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
ABSTRACT
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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Available from: Ryan Macdonald, May 18, 2016
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    • "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]. "
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    • "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. "
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    • "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. "
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