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Morin A, Chu C, Pavlidis P. Identifying Reproducible Transcription Regulator Coexpression Patterns with Single Cell Transcriptomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580581. [PMID: 38559016 PMCID: PMC10979919 DOI: 10.1101/2024.02.15.580581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The proliferation of single cell transcriptomics has potentiated our ability to unveil patterns that reflect dynamic cellular processes, rather than cell type compositional effects that emerge from bulk tissue samples. In this study, we leverage a broad collection of single cell RNA-seq data to identify the gene partners whose expression is most coordinated with each human and mouse transcription regulator (TR). We assembled 120 human and 103 mouse scRNA-seq datasets from the literature (>28 million cells), constructing a single cell coexpression network for each. We aimed to understand the consistency of TR coexpression profiles across a broad sampling of biological contexts, rather than examine the preservation of context-specific signals. Our workflow therefore explicitly prioritizes the patterns that are most reproducible across cell types. Towards this goal, we characterize the similarity of each TR's coexpression within and across species. We create single cell coexpression rankings for each TR, demonstrating that this aggregated information recovers literature curated targets on par with ChIP-seq data. We then combine the coexpression and ChIP-seq information to identify candidate regulatory interactions supported across methods and species. Finally, we highlight interactions for the important neural TR ASCL1 to demonstrate how our compiled information can be adopted for community use.
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Affiliation(s)
- Alexander Morin
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada
| | - Chingpan Chu
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada
| | - Paul Pavlidis
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
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Chen D, Keremane S, Wang S, Lei EP. CTCF regulates global chromatin accessibility and transcription during rod photoreceptor development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.27.596084. [PMID: 38853900 PMCID: PMC11160664 DOI: 10.1101/2024.05.27.596084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Chromatin architecture facilitates accurate transcription at a number of loci, but it remains unclear how much chromatin architecture is involved in global transcriptional regulation. Previous work has shown that rapid depletion of the architectural protein CTCF in cell culture strongly alters chromatin organization but results in surprisingly limited gene expression changes. This discrepancy has also been observed when other architectural proteins are depleted, and one possible explanation is that full transcriptional changes are masked by cellular heterogeneity. We tested this idea by performing multi-omics analyses with sorted post-mitotic mouse rods, which undergo synchronized development, and identified CTCF-dependent regulation of global chromatin accessibility and gene expression. Depletion of CTCF leads to dysregulation of ∼20% of the entire transcriptome (>3,000 genes) and ∼41% of genome accessibility (>26,000 sites), and these regions are strongly enriched in euchromatin. Importantly, these changes are highly enriched for CTCF occupancy, suggesting direct CTCF binding and transcriptional regulation at these active loci. CTCF mainly promotes chromatin accessibility of these direct binding targets, and a large fraction of these sites correspond to promoters. At these sites, CTCF binding frequently promotes accessibility and inhibits expression, and motifs of transcription repressors are found to be significantly enriched. Our findings provide different and often opposite conclusions from previous studies, emphasizing the need to consider cell heterogeneity and cell type specificity when performing multi-omics analyses. We conclude that the architectural protein CTCF binds chromatin and regulates global chromatin accessibility and transcription during rod development.
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Girella A, Di Bartolomeo M, Dainese E, Buzzelli V, Trezza V, D'Addario C. Fatty Acid Amide Hydrolase and Cannabinoid Receptor Type 1 Genes Regulation is Modulated by Social Isolation in Rats. Neurochem Res 2024; 49:1278-1290. [PMID: 38368587 DOI: 10.1007/s11064-024-04117-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/08/2024] [Accepted: 01/25/2024] [Indexed: 02/19/2024]
Abstract
Social isolation is a state of lack of social connections, involving the modulation of different molecular signalling cascades and associated with high risk of mental health issues. To investigate if and how gene expression is modulated by social experience at the central level, we analyzed the effects of 5 weeks of social isolation in rats focusing on endocannabinoid system genes transcription in key brain regions involved in emotional control. We observed selective reduction in mRNA levels for fatty acid amide hydrolase (Faah) and cannabinoid receptor type 1 (Cnr1) genes in the amygdala complex and of Cnr1 in the prefrontal cortex of socially isolated rats when compared to controls, and these changes appear to be partially driven by trimethylation of Lysine 27 and acetylation of Lysine 9 at Histone 3. The alterations of Cnr1 transcriptional regulation result also directly correlated with those of oxytocin receptor gene. We here suggest that to counteract the effects of SI, it is of relevance to restore the endocannabinoid system homeostasis via the use of environmental triggers able to revert those epigenetic mechanisms accounting for the alterations observed.
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Affiliation(s)
- Antonio Girella
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via Renato Balzarini, 1, 64100, Teramo, Italy
| | - Martina Di Bartolomeo
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via Renato Balzarini, 1, 64100, Teramo, Italy
| | - Enrico Dainese
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via Renato Balzarini, 1, 64100, Teramo, Italy
| | | | - Viviana Trezza
- Department of Science, Roma Tre University, Rome, Italy
- Neuroendocrinology, Metabolism and Neuropharmacology Unit, IRCSS Fondazione Santa Lucia, Rome, Italy
| | - Claudio D'Addario
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via Renato Balzarini, 1, 64100, Teramo, Italy.
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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4
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Banazadeh M, Abiri A, Poortaheri MM, Asnaashari L, Langarizadeh MA, Forootanfar H. Unexplored power of CRISPR-Cas9 in neuroscience, a multi-OMICs review. Int J Biol Macromol 2024; 263:130413. [PMID: 38408576 DOI: 10.1016/j.ijbiomac.2024.130413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/27/2023] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
The neuroscience and neurobiology of gene editing to enhance learning and memory is of paramount interest to the scientific community. The advancements of CRISPR system have created avenues to treat neurological disorders by means of versatile modalities varying from expression to suppression of genes and proteins. Neurodegenerative disorders have also been attributed to non-canonical DNA secondary structures by affecting neuron activity through controlling gene expression, nucleosome shape, transcription, translation, replication, and recombination. Changing DNA regulatory elements which could contribute to the fate and function of neurons are thoroughly discussed in this review. This study presents the ability of CRISPR system to boost learning power and memory, treat or cure genetically-based neurological disorders, and alleviate psychiatric diseases by altering the activity and the irritability of the neurons at the synaptic cleft through DNA manipulation, and also, epigenetic modifications using Cas9. We explore and examine how each different OMIC techniques can come useful when altering DNA sequences. Such insight into the underlying relationship between OMICs and cellular behaviors leads us to better neurological and psychiatric therapeutics by intelligently designing and utilizing the CRISPR/Cas9 technology.
