ChIPseq on H4K20me1 on TX1072 cell line at different times of Xist induction through Doxycycline.
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ABSTRACT:
PROVIDER: PRJNA641595 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12081751_1.fastq.gz | Fastqsanger.gz | |||
| SRR12081751_2.fastq.gz | Fastqsanger.gz | |||
| SRR12081752_1.fastq.gz | Fastqsanger.gz | |||
| SRR12081752_2.fastq.gz | Fastqsanger.gz | |||
| SRR12081753_1.fastq.gz | Fastqsanger.gz |
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Project description:During X chromosome inactivation (XCI), in female mammals, gene silencing is initiated by a long-noncoding RNA, called Xist. Xist RNA accumulation also allows for the deposition of specific chromatin marks. Among others, PRC2-dependent H3K27me3 and PrSet7-dependent H4K20me1 become enriched at the inactive X chromosome. However, the dynamics of this process in relation to Xist RNA accumulation remains unknown as is the molecular mechanism allowing for H4K20me1 enrichment. To follow XCI dynamics in living cells, we developed a genetically encoded, H3K27me3-specific intracellular antibody, or H3K27me3-mintbody. By combining it with live-imaging of H4K20me1, the X chromosome and Xist RNA we uncover striking similarities in the accumulation dynamics of H3K27me3 and H4K20me1. Further ChIP-seq analysis confirmed concurrent accumulation of H4K20me1 and H3K27me3 during XCI albeit with distinct genomic distributions. Xist B and C repeat mutant, which can silence the X but does not allow for H3K27me3 enrichment, also showed lack of H4K20me1 deposition. Thus, both H3K27me3 and H4K20me1 are deposited at the inactive X through a common molecular mechanism but are dispensable for the initiation of gene silencing.
2021-02-26 | GSE153146 | GEO
Project description:To understand the role of DPPA2 in epigenetic memory during X-Chromosome reactivation (XCR) we employed inducible Xist hybrid female embryonic stem cell line (TX1072, hybrid Bl6/Cast). Wild type or Dppa2 knockout TX1072 cells were cultured, in three or two independent biological replicates, respectively, in presence of DOX (1ug/ml) for 6 days to induce Xist overexpression and X-Chomosome inactivation (XCI) on the Bl6 allele. DOX was then washed out to silence Xist and XCR was followed in a time-series at 1, 3 or 7 days after DOX removal. Cell pellets were harvested at the following timepoints: -DOX, +DOX, 1d D-wo, 3d D-wo and 7d D-wo. RNA was extracted and 250 ng used for PolyA mRNA library preparation and Next generation sequencing.
2021-11-23 | E-MTAB-11183 | biostudies-arrayexpress
Project description:A doxycycline-inducible Xist cDNA transgene was introduced into mouse chromosome 12 at approximately 110Mb (NCBI build m36). Insertion of the transgene was heterozygous, so only one copy of chromosome 12 carried the transgene, and the other chromosome 12 was wild-type. Upon doxycycline induction, the transgene is expressed, producing Xist transgene RNA which localises to autosomal material in cis, leading to silencing of genes adjacent to the transgene. Due to the heterozygous nature of transgene insertion and the cis nature of silencing, for any silenced gene, the maximum possible downregulation in expression levels was 50%. To quantify the changes in the levels of gene expression in response to Xist transgene expression, total RNA was extracted from differentiated ES cells treated with doxycycline. As background control, total RNA was also prepared from uninduced, differentiated ES cells (cultured in parallel to doxycycline-treated cells). The total RNA was then used to make labelled cRNA, which was hybridised to an Affymetrix GeneChip Mouse Genome 430 2.0 array.
2010-05-10 | E-MEXP-2088 | biostudies-arrayexpress
Project description:A doxycycline-inducible Xist cDNA transgene was introduced into mouse chromosome 17 at approximately 71.24Mb (NCBI Build m36). Insertion of the transgene was heterozygous, so only one copy of chromosome 17 carried the transgene, and the other chromosome 17 was wild-type. Upon doxycycline induction, the transgene is expressed, producing Xist transgene RNA which localises to autosomal material in cis, leading to silencing of genes adjacent to the transgene. Due to the heterozygous nature of transgene insertion and the cis nature of silencing, for any silenced gene, the maximum possible downregulation in expression levels was 50%.<br><br><br><br>To quantify the changes in the levels of gene expression in response to Xist transgene expression, total RNA was extracted from undifferentiated and differentiated ES cells treated with doxycycline. As background control, total RNA was also prepared from uninduced cells (both undifferentiated and differentiated, cultured in parallel to doxycycline-treated cells). The total RNA was then used to make labelled cRNA, which was hybridised to an Affymetrix GeneChip Mouse Genome 430 2.0 array.
2010-05-10 | E-MEXP-2087 | biostudies-arrayexpress
Project description:A doxycycline-inducible Xist cDNA transgene was introduced into mouse chromosome 3 at approximately 99.79Mb (NCBI Build m36). Insertion of the transgene was homozygous, so only one copy of chromosome 3 carried the transgene, and the other chromosome 3 was wild-type. Upon doxycycline induction, the transgene is expressed, producing Xist transgene RNA which localises to autosomal material in cis, leading to silencing of genes adjacent to the transgene. Due to the homozygous nature of transgene insertion and the cis nature of silencing, for any silenced gene, the maximum possible downregulation in expression levels was 50%.<br><br><br><br>To quantify the changes in the levels of gene expression in response to Xist transgene expression, total RNA was extracted from undifferentiated and differentiated ES cells treated with doxycycline for three days. As background control, total RNA was also extracted from uninduced cells (both undifferentiated and differentiated, cultured in parallel to doxycycline-treated cells). cRNA was labelled from the total RNAs, and then hybridised to Affymetrix GeneChip Mouse Genome 430 2.0 arrays.
