Escape from X inactivation in mouse tissues (RNA-Seq)
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus x Mus spretus
SUBMITTER: Xinxian Deng
PROVIDER: E-GEOD-59777 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:X chromosome inactivation (XCI) silences most genes on one X chromosome in female mammals, but some genes escape XCI. To identify escape gene in vivo and to explore molecular mechanisms that regulate this process we analyzed the allele-specific expression and chromatin structure of X-linked genes in mouse tissues and cells with skewed XCI and distinguishable alleles based on single nucleotide polymorphisms. Using a new method to estimate allelic expression, we demonstrate a continuum between complete silencing and significant expression from the inactive X (Xi). Few genes (2-3%) escape XCI to a significant level and only a minority differs between mouse tissues, suggesting stringent silencing and escape controls. Allelic profiles of DNase I hypersensitivity and RNA polymerase II occupancy of genes on the Xi correlate with escape from XCI. Allelic binding profiles of the DNA binding protein CCCTC-binding factor (CTCF) in different cell types indicate that CTCF binding at the promoter correlates with escape. Importantly, CTCF binding at the boundary between escape and silenced domains may prevent the spreading of active escape chromatin into silenced domains. Examination of CTCF and RNA PolIIS5p occupancy in mouse hybrid cells and adult tissues.
2015-02-20 | E-GEOD-59778 | biostudies-arrayexpress
Project description:In mammals, genes located on the X chromosome are present in one copy in XY males and two in XX females. To balance the dosage of X-linked gene expression between the sexes one of the two X chromosomes in females is silenced by X inactivation initiated by up-regulation of the lncRNA (long non-coding RNA) Xist and recruitment of specific chromatin modifiers for silencing. The inactivated X chromosome becomes heterochromatic and visits a specific nuclear compartment adjacent to the nucleolus. We report a novel role for the X-linked lncRNA Firre in anchoring the inactive mouse X chromosome and preserving one of its main epigenetic features, trimethylation of histone H3 at lysine 27 (H3K27me3). Similar to Dxz4, Firre is expressed from a macrosatellite repeat locus associated with a cluster of CTCF and cohesin binding specifically on the inactive X. CTCF binding initially present in both male and female mouse embryonic stem cells was found to be lost from the active X during development. The Firre and Dxz4 loci on the inactive X were preferentially located adjacent to the nucleolus. Knockdown of Firre RNA disrupted perinucleolar targeting and H3K27me3 levels in mouse fibroblasts, demonstrating an important role for this lncRNA in maintenance of one of the main epigenetic features of the X chromosome. There was no X-linked gene reactivation after Firre knockdown; however, a compensatory increase in the expression of chromatin modifier genes implicated in X silencing was observed. In female ES cells Firre RNA knockdown did not disrupt Xist expression/coating nor silencing of G6pdx during differentiation, suggesting that Firre does not play a role in the onset of X inactivation. We conclude that the X-linked lncRNA Firre helps position the inactive X chromosome near the nucleolus and preserve one of its main epigenetic features. Examination of allelic expression in Patski cells upon Firre knockdown.
2015-03-05 | E-GEOD-66172 | biostudies-arrayexpress
Project description:X chromosome inactivation (XCI) silences most genes on one X chromosome in female mammals, but some genes escape XCI. To identify escape gene in vivo and to explore molecular mechanisms that regulate this process we analyzed the allele-specific expression and chromatin structure of X-linked genes in mouse tissues and cells with skewed XCI and distinguishable alleles based on single nucleotide polymorphisms. Using a new method to estimate allelic expression, we demonstrate a continuum between complete silencing and significant expression from the inactive X (Xi). Few genes (2-3%) escape XCI to a significant level and only a minority differs between mouse tissues, suggesting stringent silencing and escape controls. Allelic profiles of DNase I hypersensitivity and RNA polymerase II occupancy of genes on the Xi correlate with escape from XCI. Allelic binding profiles of the DNA binding protein CCCTC-binding factor (CTCF) in different cell types indicate that CTCF binding at the promoter correlates with escape. Importantly, CTCF binding at the boundary between escape and silenced domains may prevent the spreading of active escape chromatin into silenced domains.
