Veronica Van Heyningen

University College London and University of Edinburgh · Institute of Ophthalmology, UCL and Institute of Genetics and Molecular Medicine, UoE

Development from fertilized egg to functioning multi-cellular organism requires precision. There is no precision, and often no survival, without plasticity. Plasticity is conferred partly by stochastic variation, present inherently in all biological systems. Gene expression levels fluctuate ubiquitously through transcription, alternative splicing,...

Background Classic aniridia is a highly penetrant autosomal dominant disorder characterised by congenital absence of the iris, foveal hypoplasia, optic disc anomalies and progressive opacification of the cornea. >90% of cases of classic aniridia are caused by heterozygous, loss-of-function variants affecting the PAX6 locus. Methods Short-read whol...

When we began the identification of genes implicated in eye disease, the process was slow and laborious. It is three decades since we identified PAX6 as the gene mutated in aniridia, before the launch of the Human Genome Project. Since then there have been seismic changes in technology: in sequencing, gene expression studies, including database gen...

Classical aniridia is a congenital and progressive panocular disorder almost exclusively caused by heterozygous loss-of-function variants at the PAX6 locus. We report nine individuals from five families with severe aniridia and/or microphthalmia (with no detectable PAX6 mutation) with ultrarare monoallelic missense variants altering the Arg51 codon...

Although my engagement with human genetics emerged gradually, and sometimes serendipitously, it has held me spellbound for decades. Without my teachers, students, postdocs, colleagues, and collaborators, I would not be writing this review of my scientific adventures. Early gene and disease mapping was a satisfying puzzle-solving exercise, but build...

Identifying causative variants in cis-regulatory elements (CRE) in neurodevelopmental disorders has proven challenging. We have used in vivo functional analyses to categorize rigorously filtered CRE variants in a clinical cohort that is plausibly enriched for causative CRE mutations: 48 unrelated males with a family history consistent with X-linked...

Undiagnosed neurodevelopmental disease is significantly associated with rare variants in cis-regulatory elements (CRE) but demonstrating causality is challenging as target gene consequences may differ from a causative variant affecting the coding region. Here, we address this challenge by applying a procedure to discriminate likely diagnostic regul...

Most classical aniridia is caused by PAX6 haploinsufficiency. PAX6 missense variants can be hypomorphic or mimic haploinsufficiency. We hypothesized that missense variants also cause previously undescribed disease by altering the affinity and/or specificity of PAX6 genomic interactions. We screened PAX6 in 372 individuals with bilateral microphthal...

The development of genome sequencing technologies has revolutionized the biological sciences in ways which could not have been imagined at the time. This article sets out to document the dawning of the age of genomics and to consider the impact of this revolution on biological investigation, our understanding of life, and the relationship between s...

The autosomal dominant progressive bifocal chorioretinal atrophy (PBCRA) disease locus has been mapped to chromosome 6q14–16.2 which overlaps the North Carolina Macular Dystrophy (NCMD) locus MCDR1. NCMD is a non‐progressive developmental macular dystrophy, in which variants upstream of PRDM13 have been implicated. Whole genome sequencing was perfo...

Autosomal dominant North Carolina macular dystrophy (NCMD) is believed to represent a failure of macular development. The disorder has been linked to two loci, MCDR1 (chromosome 6q16) and MCDR3 (chromosome 5p15-p13). Recently, non-coding variants upstream of PRDM13 (MCDR1) and a duplication including IRX1 (MCDR3) have been identified. However, the...

Efficient storage and querying of large amounts of genetic and phenotypic data is crucial to contemporary clinical genetic research. This introduces computational challenges for classical relational databases, due to the sparsity and sheer volume of the data. Our Java based solution loads annotated genetic variants and well phenotyped patients into...

Table S1: Summary of validated de novo variants identified in UK10K Trio analyses

Table S2: Summary of quantitative heavy vs light labelled mass spectrometry data from GFP‐TRAP Co‐immunoprecipitates

Supporting Information

Ocular coloboma (OC) is a defect in optic fissure closure and is a common cause of severe congenital visual impairment. Bilateral OC is primarily genetically determined and shows marked locus heterogeneity. Whole exome sequencing was used to analyse twelve trios (child affected with OC and both unaffected parents), This identified de novo mutations...

Background: Developmental macular disorders are a heterogeneous group of rare retinal conditions that can cause significant visual impairment from childhood. Among these disorders, autosomal dominant North Carolina macular dystrophy (NCMD) has been mapped to 6q16 (MCDR1) with recent support for a non-coding disease mechanism of PRDM13. A second lo...

