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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 16, 2016 |
| Title |
Profiling of upstream enhancers of SHOX in idiopathic short stature and functional characterization of the cis-regulatory landscape of SHOX |
| Organisms |
Gallus gallus; Homo sapiens |
| Experiment type |
Other
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| Summary |
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..
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| Overall design |
4C-seq samples forshox gene promoter in different samples: HH28 chicken limbs and human U2OS cells
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| Contributor(s) |
Gómez-Skarmeta JL, Fernández-Miñán A |
| Citation(s) |
26631348 |
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| Submission date |
Feb 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ana Fernandez-Miñan |
| Organization name |
CABD-CSIC-UPO
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| Street address |
Crta. Utrera, km.1
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| City |
Seville |
| ZIP/Postal code |
41013 |
| Country |
Spain |
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| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL16133 |
Illumina HiSeq 2000 (Gallus gallus) |
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| Samples (2) |
| GSM1611717 |
4C-Seq for shox promoter in limbs from HH28 chicken embryos |
| GSM1611718 |
4C-Seq for shox promoter in human U2OS cells |
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| Relations |
| BioProject |
PRJNA275571 |
| SRA |
SRP055074 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE65959_RAW.tar |
2.1 Mb |
(http)(custom) |
TAR (of BEDGRAPH) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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