An SNP in an ultraconserved regulatory element affects Dlx5/Dlx6 regulation in the forebrain

Center for Advanced Research in Environmental Genomics (CAREG), Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
Development (Impact Factor: 6.46). 09/2010; 137(18):3089-97. DOI: 10.1242/dev.051052
Source: PubMed
Dlx homeobox genes play a crucial role in the migration and differentiation of the subpallial precursor cells that give rise to various subtypes of gamma-aminobutyric acid (GABA)-expressing neurons of the forebrain, including local-circuit cortical interneurons. Aberrant development of GABAergic interneurons has been linked to several neurodevelopmental disorders, including epilepsy, schizophrenia, Rett syndrome and autism. Here, we report in mice that a single-nucleotide polymorphism (SNP) found in an autistic proband falls within a functional protein binding site in an ultraconserved cis-regulatory element. This element, I56i, is involved in regulating Dlx5/Dlx6 homeobox gene expression in the developing forebrain. We show that the SNP results in reduced I56i activity, predominantly in the medial and caudal ganglionic eminences and in streams of neurons tangentially migrating to the cortex. Reduced activity is also observed in GABAergic interneurons of the adult somatosensory cortex. The SNP affects the affinity of Dlx proteins for their binding site in vitro and reduces the transcriptional activation of the enhancer by Dlx proteins. Affinity purification using I56i sequences led to the identification of a novel regulator of Dlx gene expression, general transcription factor 2 I (Gtf2i), which is among the genes most often deleted in Williams-Beuren syndrome, a neurodevelopmental disorder. This study illustrates the clear functional consequences of a single nucleotide variation in an ultraconserved non-coding sequence in the context of developmental abnormalities associated with disease.


Available from: Ryan Macdonald, May 18, 2016
  • Source
    • "For example, a rare variant implicated in autism was found in an enhancer that is active during forebrain development [Poitras et al., 2010]. The variant that may increase risk for autism alters binding of regulatory TFs and reduces enhancer activity in the developing forebrain [Poitras et al., 2010]. Another study focused on an enhancer that underwent accelerated evolution on the human lineage, after splitting from that of chimpanzees [Boyd et al., 2015]. "
    [Show abstract] [Hide abstract] ABSTRACT: Genome-wide association screens aim to identify common genetic variants contributing to the phenotypic variability of complex traits, such as human height or brain morphology. The identified genetic variants are mostly within noncoding genomic regions and the biology of the genotype-phenotype association typically remains unclear. In this article, we propose a complementary targeted strategy to reveal the genetic underpinnings of variability in subcortical brain volumes, by specifically selecting genomic loci that are experimentally validated forebrain enhancers, active in early embryonic development. We hypothesized that genetic variation within these enhancers may affect the development and ultimately the structure of subcortical brain regions in adults. We tested whether variants in forebrain enhancer regions showed an overall enrichment of association with volumetric variation in subcortical structures of >13,000 healthy adults. We observed significant enrichment of genomic loci that affect the volume of the hippocampus within forebrain enhancers (empirical P = 0.0015), a finding which robustly passed the adjusted threshold for testing of multiple brain phenotypes (cutoff of P < 0.0083 at an alpha of 0.05). In analyses of individual single nucleotide polymorphisms (SNPs), we identified an association upstream of the ID2 gene with rs7588305 and variation in hippocampal volume. This SNP-based association survived multiple-testing correction for the number of SNPs analyzed but not for the number of subcortical structures. Targeting known regulatory regions offers a way to understand the underlying biology that connects genotypes to phenotypes, particularly in the context of neuroimaging genetics. This biology-driven approach generates testable hypotheses regarding the functional biology of identified associations. Hum Brain Mapp, 2016. © 2016 Wiley Periodicals, Inc.