Cilia assembly and disassembly are coupled to actin dynamics, ensuring a coherent cellular response during environmental change. How these processes are integrated remains undefined. The histone lysine demethylase KDM3A plays important roles in organismal homeostasis. Loss-of-function mouse models of Kdm3a phenocopy features associated with human c...

Autosomal dominant North Carolina macular dystrophy (NCMD) is believed to represent a failure of macular development. The disorder has been assigned by linkage to two loci, MCDR1 on chromosome 6q16 and MCDR3 on chromosome 5p15-p13. Recently, noncoding variants upstream of PRDM13 and a large duplication including IRX1 have been identified. However,...

Mutations in more than 250 genes are implicated in inherited retinal dystrophy; the encoded proteins are involved in a broad spectrum of pathways. The presence of unsolved families after highly parallel sequencing strategies suggests that further genes remain to be identified. Whole-exome and -genome sequencing studies employed here in large cohort...

Mutations in more than 250 genes are implicated in inherited retinal dystrophy; the encoded proteins are involved in a broad spectrum of pathways. The presence of unsolved families after highly parallel sequencing strategies suggests that further genes remain to be identified. Whole-exome and -genome sequencing studies employed here in large cohort...

Arhinia, or absence of the nose, is a rare malformation of unknown etiology that is often accompanied by ocular and reproductive defects. Sequencing of 40 people with arhinia revealed that 84% of probands harbor a missense mutation localized to a constrained region of SMCHD1 encompassing the ATPase domain. SMCHD1 mutations cause facioscapulohumeral...

Although early Sox2 studies showed expression in the developing eye as well as in the brain and several additional tissues, the key role of SOX2 in eye development was revealed most clearly when heterozygous SOX2 mutations were shown to be associated with human anophthalmia. Subsequently, the phenotypic range of SOX2-associated disease broadened su...

Chapters provides overview of pathways of development and reviews of dysmorphic syndromes for which the causative gene has been identified. For each disorder, an analysis of the role of the gene in the relevant developmental pathway is provided, along with the mechanism by which mutations in the gene cause the developmental pathology. Emphasis is p...

We report molecular genetic analysis of 42 affected individuals referred with a diagnosis of aniridia who previously screened as negative for intragenic PAX6 mutations. Of these 42, the diagnoses were 31 individuals with aniridia and 11 individuals referred with a diagnosis of Gillespie syndrome (iris hypoplasia, ataxia and mild to moderate develop...

Gillespie syndrome (GS) is characterized by bilateral iris hypoplasia, congenital hypotonia, non-progressive ataxia, and progressive cerebellar atrophy. Trio-based exome sequencing identified de novo mutations in ITPR1 in three unrelated individuals with GS recruited to the Deciphering Developmental Disorders study. Whole-exome or targeted sequence...

Objective PAX6 is a pleiotropic transcription factor essential for the development of several tissues including the eyes, central nervous system, and some endocrine glands. Recently it has also been shown to be important for the maintenance and functioning of corneal and pancreatic tissues in adults. We hypothesized that PAX6 is important for the m...

Author Summary Cis-regulatory elements (CREs) play a vital role in gene regulation by providing spatial and temporal specificity to the expression of their target genes. Understanding how these regions of the genome work is of vital importance for human health as it has been demonstrated that genetic changes in these regions can result in incorrect...

Enhancers can regulate the transcription of genes over long genomic distances. This is thought to lead to selection against genomic rearrangements within such regions that may disrupt this functional linkage. Here we test this concept experimentally using the human X chromosome. We describe a scoring method to identify evolutionary maintenance of l...

Mutations in the coding sequence of SOX9 cause campomelic dysplasia (CD), a disorder of skeletal development associated with 46,XY disorders of sex development (DSDs). Translocations, deletions and duplications within a ∼2 Mb region upstream of SOX9 can recapitulate the CD-DSD phenotype fully or partially, suggesting the existence of an unusually l...

We identified four different missense mutations in the single-exon gene MAB21L2 in eight individuals with bilateral eye malformations from five unrelated families via three independent exome sequencing projects. Three mutational events altered the same amino acid (Arg51), and two were identical de novo mutations (c.151C>T [p.Arg51Cys]) in unrelated...

We identified four different missense mutations in the single-exon gene MAB21L2 in eight individuals with bilateral eye malformations from five unrelated families via three independent exome sequencing projects. Three mutational events altered the same amino acid (Arg51), and two were identical de novo mutations (c.151C>T [p.Arg51Cys]) in unrelated...

