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Klinefelter syndrome derived hiPSCs show similar XCI behavior as female hPSCs

ABSTRACT: Klinefelter syndrome derived hiPSCs show similar XCI behavior as female hPSCs

PROVIDER: PRJEB29388 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2857650_1.fastq.gz	Fastqsanger.gz
	ERR2857650_2.fastq.gz	Fastqsanger.gz
	ERR2857660_1.fastq.gz	Fastqsanger.gz
	ERR2857660_2.fastq.gz	Fastqsanger.gz
	ERR2857670_1.fastq.gz	Fastqsanger.gz

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Klinefelter syndrome derived hiPSCs show similar XCI behavior as female hPSCs

Project description:In this study, we reprogrammed fibroblasts from two azoospermic Klinefelter syndrome (KS) patients, and two healthy male and one healthy female donor with an efficient integration-free method using episomal plasmids and laminin-521 (LN521). Whole genome transcriptomics analysis showed differentially expressed genes between KS and healthy male donors with enrichment in gene ontology (GO) terms associated with fertility, cardiovascular development, ossification and brain development, for both KS hiPSCs and fibroblasts, correlating with the KS clinical phenotype. Thorough XCI analysis combining transcriptomics data, RNA FISH and H3K27me3 staining, revealed skewed XCI in one KS fibroblast line and variability in XCI state of KS hiPSCs similar to female hiPSCs, showing either XaXi or XaXe status. Furthermore, we found up-regulated X-linked genes involved in nervous system development, synaptic transmission as well as metabolic processes supporting the potential use of KS derived hiPSC as an in vitro model for KS.

2019-10-05 | E-MTAB-7340 | biostudies-arrayexpress

E-MTAB-7340

Project description:Klinefelter syndrome derived hiPSCs show similar XCI behavior as female hPSCs

2019-01-16 | E-MTAB-7340 | ExpressionAtlas

Xist exerts gene-specific silencing during XCI maintenance and impacts lineage-specific cell differentiation and proliferation during hematopoiesis [RNA-seq]

Project description:X chromosome inactivation (XCI) is a dosage compensation phenomenon that occurs in females. Initiation of XCI depends on Xist RNA, which triggers silencing of one of the two X chromosomes, except for XCI escape genes that continue to be biallelically expressed. In the soma XCI is stably maintained with continuous Xist expression. How Xist impacts XCI maintenance remains an open question. Here we conditionally deleted Xist in hematopoietic system of mice and report differentiation and cell cycle defects in female hematopoietic stem and progenitor cells (HPSCs). By utilizing female HSPCs and mouse embryonic fibroblasts, we find that X-linked genes show variable tolerance to Xist loss. Specifically, XCI escape genes exhibit preferential transcriptional upregulation, which associates with low H3K27me3 occupancy, and high chromatin accessibility that accommodates preexisting binding of transcription factors such as Yin Yang 1 (YY1) at the basal state. We conclude that Xist is necessary for gene-specific silencing during XCI maintenance and impacts lineage-specific cell differentiation and proliferation during hematopoiesis.

2022-07-15 | GSE184772 | GEO

Xist exerts gene-specific silencing during XCI maintenance and impacts lineage-specific cell differentiation and proliferation during hematopoiesis [ATAC-seq]

2022-07-15 | GSE184770 | GEO

Xist exerts gene-specific silencing during XCI maintenance and impacts lineage-specific cell differentiation and proliferation during hematopoiesis [RNA-seq MEFs]

2022-07-15 | GSE205040 | GEO

Xist exerts gene-specific silencing during XCI maintenance and impacts lineage-specific cell differentiation and proliferation during hematopoiesis [ChIP-seq MEFs]

2022-07-15 | GSE205039 | GEO

Xist exerts gene-specific silencing during XCI maintenance and impacts lineage-specific cell differentiation and proliferation during hematopoiesis [ChIP-seq Lin-]

2022-07-15 | GSE184775 | GEO

Single-cell sequencing of Klinefelter testicular biopsies

Project description:We have evaluated the transcriptome of different testicular cell types, including germ cells, at single cell level in a testicular biopsy of a man with Klinefelter syndrome (XXY karyotype)

2019-08-30 | GSE130151 | GEO

Klinefelter syndrome comorbidities induced by increased X gene dosages and altered protein interactome activity

Project description:Klinefelter syndrome (KS) is the most common male chromosomal abnormality (47,XXY). Males with KS suffers from numerous comorbidities. Gene expression data integrated with other data types can increase the knowledge and clinically handling of KS males. Gene expression microarray from eight human Klinefelter syndrome patients (47,XXY) and eight human controls. The age of the Klinefelter syndrome patients varied, which was corrected for in the pre-processing as described in the paper and also in the 'normalization data transformation protocol' of this submission.

2017-03-23 | E-MTAB-4922 | biostudies-arrayexpress

Heterozygous deletion of the SHOX gene enhancer in two females with clinical heterogeneity associating with skewed XCI and escaping XCI

Project description:Skewed X-chromosome inactivation (XCI) plays an important role in the phenotypic heterogeneity of X-linked disorders. However, the role of skewed XCI in XCI–escaping gene SHOX regulation is unclear. Here, we focused on a heterozygous deletion of SHOX gene enhancer with clinical heterogeneity. Using SNP array, we detected that the female proband with Leri-Weill dyschondrosteosis (LWD) carried an 857 kb deletion on Xp22.3 (encompassing SHOX enhancer) and a 5,707 kb large-fragment deletion on Xq25q26. XCI analysis revealed that the X-chromosome with the Xq25q26 large-fragment deletion was completely inactivated, which forced the complete activation of the other X-chromosome carrying SHOX enhancer deletion. While the Xp22.3 deletion locates on the escaping XCI region, under the combined action of skewed XCI and escaping XCI, transcription of SHOX gene was mainly from the activated X-chromosome with SHOX enhancer defect, involving in the formation of LWD phenotype. Interestingly, this SHOX enhancer deletion was inherited from her healthy mother, who also demonstrated completely skewed XCI. However, the X-chromosome with SHOX enhancer deletion was inactivated, and the normal X-chromosome was activated. Combing with escaping XCI, her phenotype was almost normal. In summary, this study was a rare report of SHOX gene enhancer deletion in a family with clinical heterogeneity due to skewed inactivation of different X-chromosomes, which can help in the genetic counseling and prenatal diagnosis of disorders in females with SHOX defect.

2019-10-08 | GSE138489 | GEO

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