Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA219131 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In order to test the hypothesis that X chromosome inactivation shows sequence specificity, we have analysed the spread of XCI into autosomal chromatin by performing DNA methylation profiling in six unbalanced X;autosome translocations. Using promoter hypermethylation as an epigenetic signature of XCI, we have determined the inactivation status of 1,050 autosomal genes after translocation onto the inactive X. By performing a comparative sequence analysis of autosomal genes that are either subject to or escape the X inactivation signal, we identified a number of common repetitive elements, including LINEs, and DNA motifs that are significantly enriched around inactive autosomal genes. We show that these same motifs predominantly map to L1P elements, are significantly enriched on the X chromosome versus the autosomes, and also occur at higher densities around X-linked genes that are subject to X inactivation compared to those that escape X inactivation. These results are consistent with a potential causal relationship between DNA sequence features such as L1s and the spread of XCI, lending strong support to Mary Lyon's 'repeat hypothesis'. Genome-wide measurement of CpG methylation levels by hybridizing bisulphite-converted DNA to Infinium HumanMethylation450 BeadChips. Eight DNA samples extracted from individuals carrying X;autosome translocations were processed according to manufacturer's recommended protocols, and array data processed using the Methylation Module of GenomeStudio v1.8 software with default parameters.
2013-09-13 | E-GEOD-50837 | biostudies-arrayexpress
Project description:In order to test the hypothesis that X chromosome inactivation shows sequence specificity, we have analysed the spread of XCI into autosomal chromatin by performing DNA methylation profiling in six unbalanced X;autosome translocations. Using promoter hypermethylation as an epigenetic signature of XCI, we have determined the inactivation status of 1,050 autosomal genes after translocation onto the inactive X. By performing a comparative sequence analysis of autosomal genes that are either subject to or escape the X inactivation signal, we identified a number of common repetitive elements, including LINEs, and DNA motifs that are significantly enriched around inactive autosomal genes. We show that these same motifs predominantly map to L1P elements, are significantly enriched on the X chromosome versus the autosomes, and also occur at higher densities around X-linked genes that are subject to X inactivation compared to those that escape X inactivation. These results are consistent with a potential causal relationship between DNA sequence features such as L1s and the spread of XCI, lending strong support to Mary Lyon's 'repeat hypothesis'.
2013-09-13 | GSE50837 | GEO
Project description:Two major genetic pathways leading to colorectal carcinoma can well be distinguished; the ‘suppressor pathway’, which is characterized by inactivation of tumor-suppressor genes and the ‘mutator pathway’, which is characterized by microsatellite instability. The purpose of this study is to explore a third putative pathway; microsatellite and chromosome stable colorectal cancer where an alternative cancer-causative mechanism might play a role.
| 2021019 | ecrin-mdr-crc
Project description:Using long-read nanopore sequencing, we obtained chromosome-wide phased methylomes of the active and inactive X in mouse placenta and neural stem cells (NSCs), overcoming the limitations if short-read bisulfite sequencing in allelic resolution. We also conducted quantitative analysis of methylation properties like symmetry and entropy, providing a more comprehensive view of epigenetic silencing in X chromosome inactivation. We also resolved the allele-specific genetics and epigenetics of structural macrosatellite Dxz4 and other repeats.
2024-03-12 | E-MTAB-13706 | biostudies-arrayexpress
Project description:Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., centric) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding, surrounded by pericentromeric LINE/L1 elements. We explored chromosome structure across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible association of centromeric chromatin, and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.
