Profiling of Conserved Non-coding Elements Upstream of SHOX and Functional Characterisation of the SHOX Cis-regulatory Landscape

Overview

Journal Sci Rep

Specialty Science

Date 2015 Dec 4

PMID 26631348

Citations 13

Authors

Hannah Verdin

Ana Fernandez-Minan

Sara Benito-Sanz

Sandra Janssens

Bert Callewaert

Kathleen De Waele

Jean De Schepper

Inge Francois

Bjorn Menten

Karen E Heath

Jose Luis Gomez-Skarmeta

Elfride De Baere

Affiliations

Soon will be listed here.

Abstract

Genetic defects such as copy number variations (CNVs) in non-coding regions containing conserved non-coding elements (CNEs) outside the transcription unit of their target gene, can underlie genetic disease. An example of this is the short stature homeobox (SHOX) gene, regulated by seven CNEs located downstream and upstream of SHOX, with proven enhancer capacity in chicken limbs. CNVs of the downstream CNEs have been reported in many idiopathic short stature (ISS) cases, however, only recently have a few CNVs of the upstream enhancers been identified. Here, we set out to provide insight into: (i) the cis-regulatory role of these upstream CNEs in human cells, (ii) the prevalence of upstream CNVs in ISS, and (iii) the chromatin architecture of the SHOX cis-regulatory landscape in chicken and human cells. Firstly, luciferase assays in human U2OS cells, and 4C-seq both in chicken limb buds and human U2OS cells, demonstrated cis-regulatory enhancer capacities of the upstream CNEs. Secondly, CNVs of these upstream CNEs were found in three of 501 ISS patients. Finally, our 4C-seq interaction map of the SHOX region reveals a cis-regulatory domain spanning more than 1 Mb and harbouring putative new cis-regulatory elements.

Citing Articles

Copy number variations residing outside the SHOX enhancer region are involved in Short Stature and Léri-Weill dyschondrosteosis.

Fanelli A, Vannelli S, Babu D, Mellone S, Cucci A, Monzani A Mol Genet Genomic Med. 2021; 10(1):e1793.

PMID: 34811950 PMC: 8801136. DOI: 10.1002/mgg3.1793.

Identification and Tissue-Specific Characterization of Novel SHOX-Regulated Genes in Zebrafish Highlights SOX Family Members Among Other Genes.

Hoffmann S, Roeth R, Diebold S, Gogel J, Hassel D, Just S Front Genet. 2021; 12:688808.

PMID: 34122528 PMC: 8191631. DOI: 10.3389/fgene.2021.688808.

Detection of Gene Variations in Patients with Skeletal Abnormalities with or without Short Stature.

Gursoy S, Hazan F, Aykut A, Nalbantoglu O, Korkmaz H, Demir K J Clin Res Pediatr Endocrinol. 2020; 12(4):358-365.

PMID: 32295321 PMC: 7711637. DOI: 10.4274/jcrpe.galenos.2020.2019.0001.

Heterozygous Deletion of the Gene Enhancer in two Females With Clinical Heterogeneity Associating With Skewed XCI and Escaping XCI.

Sun Y, Luo Y, Qian Y, Chen M, Wang L, Li H Front Genet. 2019; 10:1086.

PMID: 31781162 PMC: 6852097. DOI: 10.3389/fgene.2019.01086.

A novel conserved enhancer at zebrafish zic3 and zic6 loci drives neural expression.

Minhas R, Paterek A, Lapinski M, Bazala M, Korzh V, Winata C Dev Dyn. 2019; 248(9):837-849.

PMID: 31194899 PMC: 6771876. DOI: 10.1002/dvdy.69.

References

Rozen S, Skaletsky H . Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol. 1999; 132:365-86. DOI: 10.1385/1-59259-192-2:365. View

Rao E, Blaschke R, Marchini A, Niesler B, Burnett M, Rappold G . The Leri-Weill and Turner syndrome homeobox gene SHOX encodes a cell-type specific transcriptional activator. Hum Mol Genet. 2001; 10(26):3083-91. DOI: 10.1093/hmg/10.26.3083. View

Benito-Sanz S, Thomas N, Huber C, Gorbenko Del Blanco D, Aza-Carmona M, Crolla J . A novel class of Pseudoautosomal region 1 deletions downstream of SHOX is associated with Leri-Weill dyschondrosteosis. Am J Hum Genet. 2005; 77(4):533-44. PMC: 1275603. DOI: 10.1086/449313. View

Fukami M, Kato F, Tajima T, Yokoya S, Ogata T . Transactivation function of an approximately 800-bp evolutionarily conserved sequence at the SHOX 3' region: implication for the downstream enhancer. Am J Hum Genet. 2005; 78(1):167-70. PMC: 1380216. DOI: 10.1086/499254. View

