aav-deployment-enhancer-based-expression-constructs-vivo-mouse

AAV Deployment of Enhancer-Based Expression Constructs <em>In Vivo</em> in Mouse Brain

Enhancers are binding platforms for a diverse array of transcription factors that drive specific expression patterns of tissue- and cell-type-specific ...

University of California, Davis

The forebrain is the seat of higher-order brain functions, and many human neuropsychiatric disorders are due to genetic defects affecting forebrain development, making it imperative to understand the underlying genetic circuitry. Recent progress now makes it possible to begin fully elucidating the genomic regulatory mechanisms that control forebrain gene expression. Herein, we discuss the current knowledge of how transcription factors drive gene expression programs through their interactions with cis-acting genomic elements, such as enhancers; how analyses of chromatin and DNA modifications provide insights into gene expression states; and how these approaches yield insights into the evolution of the human brain.

Genomic perspectives of transcriptional regulation in forebrain development.

Enhancer biology is emerging as a critical area of research that informs studies of evolution, development, and disease. From early experiments that defined and mapped the first enhancers to recent enhancer models of human disease, functional experiments in the mouse have played a central role in revealing enhancer biology. Three decades of in vivo enhancer studies in mouse have laid the groundwork for the current understanding of mammalian enhancers, demonstrating the developmental and tissue-specific activity of enhancers and illuminating general features of enhancer evolution and function. Recent studies offer an emerging perspective on the importance of chromosomal context, combinatorial enhancer activity, and the functional consequences of enhancer sequence variation. This review describes the basic principles of functional testing in mouse, summarizes the contributions these studies have made to our understanding of enhancer biology, and describes limitations and future outlook of in vivo mouse enhancer studies. 

Learning about mammalian gene regulation from functional enhancer assays in the mouse.

DLX transcription factors (TFs) are master regulators of the developing vertebrate brain, driving forebrain GABAergic neuronal differentiation. Ablation of Dlx1&2 alters expression of genes that are critical for forebrain GABAergic development. We integrated epigenomic and transcriptomic analyses, complemented with in situ hybridization (ISH), and in vivo and in vitro studies of regulatory element (RE) function. This revealed the DLX-organized gene regulatory network at genomic, cellular, and spatial levels in mouse embryonic basal ganglia. DLX TFs perform dual activating and repressing functions; the consequences of their binding were determined by the sequence and genomic context of target loci. Our results reveal and, in part, explain the paradox of widespread DLX binding contrasted with a limited subset of target loci that are sensitive at the epigenomic and transcriptomic level to Dlx1&2 ablation. The regulatory properties identified here for DLX TFs suggest general mechanisms by which TFs orchestrate dynamic expression programs underlying neurodevelopment.

Genomic Resolution of DLX-Orchestrated Transcriptional Circuits Driving Development of Forebrain GABAergic Neurons.

Transcriptional enhancers are regulatory DNA elements that underlie the specificity and dynamic patterns of gene expression. Over the past decade, large-scale functional genomics projects have driven transformative progress in our understanding of enhancers. These data have relevance for identifying mechanisms of gene regulation in the CNS, elucidating the function of non-coding regulatory sequences in neurobiology and linking sequence variation within enhancers to genetic risk for neurological and psychiatric disorders. However, the sheer volume and complexity of genomic data presents a challenge to interpreting enhancer function in normal and pathogenic neurobiological processes. Here, to advance the application of genome-scale enhancer data, we offer a primer on current models of enhancer function in the CNS, we review how enhancers regulate gene expression across the neuronal lifespan, and we suggest how emerging findings regarding the role of non-coding sequence variation offer opportunities for understanding brain disorders and developing new technologies for neuroscience.

Neurobiological functions of transcriptional enhancers.

Genes with multiple co-active promoters appear common in brain, yet little is known about functional requirements for these potentially redundant genomic regulatory elements. SCN1A, which encodes the Na1.1 sodium channel alpha subunit, is one such gene with two co-active promoters. Mutations in SCN1A are associated with epilepsy, including Dravet syndrome (DS). The majority of DS patients harbor coding mutations causing SCN1A haploinsufficiency; however, putative causal non-coding promoter mutations have been identified.

Article	Year
Genomic perspectives of transcriptional regulation in forebrain development. Neuron\| PubMed ID: 25569346	2015
Learning about mammalian gene regulation from functional enhancer assays in the mouse. Genomics\| PubMed ID: 26079655	2015
Genomic Resolution of DLX-Orchestrated Transcriptional Circuits Driving Development of Forebrain GABAergic Neurons. Cell reports\| PubMed ID: 31433982	2019
Neurobiological functions of transcriptional enhancers. Nature neuroscience\| PubMed ID: 31740812	2020
Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice. Genome medicine\| PubMed ID: 33910599	2021

Alex S. Nord

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