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Affiliation(s)
- Mohammad Banazadeh
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Ardavan Abiri
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06520, USA
| | | | - Lida Asnaashari
- Student Research Committee, Kerman Universiy of Medical Sciences, Kerman, Iran
| | - Mohammad Amin Langarizadeh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Hamid Forootanfar
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran.
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5
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Moore JR, Nemera MT, D’Souza RD, Hamagami N, Clemens AW, Beard DC, Urman A, Mendoza VR, Gabel HW. Non-CG DNA methylation and MeCP2 stabilize repeated tuning of long genes that distinguish closely related neuron types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.30.577861. [PMID: 38352532 PMCID: PMC10862856 DOI: 10.1101/2024.01.30.577861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
The extraordinary diversity of neuron types in the mammalian brain is delineated at the highest resolution by subtle gene expression differences that may require specialized molecular mechanisms to be maintained. Neurons uniquely express the longest genes in the genome and utilize neuron-enriched non-CG DNA methylation (mCA) together with the Rett syndrome protein, MeCP2, to control gene expression, but the function of these unique gene structures and machinery in regulating finely resolved neuron type-specific gene programs has not been explored. Here, we employ epigenomic and spatial transcriptomic analyses to discover a major role for mCA and MeCP2 in maintaining neuron type-specific gene programs at the finest scale of cellular resolution. We uncover differential susceptibility to MeCP2 loss in neuronal populations depending on global mCA levels and dissect methylation patterns and intragenic enhancer repression that drive overlapping and distinct gene regulation between neuron types. Strikingly, we show that mCA and MeCP2 regulate genes that are repeatedly tuned to differentiate neuron types at the highest cellular resolution, including spatially resolved, vision-dependent gene programs in the visual cortex. These repeatedly tuned genes display genomic characteristics, including long length, numerous intragenic enhancers, and enrichment for mCA, that predispose them to regulation by MeCP2. Thus, long gene regulation by the MeCP2 pathway maintains differential gene expression between closely-related neurons to facilitate the exceptional cellular diversity in the complex mammalian brain.
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Affiliation(s)
- J. Russell Moore
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Mati T. Nemera
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Rinaldo D. D’Souza
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Nicole Hamagami
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Adam W. Clemens
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Diana C. Beard
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Alaina Urman
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Victoria Rodriguez Mendoza
- Opportunities in Genomic Research Program, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Harrison W. Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
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Minto M, Sotelo-Fonseca JE, Ramesh V, West AE. Genome binding properties of Zic transcription factors underlie their changing functions during neuronal maturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.04.574185. [PMID: 38260638 PMCID: PMC10802290 DOI: 10.1101/2024.01.04.574185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Background The Zic family of transcription factors (TFs) promote both proliferation and maturation of cerebellar granule neurons (CGNs), raising the question of how a single, constitutively expressed TF family can support distinct developmental processes. Here we use an integrative experimental and bioinformatic approach to discover the regulatory relationship between Zic TF binding and changing programs of gene transcription during CGN differentiation. Results We first established a bioinformatic pipeline to integrate Zic ChIP-seq data from the developing mouse cerebellum with other genomic datasets from the same tissue. In newborn CGNs, Zic TF binding predominates at active enhancers that are co-bound by developmentally-regulated TFs including Atoh1, whereas in mature CGNs, Zic TF binding consolidates toward promoters where it co-localizes with activity-regulated TFs. We then performed CUT&RUN-seq in differentiating CGNs to define both the time course of developmental shifts in Zic TF binding and their relationship to gene expression. Mapping Zic TF binding sites to genes using chromatin looping, we identified the set of Zic target genes that have altered expression in RNA-seq from Zic1 or Zic2 knockdown CGNs. Conclusion Our data show that Zic TFs are required for both induction and repression of distinct, developmentally regulated target genes through a mechanism that is largely independent of changes in Zic TF binding. We suggest that the differential collaboration of Zic TFs with other TF families underlies the shift in their biological functions across CGN development.
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Affiliation(s)
- Melyssa Minto
- Duke University, Program in Computational Biology and Bioinformatics, Durham, NC 27710
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC 27709
| | | | | | - Anne E. West
- Duke University, Department of Neurobiology, Durham, NC 27710
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Avarlaid A, Esvald E, Koppel I, Parkman A, Zhuravskaya A, Makeyev EV, Tuvikene J, Timmusk T. An 840 kb distant upstream enhancer is a crucial regulator of catecholamine-dependent expression of the Bdnf gene in astrocytes. Glia 2024; 72:90-110. [PMID: 37632136 PMCID: PMC10952894 DOI: 10.1002/glia.24463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023]
Abstract
Brain-derived neurotrophic factor (BDNF) plays a fundamental role in the developing and adult nervous system, contributing to neuronal survival, differentiation, and synaptic plasticity. Dysregulation of BDNF synthesis, secretion or signaling has been associated with many neurodevelopmental, neuropsychiatric, and neurodegenerative disorders. Although the transcriptional regulation of the Bdnf gene has been extensively studied in neurons, less is known about the regulation and function of BDNF in non-neuronal cells. The most abundant type of non-neuronal cells in the brain, astrocytes, express BDNF in response to catecholamines. However, genetic elements responsible for this regulation have not been identified. Here, we investigated four potential Bdnf enhancer regions and based on reporter gene assays, CRISPR/Cas9 engineering and CAPTURE-3C-sequencing we conclude that a region 840 kb upstream of the Bdnf gene regulates catecholamine-dependent expression of Bdnf in rodent astrocytes. We also provide evidence that this regulation is mediated by CREB and AP1 family transcription factors. This is the first report of an enhancer coordinating the transcription of Bdnf gene in non-neuronal cells.
