title: Profiling of conserved non-coding elements upstream of SHOX and functional characterisation of the SHOX cis-regulatory landscape.
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.
authors.affiliation: Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium.
authors.forename: Hannah
authors.initials: H
authors.lastname: Verdin
authors.affiliation: Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain.
authors.forename: Ana
authors.initials: A
authors.lastname: Fernández-Miñán
authors.affiliation: Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain.|Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto Carlos III, Madrid, Spain.
authors.forename: Sara
authors.initials: S
authors.lastname: Benito-Sanz
authors.affiliation: Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium.
authors.forename: Sandra
authors.initials: S
authors.lastname: Janssens
authors.affiliation: Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium.
authors.forename: Bert
authors.initials: B
authors.lastname: Callewaert
authors.affiliation: Department of Pediatrics, Ghent University Hospital, Ghent, Belgium.
authors.forename: Kathleen
authors.initials: K
authors.lastname: De Waele
authors.affiliation: Department of Pediatrics, Ghent University Hospital, Ghent, Belgium.
authors.forename: Jean
authors.initials: J
authors.lastname: De Schepper
authors.affiliation: Department of Pediatric Endocrinology, University Hospitals Leuven, Leuven, Belgium.
authors.forename: Inge
authors.initials: I
authors.lastname: François
authors.affiliation: Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium.
authors.forename: Björn
authors.initials: B
authors.lastname: Menten
authors.affiliation: Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain.|Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto Carlos III, Madrid, Spain.
authors.forename: Karen E
authors.initials: KE
authors.lastname: Heath
authors.affiliation: Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain.
authors.forename: José Luis
authors.initials: JL
authors.lastname: Gómez-Skarmeta
authors.affiliation: Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium.
authors.forename: Elfride
authors.initials: E
authors.lastname: De Baere