Huber C, Rosilio M, Munnich A, Cormier-Daire V . High incidence of SHOX anomalies in individuals with short stature. J Med Genet. 2006; 43(9):735-9. PMC: 2564573. DOI: 10.1136/jmg.2006.040998. View

Redon R, Ishikawa S, Fitch K, Feuk L, Perry G, Andrews T . Global variation in copy number in the human genome. Nature. 2006; 444(7118):444-54. PMC: 2669898. DOI: 10.1038/nature05329. View

Sabherwal N, Bangs F, Roth R, Weiss B, Jantz K, Tiecke E . Long-range conserved non-coding SHOX sequences regulate expression in developing chicken limb and are associated with short stature phenotypes in human patients. Hum Mol Genet. 2007; 16(2):210-22. DOI: 10.1093/hmg/ddl470. View

Hellemans J, Mortier G, De Paepe A, Speleman F, Vandesompele J . qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol. 2007; 8(2):R19. PMC: 1852402. DOI: 10.1186/gb-2007-8-2-r19. View

Hagege H, Klous P, Braem C, Splinter E, Dekker J, Cathala G . Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat Protoc. 2007; 2(7):1722-33. DOI: 10.1038/nprot.2007.243. View

10.

Firth H, Richards S, Bevan A, Clayton S, Corpas M, Rajan D . DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. Am J Hum Genet. 2009; 84(4):524-33. PMC: 2667985. DOI: 10.1016/j.ajhg.2009.03.010. View

11.

Dhaene B, Vandesompele J, Hellemans J . Accurate and objective copy number profiling using real-time quantitative PCR. Methods. 2010; 50(4):262-70. DOI: 10.1016/j.ymeth.2009.12.007. View

12.

Durand C, Bangs F, Signolet J, Decker E, Tickle C, Rappold G . Enhancer elements upstream of the SHOX gene are active in the developing limb. Eur J Hum Genet. 2009; 18(5):527-32. PMC: 2987325. DOI: 10.1038/ejhg.2009.216. View

13.

Dhaene B, Hellemans J, Craen M, De Schepper J, Devriendt K, Fryns J . Improved molecular diagnostics of idiopathic short stature and allied disorders: quantitative polymerase chain reaction-based copy number profiling of SHOX and pseudoautosomal region 1. J Clin Endocrinol Metab. 2010; 95(6):3010-8. DOI: 10.1210/jc.2009-2218. View

14.

Teague B, Waterman M, Goldstein S, Potamousis K, Zhou S, Reslewic S . High-resolution human genome structure by single-molecule analysis. Proc Natl Acad Sci U S A. 2010; 107(24):10848-53. PMC: 2890719. DOI: 10.1073/pnas.0914638107. View

15.

Benito-Sanz S, Barroso E, Heine-Suner D, Hisado-Oliva A, Romanelli V, Rosell J . Clinical and molecular evaluation of SHOX/PAR1 duplications in Leri-Weill dyschondrosteosis (LWD) and idiopathic short stature (ISS). J Clin Endocrinol Metab. 2010; 96(2):E404-12. DOI: 10.1210/jc.2010-1689. View

16.

Kenyon E, McEwen G, Callaway H, Elgar G . Functional analysis of conserved non-coding regions around the short stature hox gene (shox) in whole zebrafish embryos. PLoS One. 2011; 6(6):e21498. PMC: 3123344. DOI: 10.1371/journal.pone.0021498. View

17.

Noordermeer D, Leleu M, Splinter E, Rougemont J, de Laat W, Duboule D . The dynamic architecture of Hox gene clusters. Science. 2011; 334(6053):222-5. DOI: 10.1126/science.1207194. View

18.

Hirschfeldova K, Solc R, Baxova A, Zapletalova J, Kebrdlova V, Gaillyova R . SHOX gene defects and selected dysmorphic signs in patients of idiopathic short stature and Léri-Weill dyschondrosteosis. Gene. 2011; 491(2):123-7. DOI: 10.1016/j.gene.2011.10.011. View

19.

Montavon T, Soshnikova N, Mascrez B, Joye E, Thevenet L, Splinter E . A regulatory archipelago controls Hox genes transcription in digits. Cell. 2011; 147(5):1132-45. DOI: 10.1016/j.cell.2011.10.023. View

20.

Benito-Sanz S, Aza-Carmona M, Rodriguez-Estevez A, Rica-Etxebarria I, Gracia R, Campos-Barros A . Identification of the first PAR1 deletion encompassing upstream SHOX enhancers in a family with idiopathic short stature. Eur J Hum Genet. 2011; 20(1):125-7. PMC: 3234524. DOI: 10.1038/ejhg.2011.210. View