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Affiliation(s)
- Annela Avarlaid
- Department of Chemistry and BiotechnologyTallinn University of TechnologyTallinnEstonia
| | - Eli‐Eelika Esvald
- Department of Chemistry and BiotechnologyTallinn University of TechnologyTallinnEstonia
- Protobios LLCTallinnEstonia
| | - Indrek Koppel
- Department of Chemistry and BiotechnologyTallinn University of TechnologyTallinnEstonia
| | - Annabel Parkman
- Department of Chemistry and BiotechnologyTallinn University of TechnologyTallinnEstonia
| | - Anna Zhuravskaya
- Centre for Developmental NeurobiologyKing's College LondonLondonUK
| | | | - Jürgen Tuvikene
- Department of Chemistry and BiotechnologyTallinn University of TechnologyTallinnEstonia
- Protobios LLCTallinnEstonia
| | - Tõnis Timmusk
- Department of Chemistry and BiotechnologyTallinn University of TechnologyTallinnEstonia
- Protobios LLCTallinnEstonia
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R R, Devtalla H, Rana K, Panda SP, Agrawal A, Kadyan S, Jindal D, Pancham P, Yadav D, Jha NK, Jha SK, Gupta V, Singh M. A comprehensive update on genetic inheritance, epigenetic factors, associated pathology, and recent therapeutic intervention by gene therapy in schizophrenia. Chem Biol Drug Des 2024; 103:e14374. [PMID: 37994213 DOI: 10.1111/cbdd.14374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 09/15/2023] [Accepted: 09/29/2023] [Indexed: 11/24/2023]
Abstract
Schizophrenia is a severe psychological disorder in which reality is interpreted abnormally by the patient. The symptoms of the disease include delusions and hallucinations, associated with extremely disordered behavior and thinking, which may affect the daily lives of the patients. Advancements in technology have led to understanding the dynamics of the disease and the identification of the underlying causes. Multiple investigations prove that it is regulated genetically, and epigenetically, and is affected by environmental factors. The molecular and neural pathways linked to the regulation of schizophrenia have been extensively studied. Over 180 Schizophrenic risk loci have now been recognized due to several genome-wide association studies (GWAS). It has been observed that multiple transcription factors (TF) binding-disrupting single nucleotide polymorphisms (SNPs) have been related to gene expression responsible for the disease in cerebral complexes. Copy number variation, SNP defects, and epigenetic changes in chromosomes may cause overexpression or underexpression of certain genes responsible for the disease. Nowadays, gene therapy is being implemented for its treatment as several of these genetic defects have been identified. Scientists are trying to use viral vectors, miRNA, siRNA, and CRISPR technology. In addition, nanotechnology is also being applied to target such genes. The primary aim of such targeting was to either delete or silence such hyperactive genes or induce certain genes that inhibit the expression of these genes. There are challenges in delivering the gene/DNA to the site of action in the brain, and scientists are working to resolve the same. The present article describes the basics regarding the disease, its causes and factors responsible, and the gene therapy solutions available to treat this disease.
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Affiliation(s)
- Rachana R
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Harshit Devtalla
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Karishma Rana
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Siva Prasad Panda
- Institute of Pharmaceutical Research, GLA University, Mathura, India
| | - Arushi Agrawal
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Shreya Kadyan
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Divya Jindal
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
- IIT Bombay Monash Research Academy, IIT - Bombay, Bombay, India
| | - Pranav Pancham
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Deepshikha Yadav
- Bhartiya Nirdeshak Dravya Division, CSIR-National Physical Laboratory, New Delhi, India
- Physico-Mechanical Metrology Division, CSIR-National Physical Laboratory, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Niraj Kumar Jha
- Department of Biotechnology, Sharda School of Engineering and Technology (SSET), Sharda University, Greater Noida, India
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, India
- Department of Biotechnology, School of Applied and Life Sciences (SALS), Uttaranchal University, Dehradun, India
- School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, India
| | - Saurabh Kumar Jha
- Department of Biotechnology, Sharda School of Engineering and Technology (SSET), Sharda University, Greater Noida, India
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, India
- Department of Biotechnology, School of Applied and Life Sciences (SALS), Uttaranchal University, Dehradun, India
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Vivek Gupta
- Macquarie Medical School, Macquarie University (MQU), Sydney, New South Wales, Australia
| | - Manisha Singh
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
- Faculty of Health, Graduate School of Public Health, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Research Consortium in Complementary and Integrative Medicine (ARCCIM), University of Technology Sydney, Sydney, New South Wales, Australia
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Zhu K, Bendl J, Rahman S, Vicari JM, Coleman C, Clarence T, Latouche O, Tsankova NM, Li A, Brennand KJ, Lee D, Yuan GC, Fullard JF, Roussos P. Multi-omic profiling of the developing human cerebral cortex at the single-cell level. SCIENCE ADVANCES 2023; 9:eadg3754. [PMID: 37824614 PMCID: PMC10569714 DOI: 10.1126/sciadv.adg3754] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/01/2023] [Indexed: 10/14/2023]
Abstract
The cellular complexity of the human brain is established via dynamic changes in gene expression throughout development that is mediated, in part, by the spatiotemporal activity of cis-regulatory elements (CREs). We simultaneously profiled gene expression and chromatin accessibility in 45,549 cortical nuclei across six broad developmental time points from fetus to adult. We identified cell type-specific domains in which chromatin accessibility is highly correlated with gene expression. Differentiation pseudotime trajectory analysis indicates that chromatin accessibility at CREs precedes transcription and that dynamic changes in chromatin structure play a critical role in neuronal lineage commitment. In addition, we mapped cell type-specific and temporally specific genetic loci implicated in neuropsychiatric traits, including schizophrenia and bipolar disorder. Together, our results describe the complex regulation of cell composition at critical stages in lineage determination and shed light on the impact of spatiotemporal alterations in gene expression on neuropsychiatric disease.
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Affiliation(s)
- Kaiyi Zhu
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jaroslav Bendl
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Samir Rahman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - James M. Vicari
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Claire Coleman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tereza Clarence
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ovaun Latouche
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Nadejda M. Tsankova
- Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aiqun Li
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristen J. Brennand
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Donghoon Lee
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John F. Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research Education and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY 10468, USA
- Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
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10
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Gallegos DA, Minto M, Liu F, Hazlett MF, Aryana Yousefzadeh S, Bartelt LC, West AE. Cell-type specific transcriptional adaptations of nucleus accumbens interneurons to amphetamine. Mol Psychiatry 2023; 28:3414-3428. [PMID: 35173267 PMCID: PMC9378812 DOI: 10.1038/s41380-022-01466-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 01/13/2022] [Accepted: 01/26/2022] [Indexed: 11/09/2022]
Abstract
Parvalbumin-expressing (PV+) interneurons of the nucleus accumbens (NAc) play an essential role in the addictive-like behaviors induced by psychostimulant exposure. To identify molecular mechanisms of PV+ neuron plasticity, we isolated interneuron nuclei from the NAc of male and female mice following acute or repeated exposure to amphetamine (AMPH) and sequenced for cell type-specific RNA expression and chromatin accessibility. AMPH regulated the transcription of hundreds of genes in PV+ interneurons, and this program was largely distinct from that regulated in other NAc GABAergic neurons. Chromatin accessibility at enhancers predicted cell-type specific gene regulation, identifying transcriptional mechanisms of differential AMPH responses. Finally, we assessed expression of PV-enriched, AMPH-regulated genes in an Mecp2 mutant mouse strain that shows heightened behavioral sensitivity to psychostimulants to explore the functional importance of this transcriptional program. Together these data provide novel insight into the cell-type specific programs of transcriptional plasticity in NAc neurons that underlie addictive-like behaviors.
