Functional Enhancer Elements Drive Subclass-Selective Expression from Mouse to Primate Neocortex

Mich, John K.; Graybuck, Lucas T.; Hess, Erik E.; Mahoney, Joseph T.; Kojima, Yoshiyuki; Ding, Yi; Somasundaram, Saroja; Miller, Jeremy A.; Weed, Natalie; Omstead, Victoria; Bishaw, Yemeserach; Shapovalova, Nadiya V.; Martinez, Refugio A.; Fong, Olivia; Yao, Shenqin; Mortrud, Marty; Chong, Peter Han Joo; Loftus, Luke V.; Bertagnolli, Darren; Goldy, Jeff; Casper, Tamara; Dee, Nick; Opitz-Araya, Ximena; Çetin, Ali; Smith, Kimberly A.; Gwinn, Ryder P.; Cobbs, Charles; Ojemann, Jeffrey G.; Keene, C. Dirk; Silbergeld, Daniel L.; Sunkin, Susan M.; Gradinaru, Viviana; Horwitz, Gregory D.; Zeng, Hongkui; Tasic, Bosiljka; Lein, Ed; Ting, Jonathan T.

doi:10.2139/ssrn.3584741

Cited by 21 publications

(28 citation statements)

References 48 publications

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“…Other groups have taken a similar approach using mainly chromatin accessibility data from ATAC-seq experiments to identify REs for use in AAV targeting CINs ( Hrvatin et al, 2019 ; Mich et al, 2020 ; Vormstein-Schneider et al, 2020 ). Candidate regions with enrichment of H3K27ac are likely to give a better success rate than accessible regions determined by ATAC-seq alone because H3K27ac is a more specific mark of active enhancers.…”

Section: Discussionmentioning

confidence: 99%

“…One of the main drawbacks of using a genome-wide screen to identify pREs is that it may identify many false positives, as individual epigenetic markers are not sufficient to prove that a locus will function in the cell type under investigation ( Nord et al, 2015 ; Hrvatin et al, 2019 ; Mehta et al, 2019 ; Mich et al, 2020 ; Vormstein-Schneider et al, 2020 ). However, we postulated that by integrating multiple sources of data we could increase our confidence in the candidate pREs.…”

Section: Discussionmentioning

confidence: 99%

“…AAVs with CIN-specific conserved REs offer a significant advantage over the existing mouse transgenic lines because of the ease of use of these tools across species, including in humans and non-human primates ( Dimidschstein et al, 2016 ; Mehta et al, 2019 ; Mich et al, 2020 ; Vormstein-Schneider et al, 2020 ). In addition, RE AAVs injected in small volumes would facilitate effector protein expression and/or gene knock-out in restricted brain regions, and therefore could be used to uncover the physiology and function of CINs in different cortical regions.…”

Section: Discussionmentioning

confidence: 99%

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Regulatory Elements Inserted into AAVs Confer Preferential Activity in Cortical Interneurons

Rubin

Malik

Cho

et al. 2020

eNeuro

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Cortical interneuron (CIN) dysfunction is thought to play a major role in neuropsychiatric conditions like epilepsy, schizophrenia and autism. It is therefore essential to understand how the development, physiology, and functions of CINs influence cortical circuit activity and behavior in model organisms such as mice and primates. While transgenic driver lines are powerful tools for studying CINs in mice, this technology is limited in other species. An alternative approach is to use viral vectors such as AAV, which can be used in multiple species including primates and also have potential for therapeutic use in humans. Thus, we sought to discover gene regulatory enhancer elements (REs) that can be used in viral vectors to drive expression in specific cell types. The present study describes the systematic genome-wide identification of putative REs (pREs) that are preferentially active in immature CINs by histone modification chromatin immunoprecipitation and sequencing (ChIP-seq). We evaluated two novel pREs in AAV vectors, alongside the well-established Dlx I12b enhancer, and found that they drove CIN-specific reporter expression in adult mice. We also showed that the identified Arl4d pRE could drive sufficient expression of channelrhodopsin for optogenetic rescue of behavioral deficits in the Dlx5/6 +/− mouse model of fast-spiking CIN dysfunction.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Regulatory Elements Inserted into AAVs Confer Preferential Activity in Cortical Interneurons

