Filters
Technology
Platform
SRP106029
Mus musculus
36 Downloadable Samples
NextSeq 500
Description
Upon fertilisation, the highly differentiated gametes reprogram to a totipotent state to initiate a new developmental programme. Approximately half of the mammalian genome is composed of repetitive elements, including retrotransposons, some of which are transcriptionally activated after fertilisation. It is generally assumed that retrotransposons become activated as a side-effect of the large chromatin remodelling underlying the epigenetic reprogramming of the gametes. Here, we have used a targeted epigenomic approach to address whether specific families of retrotransposons play a direct role in chromatin organisation and developmental progression after fertilisation. Using this approach, we demonstrate that precocious silencing of LINE-1 reduces chromatin accessibility, while their prolonged activation prevents gradual chromatin compaction, natural to developmental progression. Preventing LINE-1 activation and interfering with their silencing results in a reduced developmental rate independently of the coding nature of the LINE-1 transcript, suggesting that LINE-1 functions primarily at the chromatin level. Our data suggest that activation of LINE-1 regulates global chromatin accessibility at the beginning of development and indicate that activation of retrotransposons is an integral part of the developmental programme. Overall design: RNAseq was done on pooled injected embryos(4-5) as indicated in methods.
Publication Title
LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Mus musculus
- 157 Downloadable Samples
- NextSeq 500
Description
Purpose: The goals of this study are to establish a roadmap of XCI and compare the transcriptomes of WT and Rlim KO embryos during X chromosome inactivation. Methods: mRNA profiles of 175 preimplantation embryos WT and KO for Rlim were elucidated by RNA-seq at various stages. Trophoblasts isolated from blastocyst outgrowths were also included. The sequence reads that samples where gender could be determined and that passed quality filters were analyzed at the level of autosomes, X xhromosomes as well as single genes. Results: Using single cell RNA-seq technology on 175 whole preimplantation embryos, we obtained about 2.95 million sequence reads per sample. Reads were normalized to autosomal gene expression. Gender of each embryo was determined by expression of Y-linked genes and Xist. Data analysis showed normal expression profiles of marker genes for epiblast and trophoblast cell types during preimplantation development. Comparing Xist expression profiles in embryos WT and KO shows that Rlim is not required for initiation of Xist transcription but for upregulation of Xist expression. Moreover, our results identify two waves of XCI during preimplantation development: One that occurs at Morula stages that is Rlim-independent and one at blastocyst stages that in dependent on Rlim. Conclusions: Our study represents the first detailed mouse preimplantation transcriptome. Our results show that Rlim is required for a second wave of imprinted XCI that occurs in female embryos at blastocyst stages. Overall design: Global mRNA profiles of whole preimplantation embryos were generated by deep sequencing.
Publication Title
Regulation of X-linked gene expression during early mouse development by <i>Rlim</i>.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 141 Downloadable Samples
- NextSeq 500
Description
Purpose: The goals of this study are to establish a dynamic roadmap of imprinted X chromosome inactivation and the role of Xist by elucidation of the transcriptome of Xist KO embryos during mouse preimplantation development. Methods: mRNA profiles of the preimplantation embryos WT and KO for Xist were elucidated by RNA-seq at various stages. Trophoblasts isolated from blastocyst outgrowths were also included. The sequence reads for samples where gender could be determined and that passed quality filters were analyzed at the level of autosomes, X chromosome as well as single genes. Results: Female embryos fail to silence the X chromosome at late preimplantation development. General autosomal gene expression is not affected in embryos lacking Xist. Conclusions: Xist is crucial for iXCI. In preimplantation embryos, the main in vivo function of Xist is to regulate iXCI in females. Overall design: Global mRNA profiles of single preimplantation embryos were generated by deep sequencing.
Publication Title
Regulation of X-linked gene expression during early mouse development by <i>Rlim</i>.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Mus musculus
- 12 Downloadable Samples
- NextSeq 500
Description
The transcriptomes of differentiated and undifferentiated E14 (male), Pgk12.1 (female; WT) and Pgk12.1 with a KO of Rlim (RlimKO) were elucidated and examined for differences in X chromosome inactivation. No significant differences between wt and RlimKO with respect to Xist expression and global X-silencing was detected. Results confirm that Rlim is not required for XCI in female ESCs. Overall design: Transciptomes of female WT (Pgk12.1) and female RlimKO ESCs were compared to those of male ESCs (E14). State of XCI in undifferentiated and differentiated ESCs was determined by comparing expression of Xist and expression of X-linked genes female versus male.
Publication Title
Rlim-Dependent and -Independent Pathways for X Chromosome Inactivation in Female ESCs.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Mus musculus
- 8 Downloadable Samples
- NextSeq 500
Description
Purpose: The goals of this study are to establish a dynamic roadmap of imprinted X chromosome inactivation and the role of Xist by elucidation of the transcriptome of Xist KO embryos during mouse preimplantation development Methods: mRNA profiles of the preimplantation embryos WT and KO for Xist were elucidated by RNA-seq at various stages. Trophoblasts isolated from blastocyst outgrowths were also included. The sequence reads that samples where gender could be determined and that passed quality filters were analyzed at the level of autosomes, X chromosome as well as single genes. Effects of genetic background on the kinetics of iXCI was evaluated by RNA-seq on E3.5 embryos with a hybrid C57BL/6 x Cast background. Results: Female embryos fail to silence the X chromosome at late preimplantation development. General autosomal gene expression is not affected in embryos lacking Xist. Conclusions: Xist is crucial for iXCI. In preimplantation embryos the main in vivo function of Xist is to regulate iXCI in females. Genetic background does not significantly influence kinetics of iXCI. Overall design: Global mRNA profiles of single preimplantation embryos were generated by deep sequencing.
Publication Title
Regulation of X-linked gene expression during early mouse development by <i>Rlim</i>.
Sample Metadata Fields
Sex, Cell line, Subject
View Samples