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Affiliation(s)
- David A Gallegos
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Melyssa Minto
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Fang Liu
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Mariah F Hazlett
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | | | - Luke C Bartelt
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Anne E West
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA.
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11
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Zhao Z, Parra OP, Musella F, Scrutton-Alvarado N, Fujita SI, Alber F, Yang Y, Yamada T. Mega-Enhancer Bodies Organize Neuronal Long Genes in the Cerebellum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.19.549737. [PMID: 37503219 PMCID: PMC10370079 DOI: 10.1101/2023.07.19.549737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Dynamic regulation of gene expression plays a key role in establishing the diverse neuronal cell types in the brain. Recent findings in genome biology suggest that three-dimensional (3D) genome organization has important, but mechanistically poorly understood functions in gene transcription. Beyond local genomic interactions between promoters and enhancers, we find that cerebellar granule neurons undergoing differentiation in vivo exhibit striking increases in long-distance genomic interactions between transcriptionally active genomic loci, which are separated by tens of megabases within a chromosome or located on different chromosomes. Among these interactions, we identify a nuclear subcompartment enriched for near-megabase long enhancers and their associated neuronal long genes encoding synaptic or signaling proteins. Neuronal long genes are differentially recruited to this enhancer-dense subcompartment to help shape the transcriptional identities of granule neuron subtypes in the cerebellum. SPRITE analyses of higher-order genomic interactions, together with IGM-based 3D genome modeling and imaging approaches, reveal that the enhancer-dense subcompartment forms prominent nuclear structures, which we term mega-enhancer bodies. These novel nuclear bodies reside in the nuclear periphery, away from other transcriptionally active structures, including nuclear speckles located in the nuclear interior. Together, our findings define additional layers of higher-order 3D genome organization closely linked to neuronal maturation and identity in the brain.
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12
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Di Liegro CM, Schiera G, Schirò G, Di Liegro I. Involvement of the H3.3 Histone Variant in the Epigenetic Regulation of Gene Expression in the Nervous System, in Both Physiological and Pathological Conditions. Int J Mol Sci 2023; 24:11028. [PMID: 37446205 DOI: 10.3390/ijms241311028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/19/2023] [Accepted: 07/01/2023] [Indexed: 07/15/2023] Open
Abstract
All the cells of an organism contain the same genome. However, each cell expresses only a minor fraction of its potential and, in particular, the genes encoding the proteins necessary for basal metabolism and the proteins responsible for its specific phenotype. The ability to use only the right and necessary genes involved in specific functions depends on the structural organization of the nuclear chromatin, which in turn depends on the epigenetic history of each cell, which is stored in the form of a collection of DNA and protein modifications. Among these modifications, DNA methylation and many kinds of post-translational modifications of histones play a key role in organizing the complex indexing of usable genes. In addition, non-canonical histone proteins (also known as histone variants), the synthesis of which is not directly linked with DNA replication, are used to mark specific regions of the genome. Here, we will discuss the role of the H3.3 histone variant, with particular attention to its loading into chromatin in the mammalian nervous system, both in physiological and pathological conditions. Indeed, chromatin modifications that mark cell memory seem to be of special importance for the cells involved in the complex processes of learning and memory.
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Affiliation(s)
- Carlo Maria Di Liegro
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Gabriella Schiera
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Giuseppe Schirò
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (Bi.N.D.), University of Palermo, 90127 Palermo, Italy
| | - Italia Di Liegro
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (Bi.N.D.), University of Palermo, 90127 Palermo, Italy
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13
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Ramirez M, Robert R, Yeung J, Wu J, Abdalla-Wyse A, Goldowitz D. Identification and characterization of transcribed enhancers during cerebellar development through enhancer RNA analysis. BMC Genomics 2023; 24:351. [PMID: 37365500 DOI: 10.1186/s12864-023-09368-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 05/08/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND The development of the brain requires precise coordination of molecular processes across many cell-types. Underpinning these events are gene expression programs which require intricate regulation by non-coding regulatory sequences known as enhancers. In the context of the developing brain, transcribed enhancers (TEs) regulate temporally-specific expression of genes critical for cell identity and differentiation. Transcription of non-coding RNAs at active enhancer sequences, known as enhancer RNAs (eRNAs), is tightly associated with enhancer activity and has been correlated with target gene expression. TEs have been characterized in a multitude of developing tissues, however their regulatory role has yet to be described in the context of embryonic and early postnatal brain development. In this study, eRNA transcription was analyzed to identify TEs active during cerebellar development, as a proxy for the developing brain. Cap Analysis of Gene Expression followed by sequencing (CAGE-seq) was conducted at 12 stages throughout embryonic and early postnatal cerebellar development. RESULTS Temporal analysis of eRNA transcription identified clusters of TEs that peak in activity during either embryonic or postnatal times, highlighting their importance for temporally specific developmental events. Functional analysis of putative target genes identified molecular mechanisms under TE regulation revealing that TEs regulate genes involved in biological processes specific to neurons. We validate enhancer activity using in situ hybridization of eRNA expression from TEs predicted to regulate Nfib, a gene critical for cerebellar granule cell differentiation. CONCLUSIONS The results of this analysis provide a valuable dataset for the identification of cerebellar enhancers and provide insight into the molecular mechanisms critical for brain development under TE regulation. This dataset is shared with the community through an online resource ( https://goldowitzlab.shinyapps.io/trans-enh-app/ ).
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Affiliation(s)
- Miguel Ramirez
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada
| | - Remi Robert
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada
| | - Joanna Yeung
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada
| | - Joshua Wu
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada
| | - Ayasha Abdalla-Wyse
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada
| | - Daniel Goldowitz
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada.
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada.