The lysine demethylase Kdm3a (Jhdm2a, Jmjd1a) is required for male fertility, sex determination and metabolic homeostasis through its nuclear role in chromatin remodeling. Many histone-modifying enzymes have additional non-histone substrates, as well as non-enzymatic functions, contributing to the full spectrum of events underlying their biological...

THE ZEBRAFISH EPITHALAMUS IS PART OF THE DIENCEPHALON AND ENCOMPASSES THREE MAJOR COMPONENTS: the pineal, the parapineal and the habenular nuclei. Using sox2 knockdown, we show here that this key transcriptional regulator has pleiotropic effects during the development of these structures. Sox2 negatively regulates pineal neurogenesis. Also, Sox2 is...

Biological differences between cell types and developmental processes are characterised by differences in gene expression profiles. Gene-distal enhancers are key components of the regulatory networks that specify the tissue-specific expression patterns driving embryonic development and cell fate decisions, and variations in their sequences are a ma...

Exome sequence analysis of affected individuals from two families with autosomal-dominant inheritance of coloboma identified two different cosegregating heterozygous nonsense mutations (c.370C>T [p.Arg124*] and c. 1066G>T [p.Glu356*]) in YAP1. The pheno-types of the affected families differed in that one included no extraocular features and the oth...

The strictly regulated expression of most pleiotropic developmental control genes is critically dependent on the activity of long-range cis-regulatory elements. This was revealed by the identification of individuals with a genetic condition lacking coding-region mutations in the gene commonly associated with the disease but having a variety of near...

Regulated gene expression is a major requirement for all living organisms. The requirement for complex spatio-temporal regulation is most obvious during development and differentiation, when precise gene switching choreographs the generation of many different cell types, at the right time and the right place, from a single fertilized cell. When thi...

Clinical evaluation and mutation analysis was performed in 51 consecutive probands with severe eye malformations - anophthalmia and/or severe microphthalmia - seen in a single specialist ophthalmology center. The mutation analysis consisted of bidirectional sequencing of the coding regions of SOX2, OTX2, PAX6 (paired domain), STRA6, BMP4, SMOC1, FO...

Pax6 is a developmental control gene essential for eye development throughout the animal kingdom. In addition, Pax6 plays key roles in other parts of the CNS, olfactory system, and pancreas. In mammals a single Pax6 gene encoding multiple isoforms delivers these pleiotropic functions. Here we provide evidence that the genomes of many other vertebra...

Multispecies alignment of the E-200 element. The novel E-200 long-range enhancer is located approximately 215 kb upstream of human PAX6. Strong sequence conservation is found between the E-200 elements of Pax6.1 loci over a 400 bp region. Conservation with the pax6.3 loci of Tetraodon and stickleback is limited to the central core of the element. H...

Depletion of Pax6.2 by morpholino knock-down. A) a Pax6.2 morpholino. and B) a control morpholino were Injected into zebrafish oocytes. Pools of embryos were fixed at 2 dpf and tested for the presence of Pax6.2 transcript by in situ hybridization. Pax6.2 ISH signal was absent or greatly reduced in the majority of pax6.2 morpholino injected embryos,...

PIP plot using the stickleback pax6.3 locus as baseline sequence. The pax6.3 loci contain several CNEs that are specifically conserved between acanthopterygian fish (arrowheads). There are no CNEs conserved between the loci of pax6.3 and pax6.1, with the exception of the E-200 element (red box). The position of the intron 7 conserved element (7CE(6...

Phylogeny and synteny relationships between the vertebratePax6 loci (extended version of Figure 7 including more species). Phylogeny/ontogeny of the Pax6 gene family is supported by comparison of gene content in the synteny regions of the genes. A) The Pax6.1 gene resides in an ancient synteny block that is perfectly conserved from elephant shark t...

Protein alignment of representative members of the vertebrate Pax6 gene family. The alignment highlights the separation into three branches representing the pax6.1, pax6.2 and pax6.3 clades. Pax6.1 is the canonical Pax6 gene found in all vertebrates. Pax6.2 encodes a paired-less form of Pax6. The pax6.3 gene lacks an alternative exon 5a and thus do...

Schematic reconstruction of the ontology of the Pax6 gene family in vertebrate evolution. Three clades of Pax6 orthologs remain in various compositions in vertebrate genomes to date: the canonical Pax6.1 loci, the paired-less Pax6.2 loci and the acanthopterygian Pax6.3 loci lacking the alternative exon5a. The duplicate Pax6 loci are proposed to hav...

