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.

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    • "Since the GxE approach identifies differentially expressed genes that are candidates for mediating the interaction, we then sought to uncover underlying single nucleotide variants (SNVs) in cis-regulatory elements within the proximal promoters of these candidate genes. SNVs within the promoters are excellent candidates for regulating expression of the nearby altered genes, as regulatory SNVs can alter the location and function of enhancers and promoters (De Gobbi et al., 2006) that change transcriptional levels (Munkhtulga et al., 2010) in specific cell types (Poitras et al., 2010) and lead to allele-specific changes in expression (Azad et al., 2013). SNV studies narrowed the list to 16 genes that showed both a GxE interaction based on gene expression studies and an SNV driven to fixation in opposite directions in the proximal promoter. "
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    • "It is plausible that the disruption or deletion of UCEs may have a strong deleterious impact on survival in complex natural environments but would have very little effect on fitness under controlled lab conditions as observed for non-coding RNA BC1 [33]. Indeed, an SNP in an ultraconserved regulatory sequence is linked with Dlx5/Dlx6 expression in the forebrain [34]. Another paper reported an enrichment of UCEs in chromosomal rearrangements, especially pathogenic deletions, identified in 200 people with idiopathic neurodevelopmental disorders [35]. "
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    • "Proteins coded by the genes from GTF2I family play a role in modification of chromatin structure and hence gene regulation (Wen et al. 2003; Tussie-Luna et al. 2002). Such effects were described for transcription of immunoglobulin heavy-chain gene (Ren et al. 2011), beta-globin gene (Crusselle-Davis et al. 2007), Dlx5/Dlx6 genes in the forebrain (Poitras et al. 2010), troponin I (Tay et al. 2003), some HIV-1 genes (Malcolm et al. 2007, 2008), Rous sarcoma virus genes (Mobley and Sealy 2000), etc. It was found that proteins from this family affect concentration of Ca ions in cytoplasm (Roy 2006; Caraveo et al. 2006). "
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