RESUMEN
To discover regulatory elements driving the specificity of gene expression in different cell types and regions of the developing human brain, we generated an atlas of open chromatin from nine dissected regions of the mid-gestation human telencephalon, as well as microdissected upper and deep layers of the prefrontal cortex. We identified a subset of open chromatin regions (OCRs), termed predicted regulatory elements (pREs), that are likely to function as developmental brain enhancers. pREs showed temporal, regional, and laminar differences in chromatin accessibility and were correlated with gene expression differences across regions and gestational ages. We identified two functional de novo variants in a pRE for autism risk gene SLC6A1, and using CRISPRa, demonstrated that this pRE regulates SCL6A1. Additionally, mouse transgenic experiments validated enhancer activity for pREs proximal to FEZF2 and BCL11A. Thus, this atlas serves as a resource for decoding neurodevelopmental gene regulation in health and disease.
Asunto(s)
Cromatina/genética , Cromatina/metabolismo , Elementos de Facilitación Genéticos , Regulación del Desarrollo de la Expresión Génica/genética , Corteza Prefrontal/embriología , Telencéfalo/embriología , Animales , Trastorno Autístico/genética , Línea Celular , Secuenciación de Inmunoprecipitación de Cromatina , Eucromatina/genética , Proteínas Transportadoras de GABA en la Membrana Plasmática/genética , Ontología de Genes , Predisposición Genética a la Enfermedad , Edad Gestacional , Humanos , Ratones , Ratones Transgénicos , Motivos de Nucleótidos , Mutación Puntual , Corteza Prefrontal/metabolismo , Proteínas Represoras/genética , Proteínas Represoras/metabolismo , Análisis Espacio-Temporal , Telencéfalo/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/metabolismoRESUMEN
In the developing subpallium, the fate decision between neurons and glia is driven by expression of Dlx1/2 or Olig1/2, respectively, two sets of transcription factors with a mutually repressive relationship. The mechanism by which Dlx1/2 repress progenitor and oligodendrocyte fate, while promoting transcription of genes needed for differentiation, is not fully understood. We identified a motif within DLX1 that binds RBBP4, a NuRD complex subunit. ChIP-seq studies of genomic occupancy of DLX1 and six different members of the NuRD complex show that DLX1 and NuRD colocalize to putative regulatory elements enriched near other transcription factor genes. Loss of Dlx1/2 leads to dysregulation of genome accessibility at putative regulatory elements near genes repressed by Dlx1/2, including Olig2. Consequently, heterozygosity of Dlx1/2 and Rbbp4 leads to an increase in the production of OLIG2+ cells. These findings highlight the importance of the interplay between transcription factors and chromatin remodelers in regulating cell-fate decisions.
Asunto(s)
Proteínas de Homeodominio , Complejo Desacetilasa y Remodelación del Nucleosoma Mi-2 , Diferenciación Celular/genética , Genes Homeobox , Proteínas de Homeodominio/metabolismo , Complejo Desacetilasa y Remodelación del Nucleosoma Mi-2/genética , Factores de Transcripción/genética , Factores de Transcripción/metabolismoRESUMEN
Deleterious genetic variants in POGZ, which encodes the chromatin regulator Pogo Transposable Element with ZNF Domain protein, are strongly associated with autism spectrum disorder (ASD). Although it is a high-confidence ASD risk gene, the neurodevelopmental functions of POGZ remain unclear. Here we reveal the genomic binding of POGZ in the developing forebrain at euchromatic loci and gene regulatory elements (REs). We profile chromatin accessibility and gene expression in Pogz-/- mice and show that POGZ promotes the active chromatin state and transcription of clustered synaptic genes. We further demonstrate that POGZ forms a nuclear complex and co-occupies loci with ADNP, another high-confidence ASD risk gene, and provide evidence that POGZ regulates other neurodevelopmental disorder risk genes as well. Our results reveal a neurodevelopmental function of an ASD risk gene and identify molecular targets that may elucidate its function in ASD.