Journal Article

H2AFY promoter deletion causes PITX1 endoactivation and Liebenberg syndrome

Digilio, Maria Cristina, Brancati, Francesco, Mundlos, Stefan, Kragesteen, Bjørt K, Spielmann, Malte

2019

Overview

Structural variants (SVs) affecting non-coding -regulatory elements are a common cause of congenital limb malformation. Yet, the functional interpretation of these non-coding variants remains challenging. The human Liebenberg syndrome is characterised by a partial transformation of the arms into legs and has been shown to be caused by SVs at the locus leading to its misregulation in the forelimb by its native enhancer element Pen. This study aims to elucidate the genetic cause of an unsolved family with a mild form of Liebenberg syndrome and investigate the role of promoters in long-range gene regulation. Here, we identify SVs by whole genome sequencing (WGS) and use CRISPR-Cas9 genome editing in transgenic mice to assign pathogenicity to the SVs. In this study, we used WGS in a family with three mildly affected individuals with Liebenberg syndrome and identified the smallest deletion described so far including the first non-coding exon of . To functionally characterise the variant, we re-engineered the 8.5 kb deletion using CRISPR-Cas9 technology in the mouse and showed that the promoter of the housekeeping gene insulates the Pen enhancer from in forelimbs; its loss leads to misexpression of by the pan-limb activity of the Pen enhancer causing Liebenberg syndrome. Our data indicate that housekeeping promoters may titrate promiscuous enhancer activity to ensure normal morphogenesis. The deletion of the promoter as a cause of Liebenberg syndrome highlights this new mutational mechanism and its role in congenital disease.

• Publisher: BMJ Publishing Group LTD
• Subject: Alleles / Animals / Brachydactyly - diagnosis / Brachydactyly - genetics / Carpal Bones - abnormalities / CRISPR / Deoxyribonucleic acid / Disease Models, Animal / DNA / Elbow Joint - abnormalities / Epistasis, Genetic / Family medical history / Fingers - abnormalities / Gene deletion / Gene Expression Regulation / Gene regulation / Gene Targeting / Genes / Genetic transformation / Genome editing / Genomes / Hand Deformities, Congenital - diagnosis / Hand Deformities, Congenital - genetics / Histones - genetics / Humans / Mice / Mice, Knockout / Morphogenesis / Morphology / Paired Box Transcription Factors - genetics / Paired Box Transcription Factors - metabolism / Pathogenicity / Pedigree / Promoter Regions, Genetic / Promoters / Regulatory sequences / Sequence Deletion / Stem cells / Synostosis - diagnosis / Synostosis - genetics / Transcriptional Activation / Transgenic mice / Whole Genome Sequencing / Wrist Joint - abnormalities