2022-03-30 | GSE199671 | GEO
Project description:X chromosome inactivation (XCI) is a dosage compensation mechanism in female cells to regulate X-linked gene expression. We report here that subcultures from established lines of female hESCs displayed variations (0-100%) in the expression of XCI markers such as XIST RNA coating and enrichment of histone H3 lysine 27 trimethylation (H3K27me3) on inactive X chromosome. Surprisingly, regardless of the presence or absence of XCI markers in different cultures, all female hESCs we examined (H7, H9, and HSF6 cells) exhibit a mono-allelic expression pattern for a majority of X-linked genes. Our results suggest that these established female hESCs have completed XCI during the process of derivation and/or propagation, and the XCI pattern of lines we investigated is already non-random. However, XIST gene expression in subsets of female hESCs is unstable and subject to epigenetic silencing through DNA methylation. Concomitant with the loss of XCI markers including XIST expression and H3K27me3, approximately 12% of X-linked CpG islands become hypomethylated and a subset of previously silenced X-linked alleles are reactivated, resulting a significant elevation of gene expression dosage. Because changes in dosage compensation of X-linked genes could impair somatic cell function, we propose that XCI status should be routinely checked in subcultures of female hESCs, with cultures displaying XCI markers better suited for use in regenerative medicine. Keywords: Genotyping, gene expression and DNA methylation We used Affymetrix Genotyping array for looking for X-linked SNPs with HSF6, H7 and H9 genomic DNA, Agilent Gene expression array for comparing gene expression patten changes between HSF6 hESCs with X-inactiation and HSF6 hESCs without X-inactivation (3 repeats). Finally, mDIP-Chip method was used to detect X-linked CpG island methylation changes differences between hESCs with X-inactivation and hESCs without X-inactivation using Agilent CpG island array (3 repeats, and one of them has dye swap)
2010-05-26 | E-GEOD-9637 | biostudies-arrayexpress
Project description:In mammals, X-linked dosage compensation involves two processes: X-inactivation to balance X chromosome dosage between males and females, and X-hyperactivation to achieve X-autosome balance. Transposable elements (TEs) are repetitive mobile DNA sequences and major sources of X chromosome dosage. Current studies in X-linked dosage compensation mainly focus on genes, with TEs still remaining elusive. Here we use “So-Smart-Seq” to comprehensively determine the allelic dynamics of TEs in the context of imprinted and random X-chromosome inactivation (XCI). We find that chromosomal loci and genetic backgrounds significantly impact TE silencing, and reveal putative roles of SINEs in shaping 3D chromatin architectures. We show remarkable difference in TE silencing between two forms of XCI and discover that X-hyperactivation is absent in TEs. Our data provide deep insight for TE studies and greatly contribute to complete understanding of X-chromosome wide dosage compensation.
2025-02-12 | GSE275192 | GEO
Project description:Mammals have evolved an XY sex chromosome system, resulting in dosage imbalance not only between sexes, but also between X-chromosome and autosome.
2015-01-07 | GSE56087 | GEO
Project description:During meiosis, gene expression is silenced in aberrantly unsynapsed chromatin and in heterogametic sex chromosomes. Initiation of sex chromosome silencing is disrupted in meiocytes with sex chromosome-autosome translocations. To determine whether this is due to aberrant synapsis or loss of continuity of sex chromosomes, we engineered Caenorhabditis elegans with non-translocated, bisected X chromosomes. In early meiocytes of mutant males and hermaphrodites, X segments were enriched with euchromatin assembly markers and active RNA polymerase II staining, indicating active transcription. Analysis of RNA-seq data showed that genes from the X chromosome were upregulated in gonads of mutant worms. Contrary to previous models, which predicted that any unsynapsed chromatin is silenced during meiosis, our data indicate that unsynapsed X segments are transcribed. Therefore, our results suggest that sex chromosome chromatin has a unique character that facilitates its meiotic expression when its continuity is lost, regardless of whether or not it is synapsed.
2021-05-24 | GSE171938 | GEO
Project description:The centromere is a pivotal chromatin domain that ensures accurate chromosome segregation during cell division. However, the epigenome regulation of the centromere and its impact on centromere function remain largely elusive. Here in the model plant Arabidopsis, we show that CCR4, the catalytic subunit of the RNA deadenylation complex CCR4-NOT, is essential for maintenance of the centromere epigenome and chromosome integrity. We demonstrate that CCR4 is involved in shortening of the poly(A) tails of transcripts originated from centromeric transposons and repeats, thereby promoting the production of small interfering RNAs (siRNAs). The CCR4-dependent siRNAs guide non-CG DNA methylation at centromere repeats, and CCR4 cooperates with canonical DNA methylation pathways to enhance centromeric H3K9 methylation and ensure mitotic chromosome stability. Our study illustrates the crucial role of RNA quality control in RNA interference and reveals the elaborate mechanism that safeguards plant centromeres through epigenomic regulation.
2024-08-24 | GSE274200 | GEO