2015-02-20 | GSE59777 | GEO
Project description:X chromosome inactivation (XCI) silences most genes on one X chromosome in female mammals, but some genes escape XCI. To identify escape gene in vivo and to explore molecular mechanisms that regulate this process we analyzed the allele-specific expression and chromatin structure of X-linked genes in mouse tissues and cells with skewed XCI and distinguishable alleles based on single nucleotide polymorphisms. Using a new method to estimate allelic expression, we demonstrate a continuum between complete silencing and significant expression from the inactive X (Xi). Few genes (2-3%) escape XCI to a significant level and only a minority differs between mouse tissues, suggesting stringent silencing and escape controls. Allelic profiles of DNase I hypersensitivity and RNA polymerase II occupancy of genes on the Xi correlate with escape from XCI. Allelic binding profiles of the DNA binding protein CCCTC-binding factor (CTCF) in different cell types indicate that CTCF binding at the promoter correlates with escape. Importantly, CTCF binding at the boundary between escape and silenced domains may prevent the spreading of active escape chromatin into silenced domains.
2015-02-20 | GSE59778 | GEO
Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of RNA polymerase II phosphorylated at serine 5 (PolII-S5p; the transcription initiation form) in female mouse cultured hybrid cells and female hybrid brain derived from mouse systems with skewed X inactivation based on crosses between C57BL/6J (BL6) and M. spretus. In these systems, alleles can be differentiated by frequent SNPs between mouse species, and the active X (Xa) compared to the haploid set of autosomes from the same species. To examine PolII-S5p occupancy in vivo, ChIP-seq was done in brain from an adult female F1 mouse in which the BL6 X is always active and the spretus X inactive. Uniquely mapped reads containing informative SNPs were assigned to each haploid chromosome set (BL6 or spretus) and were counted to establish allele-specific PolII-S5p occupancy profiles. We found that PolII-S5p allele-specific occupancy with or without normalization by input genomic DNA sequencing data showed that expressed genes on the Xa (>1RPKM) had 30% higher PolII-S5p peak levels at their promoters compared to autosomal genes from the same species (BL6). This result was confirmed by performing an independent allele-specific ChIP-seq analysis on fibroblasts derived from embryonic kidney (Patski cell line) that have the opposite X inactivation pattern from the brain sample, i.e. an Xa from M. spretus and an Xi from BL6. These findings suggest that transcription initiation of X-linked genes is enhanced to contribute to X upregulation in cell lines and in vivo. Examination of allele-specific PolII-S5p occupancy in mouse hybrid cells and brain.
2013-02-15 | E-GEOD-44255 | biostudies-arrayexpress
Project description:X-chromosome inactivation (XCI) entails a massive structural reorganization of the inactive X (Xi). However the molecular architecture of the Xi is unknown. Here we show that the Xi lacks typical autosomal features such as active/inactive compartments and topologically associating domains (TADs), except around a small number of genes that escape XCI and remain expressed. Escaping genes form TADs and retain DNA accessibility at promoter-proximal and CTCF binding sites, indicating that these loci can avoid Xist-mediated erasure of chromosomal structure. We further show that genesilencing competent Xist RNA is sufficient to induce segregation of the Xi into two ‘mega-domains’ separated by a boundary that includes the DXZ4 macrosatellite. Deletion of this boundary prior to XCI results in fusion of the megadomains and altered patterns of escape that correlate with changes in TAD structure following differentiation and XCI . Our results suggest a critical role for the boundary locus and Xist RNA in shaping the structure of the Xi and modulating escape from XCI. Our findings also point to roles of transcription and CTCF binding in TAD formation in the context of facultative heterochromatin.
2016-07-18 | GSE72697 | GEO
Project description:Although the chromatin regulator CTCF is enriched at genes escaping from X-chromosome inactivation (XCI), molecular mechanisms remain elusive. We examined CTCF and epigenetic features at escape genes on the inactive X (Xi) in mouse F1 hybrid cells and tissues. We found that escape genes are located inside topologically insulated domains limited by convergent arrays of CTCF binding sites, suggesting loop formation. Xi-specific deletion of a CTCF right boundary of the escape gene Car5b caused loss of CTCF binding and changes of histone modifications at Car5b and abolished escape, suggesting loss of insulation. This is consistent with Car5b lack of escape in mouse brain showing no CTCF binding at the boundary. Inversion of this boundary had no effect on Car5b escape, suggesting that tandem coiled looping could still function as insulation. To test whether chromatin features of the Xi could affect escape we examined mutants in which the Xi-specific compact structure is disrupted or there is loss of H3K27me3 enrichment. We found that both conditions cause an Xi-specific increase in active marks and gene expression at escape regions, suggesting that the 3D structure and heterochromatic marks of the Xi play a role in modulating escape levels of genes insulated by CTCF.