Optical Projection Tomography (OPT) movie of pax6.2 expression. The OPT movie demonstrates the highly specific expression of pax6.2 in the retina. 2 dpf zebrafish embryos were in situ hybridized with a pax6.2 antisense probe. A representative embryo was scanned by OPT and an AVI movie was created using Drishti software. (AVI)

Overview of the constructs used to evaluate cis-regulatory activity of conserved non-coding elements. For each construct the species of origin and the transgenic model system used are given, followed by the number of stable transgenic lines analysed and the observed sites of reporter expression. (DOC)

The transcription factor Pax6 is a developmental regulator with a crucial role in development of the eye, brain, and olfactory system. Pax6 is also required for correct development of the endocrine pancreas and specification of hormone producing endocrine cell types. Glucagon-producing cells are almost completely lost in Pax6-null embryos, and insu...

Aniridia is a rare congenital disorder in which there is a variable degree of hypoplasia or the absence of iris tissue associated with multiple other ocular changes, some present from birth and some arising progressively over time. Most cases are associated with dominantly inherited mutations or deletions of the PAX6 gene. This article will review...

DNase I hypersensitive site mapping across the mouse Pax6 locus. Sequences from the mouse Pax6 genomic region from 20 kb upstream of the Pax6 P0 promoter to approximately 170 kb downstream of the gene (mm9/NCBI37 position chr2:105,495,760 to chr2:105,678,886) were examined for presence of DNase I HSs by Southern blot (figures S1, S2, S3, S4, S5: Th...

DNase I hypersensitive site mapping across the Pax6 genomic locus, part 4, covering G) the 120–140 kb segment and H) the 140–160kb segment of the locus as indicated on the map of the locus at the top of the figure. Full details are given in the legend for figure S1. (TIF)

DNase I hypersensitive site mapping across the Pax6 genomic locus, part 3, covering E) the 80–100 kb segment and F) the 100–120kb segment of the locus as indicated on the map of the locus at the top of the figure. Full details are given in the legend for figure S1. (TIF)

Sequence line-up for the HS6 element. The HS6 element is conserved among mammalian species only, with platypus and wallaby being the evolutionarily most distant species with the conserved element. No conservation was detected to non-mammalian genomes. (DOC)

DNase I hypersensitive site mapping across the Pax6 genomic locus, part 2, covering C) the 40–60 kb segment and D) the 60–80kb segment of the locus as indicated on the map of the locus at the top of the figure. Full details are given in the legend for figure S1. (TIF)

DNase I hypersensitive site mapping across the Pax6 genomic locus, part 5, covering I) the 160–180 kb segment and D) the 180–200kb segment of the locus as indicated on the map of the locus at the top of the figure. Full details are given in the legend for figure S1. (TIF)

Primer sequences and genomic positions of Q-PCR primers used for H3K4me3 Chromatin Immunoprecipitation. (DOC)

The PAX6 gene plays a crucial role in development of the eye, brain, olfactory system and endocrine pancreas. Consistent with its pleiotropic role the gene exhibits a complex developmental expression pattern which is subject to strict spatial, temporal and quantitative regulation. Control of expression depends on a large array of cis-elements resid...

The characterization of transcriptional networks (TNs) is essential for understanding complex biological phenomena such as development, disease, and evolution. In this study, we have designed and implemented a procedure that combines in silico target screens with zebrafish and mouse validation, in order to identify cis-elements and genes directly r...

The European Journal of Human Genetics is the official Journal of the European Society of Human Genetics, publishing high-quality, original research papers, short reports, News and Commentary articles and reviews in the rapidly expanding field of human genetics and genomics.

Genome-wide association studies identified noncoding SNPs associated with type 2 diabetes and obesity in linkage disequilibrium (LD) blocks encompassing HHEX-IDE and introns of CDKAL1 and FTO [Sladek R, et al. (2007) Nature 445:881-885; Steinthorsdottir V, et al. (2007) Nat. Genet 39:770-775; Frayling TM, et al. (2007) Science 316:889-894]. We show...

To describe the clinical findings of a patient with an early onset retinal dystrophy and a novel mutation in OTX2, and to compare these findings with previously reported cases. Using direct sequencing, we screened 142 patients, who had either Leber congenital amaurosis (LCA) or early onset retinal dystrophy (EORD), for mutations in OTX2. All patien...