Similar Datasets
Project description:Transposable elements (TEs) have made important contributions to the evolution of the placenta, and are argued to have played a role in the wide inter-species diversification of this critical developmental organ. Co-option of TEs by host genomes has led to the genesis of important placental genes, as well as trophoblast-specific gene regulatory elements. In mice, past work has demonstrated how multiple species-specific TE subfamilies are used as transcriptional enhancers in trophoblast stem cells. However, the involvement of TEs in the regulation of mouse placental gene expression in vivo remains unclear. Here, we characterised the TE regulatory and transcriptional landscape in mouse placenta and gauged their evolutionary dynamics through a comparative approach. We found that overall, TE cis-regulatory activity is greatly diminished in differentiated mouse trophoblast when compared to their stem cell counterpart. On the other hand, evolutionarily young IAP elements are highly expressed in the placenta and create several alternative, placenta-specific transcriptional start sites for protein-coding genes. Placenta-expressed IAP elements are genetically polymorphic between mouse strains and drive species-specific expression of associated genes. These putative co-option events are therefore recent and may represent a prime example of how TE activity can drive fast placental evolution.
2026-02-04 | GSE316715 | GEO
Project description:Transposable elements (TEs) have made important contributions to the evolution of the placenta, and are argued to have played a role in the wide inter-species diversification of this critical developmental organ. Co-option of TEs by host genomes has led to the genesis of important placental genes, as well as trophoblast-specific gene regulatory elements. In mice, past work has demonstrated how multiple species-specific TE subfamilies are used as transcriptional enhancers in trophoblast stem cells. However, the involvement of TEs in the regulation of mouse placental gene expression in vivo remains unclear. Here, we characterised the TE regulatory and transcriptional landscape in mouse placenta and gauged their evolutionary dynamics through a comparative approach. We found that overall, TE cis-regulatory activity is greatly diminished in differentiated mouse trophoblast when compared to their stem cell counterpart. On the other hand, evolutionarily young IAP elements are highly expressed in the placenta and create several alternative, placenta-specific transcriptional start sites for protein-coding genes. Placenta-expressed IAP elements are genetically polymorphic between mouse strains and drive species-specific expression of associated genes. These putative co-option events are therefore recent and may represent a prime example of how TE activity can drive fast placental evolution.
2026-02-04 | GSE316711 | GEO
Project description:Transposable elements (TEs) have made important contributions to the evolution of the placenta, and are argued to have played a role in the wide inter-species diversification of this critical developmental organ. Co-option of TEs by host genomes has led to the genesis of important placental genes, as well as trophoblast-specific gene regulatory elements. In mice, past work has demonstrated how multiple species-specific TE subfamilies are used as transcriptional enhancers in trophoblast stem cells. However, the involvement of TEs in the regulation of mouse placental gene expression in vivo remains unclear. Here, we characterised the TE regulatory and transcriptional landscape in mouse placenta and gauged their evolutionary dynamics through a comparative approach. We found that overall, TE cis-regulatory activity is greatly diminished in differentiated mouse trophoblast when compared to their stem cell counterpart. On the other hand, evolutionarily young IAP elements are highly expressed in the placenta and create several alternative, placenta-specific transcriptional start sites for protein-coding genes. Placenta-expressed IAP elements are genetically polymorphic between mouse strains and drive species-specific expression of associated genes. These putative co-option events are therefore recent and may represent a prime example of how TE activity can drive fast placental evolution.
2026-02-04 | GSE316712 | GEO
Project description:IAP retrotransposons contribute to the transcriptional diversity of the murine placenta
| PRJNA1404109 | ENA
Project description:IAP retrotransposons contribute to the transcriptional diversity of the murine placenta [ATAC-Seq]
| PRJNA1403817 | ENA
Project description:IAP retrotransposons contribute to the transcriptional diversity of the murine placenta [RNA-Seq]
| PRJNA1403818 | ENA
Project description:IAP retrotransposons contribute to the transcriptional diversity of the murine placenta [Cut & Tag]
| PRJNA1403816 | ENA
Project description:We have cloned and characterized a novel cellular gene that is promoted by an intracisternal A-particle (IAP) LTR and expressed in the mouse placenta (mouse IAP promoted placental gene, MIPP). A 1067bp cDNA clone containing an IAP LTR U5 region duplicated in its 5' terminus and an ORF coding for a potential 202 amino acids protein was isolated from an 8.5 day old mouse embryo cDNA library. Sequence analysis of the 5' region of a genomic clone revealed the presence of a solo IAP LTR with the same U5 duplication, and primer extension analysis confirmed that transcription of the MIPP gene is under the control of the IAP LTR. Expression of the MIPP gene parallels that of IAP genes in normal mouse tissues with abundant transcripts present in the placenta and also in the myeloma MOPC-315. The MIPP-encoded protein is composed of four 48-amino acid repeat units and shares homology with a vaccinia virus gene product. MIPP-related sequences were also detected in higher eukaryotic genomes including human.
| S-EPMC328396 | biostudies-other
Project description:BackgroundIn the mouse, culture of embryonic stem (ES) cells may decrease their pluripotency and give rise to foetal abnormalities in recipient embryos. These abnormalities are frequently associated with both, chromosome abnormalities or epigenetic alteration of imprinting genes; however, little is known about the epigenetic stability of endogenous retrotransposable elements (REs). In our laboratory, we came across a R1 ES cell line, which at passage 27, lost the ability of germline transmission and started inducing the kinky tail phenotype in all chimeric animals produced with it.MethodsIn order to investigate whether this phenotype was associated with chromosome alteration, inadvertent differentiation, or epigenetic modification, we characterized and compared this R1 ES cell line at passage 27 with an early passage and with a second ES cell line C57/CBAF1 generated in our laboratory. We assessed: i) karyotype; ii) expression of pluripotent and differentiation markers, iii) mRNA transcription by qRT-PCR of two REs, intracisternal-A particle (IAP) and murine endogenous-retrovirus-L (MuERV-L), and iv) methylation of IAP and MuERV-L.ResultsThe R1 ES cell at passage 27, presented normal morphology, karyotype, and expression of genetic markers characteristic of pluripotent; however, it was detected an altered mRNA transcription of sense and antisense RNA strands of both REs, concomitantly with an altered methylation pattern for the IAP element but not for MuERV-L. These results indicate that besides methylation, other post-transcriptional processes are involved in gene silencing of some REs; and that culture of ES cells may decrease their pluripotency by producing inadvertent alterations in the expression of REs without significantly affecting the morphology, chromosome structure, and expression of pluripotent or differentiation markers.ConclusionInadvertent REs instability may have important consequences for the use of ES cells in transgenesis (chimera formation) or in cell therapy.
| S-EPMC1636644 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2012-11-26 | E-GEOD-41643 | biostudies-arrayexpress