

2022-02-17 | PXD025245 | Pride

Pervasive transcription and endosiRNAs restrain transposons during global demethylation in embryonic stem cells [smallRNA-Seq 2]

Project description:DNA methylation and other repressive epigenetic marks are erased in the mammalian germline and transposable elements (TEs) acquire the potential to be transcribed. This is a critical phase for genome defense and complementary TE silencing pathways are required to limit their activity. We find overlapping sense/antisense transcription in TEs in mouse embryonic stem cells, with an increase of sense transcription induced by acute deletion of Dnmt1, leading to increased abundance of small RNAs. These small RNAs are loaded into ARGONAUTE2 (AGO2) suggesting an endosiRNA based silencing mechanism. Reduction of Dicer and Ago2 levels reveals that small RNAs are involved in an immediate response to transposon activation by demethylation, while the deposition of repressive histone marks represents an ensuing chronic response. Dicer dependent endosiRNAs which map to TEs are also found in vivo during primordial germ cell development. Our results suggest that TE antisense transcription acts as a trap that restrains acute transposon activity through small RNAs during epigenetic reprogramming in the germline.

2017-11-01 | GSE102447 | GEO

Pervasive transcription and endosiRNAs restrain transposons during global demethylation in embryonic stem cells [ChIP-Seq 2]

2017-11-01 | GSE102445 | GEO

Pervasive transcription and endosiRNAs restrain transposons during global demethylation in embryonic stem cells [RNA-Seq 2]

2017-11-01 | GSE102446 | GEO

A transposon sensor during epigenetic reprogramming consists of pervasive transcription and endosiRNAs in mouse ES cells [BS-Seq]

Project description:DNA methylation and other repressive epigenetic marks are erased genome-wide in mammalian primordial germ cells (PGCs), the early embryo and in naïve embryonic stem cells (ESCs). This is a critical phase for transposon element (TE) defense since presumably alternative pathways need to be employed to limit their activity. It has been reported that pervasive transcription is enriched for TEs in ESCs in comparison to somatic cells. Here we test the hypothesis that pervasive transcription overlapping TEs forms a sensor for loss of their transcriptional repression. Overlapping sense and antisense transcription is found in TEs, and the increase of sense transcription induced by acute deletion of DNMT1 leads to the emergence of small RNAs. These small RNAs are loaded into ARGONAUTE 2 suggesting an endosiRNA mechanism for transposon silencing. Indeed, deletion of DICER reveals this mechanism to be important for silencing of certain transposon classes, while others are additionally repressed by deposition of repressive histone marks. Our observations suggest that pervasive transcription overlapping with TEs resulting in endosiRNAs is a transposon sensor that restrains their activity during epigenetic reprogramming in the germline.

2017-11-01 | GSE89697 | GEO

A transposon sensor during epigenetic reprogramming consists of pervasive transcription and endosiRNAs in mouse ES cells [RNA-Seq]

2017-11-01 | GSE89695 | GEO

A transposon sensor during epigenetic reprogramming consists of pervasive transcription and endosiRNAs in mouse ES cells [ChIP-Seq]

2017-11-01 | GSE89694 | GEO

A transposon sensor during epigenetic reprogramming consists of pervasive transcription and endosiRNAs in mouse ES cells [smallRNA-Seq]

2017-11-01 | GSE89696 | GEO

RNA Ligase RTCB-mediated mRNA Alternative Splicing is Required for Mouse Oocyte Development and Maintenance

Project description:Intron splicing of the pre-mRNA is usually coupled with the transcription elongation catalyzed by RNA polymerase. However, recent large-scale mRNA sequencing showed that introns are still retained in 5-10% of mRNA, these introns are named as exitrons. They are deleted in some special cells or conditions to deal with developmental transition or cellular stress response. The role of this mechanism in mammalian female reproduction is elusive so far. We found that RNA terminal phosphate cyclase B (RTCB) mainly regulated splicing of these transcripts related to p-CDK1, DNA methylation and DNA damage repair. On the one hand, it regulated the recovery of oocyte meiosis by affecting CDK1 activation. On the other hand, it also regulated the developmental potential of oocytes by influencing splicing of DNA methylation and DNA damage repair-related mRNA. In addition, it could also play a crucial role in follicular development. Rtcb deletion resulted in the accumulation of these maternal mRNAs containing unspliced introns, and the decline of the overall level of transcripts. As a result, Rtcb-/- female are sterile. Our study highlights the important role of RTCB-regulated non-canonical alternative splicing in female reproduction.

2022-10-10 | GSE190681 | GEO

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