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14
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Hamagami N, Wu DY, Clemens AW, Nettles SA, Li A, Gabel HW. NSD1 deposits histone H3 lysine 36 dimethylation to pattern non-CG DNA methylation in neurons. Mol Cell 2023; 83:1412-1428.e7. [PMID: 37098340 PMCID: PMC10230755 DOI: 10.1016/j.molcel.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 02/16/2023] [Accepted: 03/30/2023] [Indexed: 04/27/2023]
Abstract
During postnatal development, the DNA methyltransferase DNMT3A deposits high levels of non-CG cytosine methylation in neurons. This methylation is critical for transcriptional regulation, and loss of this mark is implicated in DNMT3A-associated neurodevelopmental disorders (NDDs). Here, we show in mice that genome topology and gene expression converge to shape histone H3 lysine 36 dimethylation (H3K36me2) profiles, which in turn recruit DNMT3A and pattern neuronal non-CG methylation. We show that NSD1, an H3K36 methyltransferase mutated in NDD, is required for the patterning of megabase-scale H3K36me2 and non-CG methylation in neurons. We find that brain-specific deletion of NSD1 causes altered DNA methylation that overlaps with DNMT3A disorder models to drive convergent dysregulation of key neuronal genes that may underlie shared phenotypes in NSD1- and DNMT3A-associated NDDs. Our findings indicate that H3K36me2 deposited by NSD1 is important for neuronal non-CG DNA methylation and suggest that the H3K36me2-DNMT3A-non-CG-methylation pathway is likely disrupted in NSD1-associated NDDs.
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Affiliation(s)
- Nicole Hamagami
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO 63110-1093, USA
| | - Dennis Y Wu
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO 63110-1093, USA
| | - Adam W Clemens
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO 63110-1093, USA
| | - Sabin A Nettles
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO 63110-1093, USA
| | - Aidan Li
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO 63110-1093, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO 63110-1093, USA.
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15
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Morin A, Chu ECP, Sharma A, Adrian-Hamazaki A, Pavlidis P. Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets. Genome Res 2023; 33:763-778. [PMID: 37308292 PMCID: PMC10317128 DOI: 10.1101/gr.277273.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 04/26/2023] [Indexed: 06/14/2023]
Abstract
Mapping the gene targets of chromatin-associated transcription regulators (TRs) is a major goal of genomics research. ChIP-seq of TRs and experiments that perturb a TR and measure the differential abundance of gene transcripts are a primary means by which direct relationships are tested on a genomic scale. It has been reported that there is a poor overlap in the evidence across gene regulation strategies, emphasizing the need for integrating results from multiple experiments. Although research consortia interested in gene regulation have produced a valuable trove of high-quality data, there is an even greater volume of TR-specific data throughout the literature. In this study, we show a workflow for the identification, uniform processing, and aggregation of ChIP-seq and TR perturbation experiments for the ultimate purpose of ranking human and mouse TR-target interactions. Focusing on an initial set of eight regulators (ASCL1, HES1, MECP2, MEF2C, NEUROD1, PAX6, RUNX1, and TCF4), we identified 497 experiments suitable for analysis. We used this corpus to examine data concordance, to identify systematic patterns of the two data types, and to identify putative orthologous interactions between human and mouse. We build upon commonly used strategies to forward a procedure for aggregating and combining these two genomic methodologies, assessing these rankings against independent literature-curated evidence. Beyond a framework extensible to other TRs, our work also provides empirically ranked TR-target listings, as well as transparent experiment-level gene summaries for community use.
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Affiliation(s)
- Alexander Morin
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Eric Ching-Pan Chu
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Aman Sharma
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Alex Adrian-Hamazaki
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Paul Pavlidis
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada;
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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16
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Jiang K, Koob J, Chen XD, Krajeski RN, Zhang Y, Volf V, Zhou W, Sgrizzi SR, Villiger L, Gootenberg JS, Chen F, Abudayyeh OO. Programmable eukaryotic protein synthesis with RNA sensors by harnessing ADAR. Nat Biotechnol 2023; 41:698-707. [PMID: 36302988 DOI: 10.1038/s41587-022-01534-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022]
Abstract
Programmable approaches to sense and respond to the presence of specific RNAs in biological systems have broad applications in research, diagnostics, and therapeutics. Here we engineer a programmable RNA-sensing technology, reprogrammable ADAR sensors (RADARS), which harnesses RNA editing by adenosine deaminases acting on RNA (ADAR) to gate translation of a cargo protein by the presence of endogenous RNA transcripts. Introduction of a stop codon in a guide upstream of the cargo makes translation contingent on binding of an endogenous transcript to the guide, leading to ADAR editing of the stop codon and allowing translational readthrough. Through systematic sensor engineering, we achieve 277 fold improvement in sensor activation and engineer RADARS with diverse cargo proteins, including luciferases, fluorescent proteins, recombinases, and caspases, enabling detection sensitivity on endogenous transcripts expressed at levels as low as 13 transcripts per million. We show that RADARS are functional as either expressed DNA or synthetic mRNA and with either exogenous or endogenous ADAR. We apply RADARS in multiple contexts, including tracking transcriptional states, RNA-sensing-induced cell death, cell-type identification, and control of synthetic mRNA translation.
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Affiliation(s)
- Kaiyi Jiang
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeremy Koob
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Xi Dawn Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Systems, Synthetic, and Quantitative Biology Program, Harvard Medical School, Boston, MA, USA
| | - Rohan N Krajeski
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yifan Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Verena Volf
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Wenyuan Zhou
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Samantha R Sgrizzi
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lukas Villiger
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Fei Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Omar O Abudayyeh
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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17
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Ramesh V, Liu F, Minto MS, Chan U, West AE. Bidirectional regulation of postmitotic H3K27me3 distributions underlie cerebellar granule neuron maturation dynamics. eLife 2023; 12:e86273. [PMID: 37092728 PMCID: PMC10181825 DOI: 10.7554/elife.86273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/21/2023] [Indexed: 04/25/2023] Open
Abstract
The functional maturation of neurons is a prolonged process that extends past the mitotic exit and is mediated by the chromatin-dependent orchestration of gene transcription programs. We find that expression of this maturation gene program in mouse cerebellar granule neurons (CGNs) requires dynamic changes in the genomic distribution of histone H3 lysine 27 trimethylation (H3K27me3), demonstrating a function for this chromatin modification beyond its role in cell fate specification. The developmental loss of H3K27me3 at promoters of genes activated as CGNs mature is facilitated by the lysine demethylase and ASD-risk gene, Kdm6b. Interestingly, inhibition of the H3K27 methyltransferase EZH2 in newborn CGNs not only blocks the repression of progenitor genes but also impairs the induction of mature CGN genes, showing the importance of bidirectional H3K27me3 regulation across the genome. These data demonstrate that H3K27me3 turnover in developing postmitotic neurons regulates the temporal coordination of gene expression programs that underlie functional neuronal maturation.
