A novel long-range enhancer regulates postnatal expression of Zeb2: Implications for Mowat-Wilson syndrome phenotypes
The zinc-finger, E-box-binding homeobox-2 (Zeb2) gene encodes a SMAD-interacting transcription factor that has diverse roles in development and disease. Mutations at the hZeb2 locus cause Mowat-Wilson syndrome (MWS), a genetic disorder that is associated with mental retardation and other, case- and sex-dependent clinical features. Recent studies have detailed microRNA-mediated control of Zeb2, but little is known about the genomic context of this gene or of enhancer sequences that may direct its diverse functions. Here, we describe a novel transgenic rodent model in which Zeb2 regulatory sequence has been disrupted, resulting in a postnatal developmental phenotype that is autosomal dominant. The phenotype exhibits a genotype-by-sex interaction and manifests primarily as an acute attenuation of postnatal kidney development in males. Other aspects of embryonic and neonatal development, including neuronal, are unaffected. The transgene insertion site is associated with a 12 kb deletion, 1.2 Mb upstream of Zeb2, within a 4.1 Mb gene desert. A conserved sequence, derived from the deleted region, enhanced Zeb2 promoter activity in transcription assays. Tissue and temporal restriction of this enhancer activity may involve postnatal changes in proteins that bind this sequence. A control human/mouse VISTA enhancer (62 kb upstream of Zeb2) also up-regulated the Zeb2 promoter, providing evidence of a string of conserved distal enhancers. The phenotype arising from deletion of one copy of the extreme long-range enhancer indicates a critical role for this enhancer at one developmental stage. Haploinsufficiency of Zeb2 in this developmental context reflects inheritance of MWS and may underlie some sex-dependent, non-neural characteristics of this human inherited disorder.
Available from: Maëlle Pannetier
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ABSTRACT: Polled and Multisystemic Syndrome (PMS) is a novel developmental disorder occurring in the progeny of a single bull. Its clinical spectrum includes polledness (complete agenesis of horns), facial dysmorphism, growth delay, chronic diarrhea, premature ovarian failure, and variable neurological and cardiac anomalies. PMS is also characterized by a deviation of the sex-ratio, suggesting male lethality during pregnancy. Using Mendelian error mapping and whole-genome sequencing, we identified a 3.7 Mb deletion on the paternal bovine chromosome 2 encompassing ARHGAP15, GTDC1 and ZEB2 genes. We then produced control and affected 90-day old fetuses to characterize this syndrome by histological and expression analyses. Compared to wild type individuals, affected animals showed a decreased expression of the three deleted genes. Based on a comparison with human Mowat-Wilson syndrome, we suggest that deletion of ZEB2, is responsible for most of the effects of the mutation. Finally sperm-FISH, embryo genotyping and analysis of reproduction records confirmed somatic mosaicism in the founder bull and male-specific lethality during the first third of gestation. In conclusion, we identified a novel locus involved in bovid horn ontogenesis and suggest that epithelial-to-mesenchymal transition plays a critical role in horn bud differentiation. We also provide new insights into the pathogenicity of ZEB2 loss of heterozygosity in bovine and humans and describe the first case of male-specific lethality associated with an autosomal locus in a non-murine mammalian species. This result sets PMS as a unique model to study sex-specific gene expression/regulation.
PLoS ONE 11/2012; 7(11):e49084. DOI:10.1371/journal.pone.0049084 · 3.23 Impact Factor
Available from: PubMed Central
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ABSTRACT: Gene-regulatory enhancers have been identified by many lines of evidence,
including evolutionary conservation, regulatory protein binding, chromatin
modifications, and DNA sequence motifs. To integrate these different
approaches, we developed EnhancerFinder, a novel method for predicting
developmental enhancers and their tissue specificity. EnhancerFinder uses a
two-step multiple-kernel learning approach to integrate DNA sequence motifs,
evolutionary patterns, and thousands of diverse functional genomics datasets
from a variety of cell types and developmental stages. We trained
EnhancerFinder on hundreds of experimentally verified human developmental
enhancers from the VISTA Enhancer Browser, in contrast to histone mark or
sequence-based enhancer definitions commonly used. We comprehensively evaluated
EnhancerFinder, and found that our integrative approach improves enhancer
prediction accuracy over previous approaches that consider a single type of
data. Our evaluation highlights the importance of considering information from
many tissues when predicting specific types of enhancers. We find that VISTA
enhancers active in embryonic heart are easier to predict than enhancers active
in several other tissues due to their uniquely high GC content. We applied
EnhancerFinder to the entire human genome and predicted 84,301 developmental
enhancers and their tissue specificity. These predictions provide specific
functional annotations for large amounts of human non-coding DNA, and are
significantly enriched near genes with annotated roles in their predicted
tissues and hits from genome-wide association studies. We demonstrate the
utility of our enhancer predictions by identifying and validating a novel
cranial nerve enhancer in the ZEB2 locus. Our genome-wide developmental
enhancer predictions will be freely available as a UCSC Genome Browser track.
PLoS Computational Biology 09/2013; 10(6). DOI:10.1371/journal.pcbi.1003677 · 4.62 Impact Factor
Available from: Isaac Adeyemi Babarinde
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ABSTRACT: Conserved noncoding sequences (CNSs) of vertebrates are considered to be closely linked with protein coding gene regulatory functions. We examined the abundance and the genomic distribution of CNSs in four mammalian orders; primates, rodents, carnivores, and cetartiodactyls. We defined the two thresholds for CNS by using conservation level of coding genes; using all the three coding positions and using only first and second codon positions. The abundance of CNSs varied among lineages with primates and rodents having highest and lowest number of CNSs respectively, while carnivores and cetartiodactyls had intermediate values. These CNSs cover 1.3∼5.5% of the mammalian genomes and have signatures of selective constraints which are stronger in more ancestral than the recent ones. Evolution of new CNSs as well as retention of ancestral CNSs contribute to the differences in abundance. The genomic distribution of CNSs is dynamic with higher proportions of rodent and primate CNSs located in the introns compared to carnivores and cetartiodactyls. In fact, 19% of orthologous single-copy CNSs between human and dog are located in different genomic regions. If CNSs can be considered as candidates of gene expression regulatory sequences, heterogeneity of CNSs among the four mammalian orders may have played an important role in creating the order-specific phenotypes. Fewer CNSs in rodents suggests that rodent diversity is related to lower regulatory conservation. With CNSs shown to cluster around genes involved in nervous systems and the higher number of primate CNSs, our result suggests that CNSs may be involved in the higher complexity of the primate nervous system.
Genome Biology and Evolution 11/2013; 5(12). DOI:10.1093/gbe/evt177 · 4.23 Impact Factor
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