Rubin

Malik

Cho

et al. 2020

eNeuro

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“…More recently, many developers have turned toward virus-based cell type-specific tools (Dimidschstein et al, 2016;Graybuck et al, 2021;Hrvatin et al, 2019;Mich et al, 2021;Nair et al, 2020;Vormstein-Schneider et al, 2020). Adeno-associated virus (AAV) technologies became particularly attractive with the invention of AAV variants that cross the blood-brain barrier to transduce the central nervous system, AAV-PHP.B and AAV-PHP.eB (Chan et al, 2017;Deverman et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Machine learning sequence prioritization for cell type-specific enhancer design

Lawler

Ramamurthy

Brown

et al. 2021

Preprint

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Recent discoveries of extreme cellular diversity in the brain warrant rapid development of technologies to access specific cell populations, enabling characterization of their roles in behavior and in disease states. Available approaches for engineering targeted technologies for new neuron subtypes are low-yield, involving intensive transgenic strain or virus screening. Here, we introduce SNAIL (Specific Nuclear-Anchored Independent Labeling), a new virus-based strategy for cell labeling and nuclear isolation from heterogeneous tissue. SNAIL works by leveraging machine learning and other computational approaches to identify DNA sequence features that confer cell type-specific gene activation and using them to make a probe that drives an affinity purification-compatible reporter gene. As a proof of concept, we designed and validated two novel SNAIL probes that target parvalbumin-expressing (PV) neurons. Furthermore, we show that nuclear isolation using SNAIL in wild type mice is sufficient to capture characteristic open chromatin features of PV neurons in the cortex, striatum, and external globus pallidus. Expansion of this technology has broad applications in cell type-specific observation, manipulation, and therapeutics across species and disease models.

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“…The continued improvement of blood-brain barrier penetrant AAV vectors will greatly facilitate the systemic delivery of the CRISPR/Cas system for somatic cell genetic manipulations in the whole brain (15). In addition, ongoing efforts to identify cell type-specific promoters and enhancers will add another layer of sophistication for somatic genetic manipulations (16).…”

mentioning

confidence: 99%

Opportunities and limitations of genetically modified nonhuman primate models for neuroscience research

Feng

Jensen

Greely

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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The recently developed new genome-editing technologies, such as the CRISPR/Cas system, have opened the door for generating genetically modified nonhuman primate (NHP) models for basic neuroscience and brain disorders research. The complex circuit formation and experience-dependent refinement of the human brain are very difficult to model in vitro, and thus require use of in vivo whole-animal models. For many neurodevelopmental and psychiatric disorders, abnormal circuit formation and refinement might be at the center of their pathophysiology. Importantly, many of the critical circuits and regional cell populations implicated in higher human cognitive function and in many psychiatric disorders are not present in lower mammalian brains, while these analogous areas are replicated in NHP brains. Indeed, neuropsychiatric disorders represent a tremendous health and economic burden globally. The emerging field of genetically modified NHP models has the potential to transform our study of higher brain function and dramatically facilitate the development of effective treatment for human brain disorders. In this paper, we discuss the importance of developing such models, the infrastructure and training needed to maximize the impact of such models, and ethical standards required for using these models.

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Functional Enhancer Elements Drive Subclass-Selective Expression from Mouse to Primate Neocortex

Cited by 21 publications

References 48 publications

Regulatory Elements Inserted into AAVs Confer Preferential Activity in Cortical Interneurons

Regulatory Elements Inserted into AAVs Confer Preferential Activity in Cortical Interneurons

Machine learning sequence prioritization for cell type-specific enhancer design

Opportunities and limitations of genetically modified nonhuman primate models for neuroscience research

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