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Affiliation(s)
- Vijyendra Ramesh
- Molecular Cancer Biology Program, Duke UniversityDurhamUnited States
| | - Fang Liu
- Department of Neurobiology, Duke UniversityDurhamUnited States
| | - Melyssa S Minto
- Department of Neurobiology, Duke UniversityDurhamUnited States
| | - Urann Chan
- Department of Neurobiology, Duke UniversityDurhamUnited States
| | - Anne E West
- Molecular Cancer Biology Program, Duke UniversityDurhamUnited States
- Department of Neurobiology, Duke UniversityDurhamUnited States
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18
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Whole Genome Analysis of Dizygotic Twins With Autism Reveals Prevalent Transposon Insertion Within Neuronal Regulatory Elements: Potential Implications for Disease Etiology and Clinical Assessment. J Autism Dev Disord 2023; 53:1091-1106. [PMID: 35759154 DOI: 10.1007/s10803-022-05636-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2022] [Indexed: 10/17/2022]
Abstract
Transposable elements (TEs) have been implicated in autism spectrum disorder (ASD). However, our understanding of their roles is far from complete. Herein, we explored de novo TE insertions (dnTEIs) and de novo variants (DNVs) across the genomes of dizygotic twins with ASD and their parents. The neuronal regulatory elements had a tendency to harbor dnTEIs that were shared between twins, but ASD-risk genes had dnTEIs that were unique to each twin. The dnTEIs were 4.6-fold enriched in enhancers that are active in embryonic stem cell (ESC)-neurons (p < 0.001), but DNVs were 1.5-fold enriched in active enhancers of astrocytes (p = 0.0051). Our findings suggest that dnTEIs and DNVs play a role in ASD etiology by disrupting enhancers of neurons and astrocytes.
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19
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Hamagami N, Wu DY, Clemens AW, Nettles SA, Gabel HW. NSD1 deposits histone H3 lysine 36 dimethylation to pattern non-CG DNA methylation in neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.17.528965. [PMID: 36824816 PMCID: PMC9949142 DOI: 10.1101/2023.02.17.528965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
During postnatal development the DNA methyltransferase DNMT3A deposits high levels of non-CG cytosine methylation in neurons. This unique methylation is critical for transcriptional regulation in the mature mammalian brain, and loss of this mark is implicated in DNMT3A-associated neurodevelopmental disorders (NDDs). The mechanisms determining genomic non-CG methylation profiles are not well defined however, and it is unknown if this pathway is disrupted in additional NDDs. Here we show that genome topology and gene expression converge to shape histone H3 lysine 36 dimethylation (H3K36me2) profiles, which in turn recruit DNMT3A and pattern neuronal non-CG methylation. We show that NSD1, the H3K36 methyltransferase mutated in the NDD, Sotos syndrome, is required for megabase-scale patterning of H3K36me2 and non-CG methylation in neurons. We find that brain-specific deletion of NSD1 causes alterations in DNA methylation that overlap with models of DNMT3A disorders and define convergent disruption in the expression of key neuronal genes in these models that may contribute to shared phenotypes in NSD1- and DNMT3A-associated NDD. Our findings indicate that H3K36me2 deposited by NSD1 is an important determinant of neuronal non-CG DNA methylation and implicates disruption of this methylation in Sotos syndrome. Highlights Topology-associated DNA methylation and gene expression independently contribute to neuronal gene body and enhancer non-CG DNA methylation patterns.Topology-associated H3K36me2 patterns and local enrichment of H3K4 methylation impact deposition of non-CG methylation by DNMT3A. Disruption of NSD1 in vivo leads to alterations in H3K36me2, DNA methylation, and gene expression that overlap with models of DNMT3A disorders.
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Affiliation(s)
- Nicole Hamagami
- Department of Neuroscience, Washington University School of Medicine, St Louis MO 63110-1093, USA
- These authors contributed equally
| | - Dennis Y Wu
- Department of Neuroscience, Washington University School of Medicine, St Louis MO 63110-1093, USA
- These authors contributed equally
| | - Adam W Clemens
- Department of Neuroscience, Washington University School of Medicine, St Louis MO 63110-1093, USA
| | - Sabin A Nettles
- Department of Neuroscience, Washington University School of Medicine, St Louis MO 63110-1093, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St Louis MO 63110-1093, USA
- Lead contact
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20
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Modulating the activity of human nociceptors with a SCN10A promoter-specific viral vector tool. NEUROBIOLOGY OF PAIN (CAMBRIDGE, MASS.) 2023; 13:100120. [PMID: 36816616 PMCID: PMC9932673 DOI: 10.1016/j.ynpai.2023.100120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023]
Abstract
Despite the high prevalence of chronic pain as a disease in our society, there is a lack of effective treatment options for patients living with this condition. Gene therapies using recombinant AAVs are a direct method to selectively express genes of interest in target cells with the potential of, in the case of nociceptors, reducing neuronal firing in pain conditions. We designed a recombinant AAV vector expressing cargos whose expression was driven by a portion of the SCN10A (NaV1.8) promoter, which is predominantly active in nociceptors. We validated its specificity for nociceptors in mouse and human dorsal root ganglia and showed that it can drive the expression of functional proteins. Our viral vector and promoter package drove the expression of both excitatory or inhibitory DREADDs in primary human DRG cultures and in whole cell electrophysiology experiments, increased or decreased neuronal firing, respectively. Taken together, we present a novel viral tool that drives expression of cargo specifically in human nociceptors. This will allow for future specific studies of human nociceptor properties as well as pave the way for potential future gene therapies for chronic pain.