    Full-text · Article · Feb 2016 · Human Brain Mapping
  • Source
    • "Evf2 was discovered in the developing mouse forebrain and it is transcribed from the ultra-conserved Dlx5/6 region encoding the homeodomain transcription factors DLx5 and DLx6 (Feng et al., 2006). Dlx homeobox genes products play a crucial role in migration and differentiation of the subpallial precursor cells that give rise to various subtypes of gamma-aminobutiric acid (GABA)-expressing neurons of the forebrain, including localcircuit cortical interneurons (Poitras et al., 2010). Interneurons play a vital role in modulating the activity of the cerebral cortex and they rely on the enzyme glutamic acid decarboxylase 67 (GAD67) for the synthesis of GABA (Addington et al., 2005), the major inhibitory neurotransmitter in the brain. "
    [Show abstract] [Hide abstract] ABSTRACT: Several lines of evidence indicate that schizophrenia has a strong genetic component. But the exact nature and functional role of this genetic component in the pathophysiology of this mental illness remains a mystery. Long non-coding RNAs (lncRNAs) are a recently discovered family of molecules that regulate gene transcription through a variety of means. Consequently, lncRNAs could help us bring together apparent unrelated findings in schizophrenia; namely, genomic deficiencies on one side and neuroimaging, as well as postmortem results on the other. In fact, the most consistent finding in schizophrenia is decreased brain size together with enlarged ventricles. This anomaly appears to originate from shorter and less ramified dendrites and axons. But a decrease in neuronal arborizations cannot explain the complex pathophysiology of this psychotic disorder; however, dynamic changes in neuronal structure present throughout life could. It is well recognized that the structure of developing neurons is extremely plastic. This structural plasticity was thought to stop with brain development. However, breakthrough discoveries have shown that neuronal structure retains some degree of plasticity throughout life. What the neuroscientific field is still trying to understand is how these dynamic changes are regulated and lncRNAs represent promising candidates to fill this knowledge gap. Here, we present evidence that associates specific lncRNAs with schizophrenia. We then discuss the potential role of lncRNAs in neurostructural dynamics. Finally, we explain how dynamic neurostructural modifications present throughout life could, in theory, reconcile apparent unrelated findings in schizophrenia.
    Full-text · Article · Sep 2015 · Frontiers in Molecular Neuroscience
  • Source
    • "Dlx1/2 antagonize MECP2 repression of Dlx5 (Berghoff et al., 2013). A Dlx5/6 ei SNP that disrupts DLX1/2 binding was identified in an autistic proband (Poitras et al., 2010). Given the global DNA-binding properties of MECP2, it has been difficult to envision how this may cause such specific neurological phenotypes, as in Rett syndrome. "
    [Show abstract] [Hide abstract] ABSTRACT: Transcription-regulating long non-coding RNAs (lncRNAs) have the potential to control site-specific gene expression of thousands of targets. Previously, we showed that Evf2, the first described ultraconserved lncRNA, increases association of transcriptional activators (DLX homeodomain proteins) to key DNA enhancers, but represses gene expression. In this report, mass spectrometry shows that the Evf2/DLX1 ribonucleoprotein (RNP) contains SWI/SNF related chromatin-remodelers, Brahma related gene 1 (BRG1, SMARCA4) and Brahma-associated factor (BAF170, SMARCC2) in developing forebrain. Evf2 RNA co-localizes with BRG1 in nuclear clouds and increases BRG1 association with key DNA regulatory enhancers in developing forebrain. While BRG1 directly interacts with DLX1 and Evf2 through distinct binding sites, Evf2 directly inhibits BRG1 ATPase and chromatin remodeling activities. In vitro studies show that both RNA/BRG1 binding and RNA inhibition of BRG1 ATPase/remodeling activity is promiscuous, suggesting that context is a critical factor in RNA-dependent chromatin remodeling inhibition. Together, these experiments support a model where RNAs convert an active enhancer to a repressed enhancer by directly inhibiting chromatin-remodeling activity, and address the apparent paradox of RNA-mediated stabilization of transcriptional activators at enhancers, with a repressive outcome. The importance of BRG1/RNA and BRG1/homeodomain interactions in neurodevelopmental disorders is underscored by the finding that mutations in Coffin Siris Syndrome, a human intellectual disability disorder, localize to the BRG1 RNA binding and DLX1 binding domains. © 2015. Published by The Company of Biologists Ltd.
    Full-text · Article · Jul 2015 · Development
Show more