2010-05-10 | E-MEXP-2086 | biostudies-arrayexpress
Project description:Developmental genes are controlled by complex cis-regulatory landscapes that integrate multiple signals to ensure the correct spatio-temporal expression pattern. To investigate the underlying regulatory principles, we use the Xist locus as a model, which encodes the master regulator of X-chromosome inactivation. Xist is upregulated at the primed pluripotent state in a female-specific manner, thus integrating developmental cues and X-dosage information. It remains poorly understood how these signals are decoded by the ~800kb genomic region that controls Xist. While a series of repressive cis-regulatory elements have been identified, the distal enhancers that activate Xist transcription remain largely unknown. Here we use polyA-tail enriched RNA-seq within the wildtype TX1072 XX cell line after two days of differentiation.
2021-03-04 | GSE167354 | GEO
Project description:JARID2 ChIP-seq profile mediated by Xist was investigated using two separate approaches: In the first approach, we use the TX1072 female embryonic stem cell (ESC) line; this is a genetically polymorphic ESC line derived from a mouse with one X-chromosome (X-chr) from the Mus musculus castaneus (Cast) origin and the other of Mus musculus domesticus, C57BL/6 (BL6) strain origin, containing an inducible promoter on the BL6 Xist allele; differentiation and simultaneous induction of Xist for 4 days results in the inactivation of ONLY the BL6-derived X-chr and coating by JARID2 protein. We analysed this ESC line in the undifferentiated state, in which both X-chrs are active (and not coated by JARID2), and also after 4 days of differentiation under Xist inducible conditions, in which cells display one inactive X-chr from BL6 origin and one Xa of the Cast origin; the presence of SNPs allows for the comparison of the degree and localisation of JARID2 enrichment on the inactive X-chr versus the active X-chr; our results suggests that JARID2 is enriched on the inactive X-chr chromosome-wide and not in confined peaks as elsewhere in the genome; This pattern resembles patterns of Xist enrichment published before (Engreitz et al., 2013). In the second approach, we use a male ESC line that carries an inducible Xist transgene (TG) on chromosome 11 (chr11) (Wutz et al., 2000) in the presence (36:11 WT) or the absence of Eed (36:11 Eed-/-) Induction of Xist TG results in Xist coating and enrichment of JARID2 across the chr11, regardless of the presence of Eed when assess by IF/Xist RNA FISH experiments. We compare inducible and uninducible condition in both the 36:11 WT and Eed-/- ESCs; this way, we could assess the Xist-mediated JARID2 recruitment and the effect of the absence of Eed-/-; Our results shows that Xist induction result in a chromosome-wide enrichment of JARID2 on chr11, in a manner that resembles enrichment on the inactive X-chr; this pattern seem to be independent of EED, showing that in contrast to other regions in the genome where JARID2 occupancy is abrogated in the absence of EED, Xist-mediated JARID2 recruitment is not affected. JARID2 ChIP-seq analysis in differentiating female ESCs (TX1072) and in a male ESC harbouring a Xist transgene on chromosome 11 in WT and Eed-/- genetics settings
2014-01-23 | E-GEOD-52073 | biostudies-arrayexpress
Project description:In vertebrates, the catalytic core of PRC1 comprises RING1A/B and one of six homologues of the Polycomb group RING finger (PCGF) protein. Unique characteristics of PCGF1-6 in turn define distinct subunit assemblies, broadly subdivided into canonical and non-canonical PRC1 complexes. This RNA-seq experiment aimed to test the hypothesis that Pcgf3/5 gene knockout abrogates Xist mediated gene repression. In this experiment, Pcgf3fl/flPcgf5-/- and Pcgf3-/-Pcgf5-/- mESCs bearing Xist transgene on chromosome 16 (clone C3F8) were cultured in differentiating conditions: plated on non-gelatinized TC dish in ES medium without LIF for 72 hours with (+dox) and without doxycycline. RNA was isolated from 4 biological replicates. In analysed cells chromosome 16 bears inducible Xist and the whole study investigates role of PCGF3 and PCGF5 in Xist-dependednt gene silencing, therefore both bam files containing alignments and counts per gene were uploaded to ArrayExpress only for chromosome 16. Genome-wide data can be provided upon request.
2018-04-04 | E-MTAB-5642 | biostudies-arrayexpress
Project description:RNAseq in Dppa2 knockout or wildtype TX1072 ESC during and after Xist over-expression
| PRJEB48826 | ENA
Project description:Purpose: Compare the transcriptome of homogeneous XIST+ and XIST- hES cell populations. Methods: We isolated homogeneous XIST+ and XIST- cell populations. The XIST+ cells correspond to cells with a XIST cloud and one ATRX pinpoint. The XIST- cells correspond to cells with no XIST cloud and one ATRX pinpoint. Results: We took advantage of the clonal pattern of X-chromosome inactivation in H9 cells and analyzed the data in an allelic manner. By comparing the RNA-Seq data with known H9 SNPs, we identified genomic positions which were relaxed from XCI in XIST- cells compared to XIST+ cells. Conclusions: Genic as well as unannotated transcripts are massively relaxed from XCI in H9 cells when XIST expression is lost, however, this reactivation is only partial and a large region around the centromere is protected from relaxation of silencing. Total RNA (rRNA depleted) profiles of XIST+ and XIST- human embryonic stem cells
2012-12-21 | E-GEOD-39757 | biostudies-arrayexpress