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21
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Zheng A, Shen Z, Glass CK, Gymrek M. Deep learning predicts the impact of regulatory variants on cell-type-specific enhancers in the brain. BIOINFORMATICS ADVANCES 2023; 3:vbad002. [PMID: 36726730 PMCID: PMC9887460 DOI: 10.1093/bioadv/vbad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/11/2022] [Accepted: 01/11/2023] [Indexed: 01/13/2023]
Abstract
Motivation Previous studies have shown that the heritability of multiple brain-related traits and disorders is highly enriched in transcriptional enhancer regions. However, these regions often contain many individual variants, while only a subset of them are likely to causally contribute to a trait. Statistical fine-mapping techniques can identify putative causal variants, but their resolution is often limited, especially in regions with multiple variants in high linkage disequilibrium. In these cases, alternative computational methods to estimate the impact of individual variants can aid in variant prioritization. Results Here, we develop a deep learning pipeline to predict cell-type-specific enhancer activity directly from genomic sequences and quantify the impact of individual genetic variants in these regions. We show that the variants highlighted by our deep learning models are targeted by purifying selection in the human population, likely indicating a functional role. We integrate our deep learning predictions with statistical fine-mapping results for 8 brain-related traits, identifying 63 distinct candidate causal variants predicted to contribute to these traits by modulating enhancer activity, representing 6% of all genome-wide association study signals analyzed. Overall, our study provides a valuable computational method that can prioritize individual variants based on their estimated regulatory impact, but also highlights the limitations of existing methods for variant prioritization and fine-mapping. Availability and implementation The data underlying this article, nucleotide-level importance scores, and code for running the deep learning pipeline are available at https://github.com/Pandaman-Ryan/AgentBind-brain. Contact mgymrek@ucsd.edu. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
| | | | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA,Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
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22
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Edwards-Faret G, de Vin F, Slezak M, Gollenbeck L, Karaman R, Shinmyo Y, Batiuk MY, Pando CM, Urschitz J, Rincon MY, Moisyadi S, Schnütgen F, Kawasaki H, Schmucker D, Holt MG. A New Technical Approach for Cross-species Examination of Neuronal Wiring and Adult Neuron-glia Functions. Neuroscience 2023; 508:40-51. [PMID: 36464177 DOI: 10.1016/j.neuroscience.2022.11.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022]
Abstract
Advances in single cell sequencing have enabled the identification of a large number of genes, expressed in many different cell types, and across a variety of model organisms. In particular, the nervous system harbors an immense number of interacting cell types, which are poorly characterized. Future loss- and gain-of-function experiments will be essential in determining how novel genes play critical roles in diverse cellular, as well as evolutionarily adapted, contexts. However, functional analysis across species is often hampered by technical limitations, in non-genetic animal systems. Here, we describe a new single plasmid system, misPiggy. The system is based around the hyperactive piggyBac transposon system, which combines stable genomic integration of transgenes (for long-term expression) with large cargo capacity. Taking full advantage of these characteristics, we engineered novel expression modules into misPiggy that allow for cell-type specific loss- and gain-of-gene function. These modules work widely across species from frog to ferret. As a proof of principle, we present a loss-of-function analysis of the neuronal receptor Deleted in Colorectal Cancer (DCC) in retinal ganglion cells (RGCs) of Xenopus tropicalis tadpoles. Single axon tracings of mosaic knock-out cells reveal a specific cell-intrinsic requirement of DCC, specifically in axonal arborization within the frog tectum, rather than retina-to-brain axon guidance. Furthermore, we report additional technical advances that enable temporal control of knock-down or gain-of-function analysis. We applied this to visualize and manipulate labeled neurons, astrocytes and other glial cells in the central nervous system (CNS) of mouse, rat and ferret. We propose that misPiggy will be a valuable tool for rapid, flexible and cost-effective screening of gene function across a variety of animal models.
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Affiliation(s)
- Gabriela Edwards-Faret
- VIB Center for Brain and Disease Research, Herestraat 49, Leuven 3000, Belgium; KU Leuven Department of Neuroscience, Herestraat 49, Leuven 3000, Belgium; Neuronal Wiring Group, Life & Medical Sciences Institute, University of Bonn, Carl-Troll-Straße 31, Bonn D53115, Germany
| | - Filip de Vin
- VIB Center for Brain and Disease Research, Herestraat 49, Leuven 3000, Belgium; KU Leuven Department of Neuroscience, Herestraat 49, Leuven 3000, Belgium
| | - Michal Slezak
- VIB Center for Brain and Disease Research, Herestraat 49, Leuven 3000, Belgium; KU Leuven Department of Neuroscience, Herestraat 49, Leuven 3000, Belgium
| | - Lennart Gollenbeck
- Neuronal Wiring Group, Life & Medical Sciences Institute, University of Bonn, Carl-Troll-Straße 31, Bonn D53115, Germany
| | - Ruçhan Karaman
- VIB Center for Cancer Biology, Herestraat 49, Leuven 3000, Belgium; KU Leuven Department of Oncology, Herestraat 49, Leuven 3000, Belgium
| | - Yohei Shinmyo
- Department of Medical Neuroscience, Graduate School of Medicine, Kanazawa University, Ishikawa 920-1192, Japan
| | - Mykhailo Y Batiuk
- VIB Center for Brain and Disease Research, Herestraat 49, Leuven 3000, Belgium; KU Leuven Department of Neuroscience, Herestraat 49, Leuven 3000, Belgium
| | - Carmen Menacho Pando
- VIB Center for Brain and Disease Research, Herestraat 49, Leuven 3000, Belgium; KU Leuven Department of Neuroscience, Herestraat 49, Leuven 3000, Belgium
| | - Johann Urschitz
- Institute for Biogenesis Research, University of Hawaii, 1960 East-West Rd. E-124, Honolulu, HI 96822, USA
| | - Melvin Y Rincon
- VIB Center for Brain and Disease Research, Herestraat 49, Leuven 3000, Belgium; KU Leuven Department of Neuroscience, Herestraat 49, Leuven 3000, Belgium
| | - Stefan Moisyadi
- Institute for Biogenesis Research, University of Hawaii, 1960 East-West Rd. E-124, Honolulu, HI 96822, USA
| | - Frank Schnütgen
- Department of Medicine 2, University Hospital Frankfurt, Goethe University, Theodor Stern Kai 7, Frankfurt am Main D60590, Germany; LOEWE Center for Cell and Gene Therapy, University Hospital Frankfurt, Goethe University, Theodor Stern Kai 7, Frankfurt am Main D60590, Germany; FCI, Frankfurt Cancer Institute, University Hospital Frankfurt, Goethe University, Theodor Stern Kai 7, Frankfurt am Main D60590, Germany
| | - Hiroshi Kawasaki
- Department of Medical Neuroscience, Graduate School of Medicine, Kanazawa University, Ishikawa 920-1192, Japan
| | - Dietmar Schmucker
- VIB Center for Brain and Disease Research, Herestraat 49, Leuven 3000, Belgium; KU Leuven Department of Neuroscience, Herestraat 49, Leuven 3000, Belgium; Neuronal Wiring Group, Life & Medical Sciences Institute, University of Bonn, Carl-Troll-Straße 31, Bonn D53115, Germany; Leuven Brain Institute, Herestraat 49, Leuven 3000, Belgium.
| | - Matthew G Holt
- VIB Center for Brain and Disease Research, Herestraat 49, Leuven 3000, Belgium; KU Leuven Department of Neuroscience, Herestraat 49, Leuven 3000, Belgium; Leuven Brain Institute, Herestraat 49, Leuven 3000, Belgium; University of Porto, Instituto de Investigaçāo e Inovaçāo em Saúde (i3S), Rua Alfredo Allen 208, 4200-135 Porto, Portugal.