2023-05-18 | GSE231626 | GEO
Project description:The three-dimensional organization of chromatin has a critical impact on the regulation of gene expression. However, little is known about the effect of DNA copy number variants (CNVs) on chromatin organization. We performed an allele-specific chromatin conformation and gene expression analysis of wild-type (WT) mouse chromosome 4 and an engineered 4.3Mb chromosome 4 deletion in mouse embryonic fibroblasts. A newly developed quantitative framework for the analysis of paired-end 4C-seq data revealed a number of significant differentially interacting regions (DIRs) and higher-order chromatin compaction changes present in the deletion chromosome. Selected DIRs were validated by 3D DNA FISH experiments. We discovered a significant enrichment of CTCF and Smc1 binding sites within DIRs, as well as differentially expressed genes determined by RNA-Seq. Together, our findings highlight the complex effects of a 4E2 CNV on chromatin structure and function, both locally in the deletion chromosome and globally in the WT copy. Examination of chromatin contacts and gene expression in wild type chromosome 4 and a 4.3Mb deletion in chromosome 4 in mouse
2016-07-03 | E-GEOD-64359 | biostudies-arrayexpress
Project description:Background: During early embryonic development, one of the two X chromosomes in mammalian female cells is inactivated to compensate for a potential imbalance in transcript levels with male cells containing a single X chromosome. We use mouse female Embryonic Stem Cells (ESCs) with nonrandom XCI and polymorphic X chromosomes to study the dynamics of gene silencing over the inactive X chromosome (Xi) by high-resolution allele-specific RNA-Seq. Results: Induction of XCI by differentiation of female ESCs shows that genes proximal to the X-inactivation center (XIC) are silenced earlier than distal genes, while lowly expressed genes show faster XCI dynamics than highly expressed genes. The active X chromosome shows a minor but significant increase in gene activity during differentiation, resulting in complete dosage compensation in differentiated cell types. Genes escaping XCI show little or no silencing during early propagation of XCI. Using allele-specific RNA-Seq of Neural Progenitor Cells (NPCs) generated from the female ESCs, we identify three regions distal to the XIC that stably escape XCI during differentiation of the female ESCs, as well as during propagation of the NPCs. These regions coincide with Topologically Associated Domains (TADs) as determined in the undifferentiated female ESCs. Also the previously characterized human gene clusters escaping XCI correlate with TADs. Conclusions: Together, the dynamics of gene silencing observed over the Xi during XCI provide further insight in the formation and maintenance of the repressive Xi complex. The association of regions of escape with TADs, in mouse and human, suggests a regulatory role for TADs during propagation of XCI. 19 RNA-Seq profiles of mouse ESCs, EpiSCs and NPCs, mostly from distant crosses to allow allele specific mapping. 1 HiC profile of an undifferentiated mouse female ESC line containing a Tsix mutation. Mainly focusing on X inactivation.
2015-06-15 | E-GEOD-60738 | biostudies-arrayexpress
Project description:X-chromosome inactivation (XCI) achieves dosage compensation between males and females through the silencing of the majority of genes on one X chromosome, with approximately 15% of genes reported to show inactive X (Xi) expression. We examined the interplay between ChromHMM states, CpG density, expression and DNAm from over 1800 female samples with the Illumina 450K array. The interaction between CpG density and histone marks differed between the active X (Xa) and the Xi, with X-linked promoters reflecting transcriptional status, while the Xi showed lower DNAm than the Xa at all non-promoter regions. Promoter DNAm was used to determine a novel XCI status for more than 100 transcription start sites and a comparison across 27 tissues revealed the majority of genes were consistently subject to XCI. Inter-female and twin data supported a model of predominately cis-acting influences on escape, or variable escape, from XCI. Increased promoter DNAm at escape genes correlated with decreased relative Xi expression up to ~15% female DNAm but above this threshold DNAm was not correlated with the stability of silencing. Xi DNAm was ~12% lower than Xa DNAm within the gene bodies of subject genes and between genes while there was equivalent DNAm at escape genes. In addition to offering insight into sex-specific difference in disease, female X chromosomes provide the opportunity to compare euchromatin and heterochromatin of allelic regions within the same nuclear environment and demonstrate the correlation of DNAm with transcription and the influences of CpG density and chromatin marks.
2014-11-29 | GSE60275 | GEO