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

Abstract

SUMMARYDlx homeobox genes play a crucial role in the migration and differentiation of the subpallial precursor cells that give rise to various subtypes of -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.

Dlx5 Homeodomain:DNA Complex: Structure, Binding and Effect of Mutations Related to Split Hand and Foot Malformation Syndrome

“…We also observed that once a complex with DNA was formed, Dlx5 was more stable and that we could cleave GB1 from the DNA-bound Dlx5 before starting crystallization trials. A 21 bp DNA sequence, AAATGCAGCCA TAAT TAGAGT, had previously been identified to target expression of the Dlx5/Dlx6 bi-gene cluster to the developing forebrain in mice [24]. This sequence includes the TAAT motif typically recognized by homeodomains, including all six Dlx proteins [25].…”

Evf2 (Dlx6as) lncRNA regulates ultraconserved enhancer methylation and the differential transcriptional control of adjacent genes

“…The biological significance of Evf2-Dlx5/6ei interactions is supported by altered adult hippocampal GABA circuitry in mice lacking Evf2 (Bond et al, 2009), transcriptional effects of a single nucleotide polymorphism (SNP) in Dlx5/6ei linked to autism (Poitras et al, 2010), and the established role of MECP2 in autism (Guy et al, 2007;Guy et al, 2001). Loss of Evf2 results in increased Dlx5 and Dlx6 expression in E13.5 MGE, a major site of sonic hedgehog-activated Dlx and Evf2 gene regulatory events crucial for GABAergic interneuron development (Anderson et al, 1997a;Feng et al, 2006;Kohtz et al, 1998).…”

Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent chromatin remodeling inhibition

“…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.…”