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Expression profiles of wildtype and SHOX transgenic embryonic mouse limbs

ABSTRACT: Deficiency of the human short stature homeobox-containing gene (SHOX) has been identified in several disorders characterized by reduced height and skeletal anomalies such as Turner, Leri-Weill and Langer syndrome as well as idiopathic short stature. Although highly conserved in vertebrates, rodents lack a SHOX orthologue. Here, we compared gene expression profiles of wildtype and SHOX transgenic mouse limbs using microarray experiments to identify SHOX target genes in the developing limb.

ORGANISM(S): Mus musculus

PROVIDER: GSE47902 | GEO | 2014/08/13

SECONDARY ACCESSION(S): PRJNA208290

REPOSITORIES: GEO

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Expression profiles of wildtype and SHOX transgenic embryonic mouse limbs

Project description:Deficiency of the human short stature homeobox-containing gene (SHOX) has been identified in several disorders characterized by reduced height and skeletal anomalies such as Turner, Leri-Weill and Langer syndrome as well as idiopathic short stature. Although highly conserved in vertebrates, rodents lack a SHOX orthologue. Here, we compared gene expression profiles of wildtype and SHOX transgenic mouse limbs using microarray experiments to identify SHOX target genes in the developing limb. Limbs of E12.5 mouse embryos were dissected, fore- and hindlimbs were pooled and genotyped for RNA extraction. RNA from 2 to 4 littermates was pooled per genotype (Wildtype and SHOX transgene) and compared. In total, 2 microarray hybridization experiments were performed using RNA from 2 biological replicate samples for each genotype.

2014-08-13 | E-GEOD-47902 | biostudies-arrayexpress

Profiling of upstream enhancers of SHOX in idiopathic short stature and functional characterization of the cis-regulatory landscape of SHOX

Project description:SHOX mutations and deletions of the downstream regulatory region have been reported in cases with idiopathic short stature (ISS) and Leri-Weill dyschondrosteosis (LWD). Recently, a deletion and duplication of upstream enhancers have been described in ISS. Here, we aimed to evaluate the contribution of upstream copy number variations (CNVs) to the pathogenesis of ISS, to validate the enhancer role of the upstream enhancers in human cells, and to characterize the chromatin architecture of the cis-regulatory landscape of SHOX. CNV analysis of three upstream conserved non-coding elements (CNEs), CNE-5, CNE-3 and CNE-2, in 501 ISS referrals with no established molecular diagnosis revealed two deletions and one duplication. Enhancer activity of the upstream CNEs was corroborated by luciferase assays in human osteosarcoma U2OS cells. In addition, all three CNEs overlap with reported H3K27ac ChIP-seq marks in human embryonic limb buds. To characterize the chromatin interaction profile of the SHOX region, chromosome conformation capture (4C-seq) was performed in chicken embryo limb buds and in U2OS cells, revealing interactions of the upstream CNEs with the SHOX promoter. Moreover, the 4C-seq interaction maps and H3K27ac marks indicated that the cis-regulatory landscape of SHOX encompasses 1 Mb, suggesting additional cis-regulatory elements controlling SHOX.In conclusion, we showed that upstream CNVs of SHOX are rare in ISS and have incomplete penetrance. Chromatin interaction maps, luciferase assays and H3K27ac marks further support an enhancer function for the upstream CNEs. Finally, we demonstrated that the cis-regulatory landscape of SHOX is larger than previously anticipated potentially harboring novel cis-regulatory elements, which may be involved in the pathogenesis of molecularly unsolved ISS cases..

2016-06-16 | GSE65959 | GEO

Genome-wide analysis of SHOX targets in NHDF cells expressing SHOX WT vs SHOX HM mutant

Project description:To elucidate the underlying molecular mechanisms and to better understand the broad phenotypic spectrum of SHOX deficiency, we aimed to identify novel SHOX targets. We analyzed differentially expressed genes in SHOX-overexpressing human fibroblasts (NHDF)

2021-06-01 | GSE169732 | GEO

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

Profiling of upstream enhancers of SHOX in idiopathic short stature and functional characterization of the cis-regulatory landscape of SHOX

Project description:Profiling of upstream enhancers of SHOX in idiopathic short stature and functional characterization of the cis-regulatory landscape of SHOX

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WRN promotes bone development and growth by unwinding SHOX-G-quadruplexes via its helicase activity in Werner Syndrome [ChIP-seq]

Project description:Werner Syndrome (WS) is an autosomal recessive disorder characterized by premature aging due to mutations of the WRN gene. A classical sign in WS patients is short stature, but the underlying mechanisms are not well understood. Here we report that WRN is indispensable for chondrogenesis, which is the engine driving the elongation of bones and determines height.

2022-07-28 | GSE206210 | GEO

WRN promotes bone development and growth by unwinding SHOX-G-quadruplexes via its helicase activity in Werner Syndrome [RNA-seq]

2022-07-28 | GSE206213 | GEO

Genetic analysis, ultrasound phenotype, and pregnancy outcome of fetuses with Xp22.33 or Yp11.32 microdeletion

Project description:The phenotypes of Xp22.33 or Yp11.32 microdeletions containing short-stature homeobox (SHOX) gene have been extensively described in adults and children, however, few have been reported in prenatal fetuses. We analyzed the prenatal ultrasound phenotype and pregnancy outcomes of fetuses with Xp22.33 or Yp11.32 microdeletion containing SHOX gene to improve the understanding, diagnosis, and monitoring of the disease in the fetal period.

2023-01-24 | GSE223242 | GEO

Genome-wide analysis of SHOX targets in NHDF cells expressing SHOX WT vs SHOX HM mutant

Project description:Genome-wide analysis of SHOX targets in NHDF cells expressing SHOX WT vs SHOX HM mutant

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Different expression of ceRNAs (lncRNAs, circRNAs and mRNAs) in peripheral blood exosomes from idiopathic short stature patients and healthy controls

Project description:Idiopathic short stature is diagnosed by a standing height of less than two standard deviation scores in a specific population adjusted for age and gender and the exclusion of identifiable diseases. A series of studies have confirmed that noncoding RNAs can regulate the chondrocyte proliferation, hypertrophy, and endochondral ossification in the growth plate. In order to analyze and find differentially expressed ceRNAs (lncRNAs, circRNAs and mRNAs in peripheral blood exosomes of idiopathic short stature and healthy controls, we aimed to explore whether differentially expressed ceRNAs (lncRNAs, circRNAs and mRNAs) in peripheral blood exosomes of idiopathic short stature. Three pairs of peripheral blood exosomes samples were subjected to microarray analysis using the SBC human ceRNA Microarray.

2023-01-31 | GSE193994 | GEO

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