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23
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Giacoman-Lozano M, Meléndez-Ramírez C, Martinez-Ledesma E, Cuevas-Diaz Duran R, Velasco I. Epigenetics of neural differentiation: Spotlight on enhancers. Front Cell Dev Biol 2022; 10:1001701. [PMID: 36313573 PMCID: PMC9606577 DOI: 10.3389/fcell.2022.1001701] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/03/2022] [Indexed: 11/28/2022] Open
Abstract
Neural induction, both in vivo and in vitro, includes cellular and molecular changes that result in phenotypic specialization related to specific transcriptional patterns. These changes are achieved through the implementation of complex gene regulatory networks. Furthermore, these regulatory networks are influenced by epigenetic mechanisms that drive cell heterogeneity and cell-type specificity, in a controlled and complex manner. Epigenetic marks, such as DNA methylation and histone residue modifications, are highly dynamic and stage-specific during neurogenesis. Genome-wide assessment of these modifications has allowed the identification of distinct non-coding regulatory regions involved in neural cell differentiation, maturation, and plasticity. Enhancers are short DNA regulatory regions that bind transcription factors (TFs) and interact with gene promoters to increase transcriptional activity. They are of special interest in neuroscience because they are enriched in neurons and underlie the cell-type-specificity and dynamic gene expression profiles. Classification of the full epigenomic landscape of neural subtypes is important to better understand gene regulation in brain health and during diseases. Advances in novel next-generation high-throughput sequencing technologies, genome editing, Genome-wide association studies (GWAS), stem cell differentiation, and brain organoids are allowing researchers to study brain development and neurodegenerative diseases with an unprecedented resolution. Herein, we describe important epigenetic mechanisms related to neurogenesis in mammals. We focus on the potential roles of neural enhancers in neurogenesis, cell-fate commitment, and neuronal plasticity. We review recent findings on epigenetic regulatory mechanisms involved in neurogenesis and discuss how sequence variations within enhancers may be associated with genetic risk for neurological and psychiatric disorders.
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Affiliation(s)
- Mayela Giacoman-Lozano
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, NL, Mexico
| | - César Meléndez-Ramírez
- Instituto de Fisiología Celular—Neurociencias, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
- Laboratorio de Reprogramación Celular, Instituto Nacional de Neurología y Neurocirugía “Manuel Velasco Suárez”, Mexico City, Mexico
| | - Emmanuel Martinez-Ledesma
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, NL, Mexico
- Tecnologico de Monterrey, The Institute for Obesity Research, Monterrey, NL, Mexico
| | - Raquel Cuevas-Diaz Duran
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, NL, Mexico
- *Correspondence: Raquel Cuevas-Diaz Duran, ; Iván Velasco,
| | - Iván Velasco
- Instituto de Fisiología Celular—Neurociencias, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
- Laboratorio de Reprogramación Celular, Instituto Nacional de Neurología y Neurocirugía “Manuel Velasco Suárez”, Mexico City, Mexico
- *Correspondence: Raquel Cuevas-Diaz Duran, ; Iván Velasco,
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24
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Griffin A, Mahesh A, Tiwari VK. Disruption of the gene regulatory programme in neurodevelopmental disorders. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194860. [PMID: 36007842 DOI: 10.1016/j.bbagrm.2022.194860] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Cortical development consists of a series of synchronised events, including fate transition of cortical progenitors, neuronal migration, specification and connectivity. It is becoming clear that gene expression programs governing these events rely on the interplay between signalling molecules, transcription factors and epigenetic mechanisms. When genetic or environmental factors disrupt expression of genes involved in important brain development processes, neurodevelopmental disorders can occur. This review aims to highlight how recent advances in technologies have helped uncover and imitate the gene regulatory mechanisms commonly disrupted in neurodevelopmental disorders.
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Affiliation(s)
- Aoife Griffin
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry & Biomedical Science, Queens University, Belfast BT9 7BL, United Kingdom
| | - Arun Mahesh
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry & Biomedical Science, Queens University, Belfast BT9 7BL, United Kingdom
| | - Vijay K Tiwari
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry & Biomedical Science, Queens University, Belfast BT9 7BL, United Kingdom.
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25
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McAfee JC, Bell JL, Krupa O, Matoba N, Stein JL, Won H. Focus on your locus with a massively parallel reporter assay. J Neurodev Disord 2022; 14:50. [PMID: 36085003 PMCID: PMC9463819 DOI: 10.1186/s11689-022-09461-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 09/01/2022] [Indexed: 01/01/2023] Open
Abstract
A growing number of variants associated with risk for neurodevelopmental disorders have been identified by genome-wide association and whole genome sequencing studies. As common risk variants often fall within large haplotype blocks covering long stretches of the noncoding genome, the causal variants within an associated locus are often unknown. Similarly, the effect of rare noncoding risk variants identified by whole genome sequencing on molecular traits is seldom known without functional assays. A massively parallel reporter assay (MPRA) is an assay that can functionally validate thousands of regulatory elements simultaneously using high-throughput sequencing and barcode technology. MPRA has been adapted to various experimental designs that measure gene regulatory effects of genetic variants within cis- and trans-regulatory elements as well as posttranscriptional processes. This review discusses different MPRA designs that have been or could be used in the future to experimentally validate genetic variants associated with neurodevelopmental disorders. Though MPRA has limitations such as it does not model genomic context, this assay can help narrow down the underlying genetic causes of neurodevelopmental disorders by screening thousands of sequences in one experiment. We conclude by describing future directions of this technique such as applications of MPRA for gene-by-environment interactions and pharmacogenetics.
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Affiliation(s)
- Jessica C. McAfee
- grid.10698.360000000122483208Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA ,grid.10698.360000000122483208UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Jessica L. Bell
- grid.10698.360000000122483208Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA ,grid.10698.360000000122483208UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Oleh Krupa
- grid.10698.360000000122483208Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA ,grid.10698.360000000122483208UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Nana Matoba
- grid.10698.360000000122483208Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA ,grid.10698.360000000122483208UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Jason L. Stein
- grid.10698.360000000122483208Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA ,grid.10698.360000000122483208UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA. .,UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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26
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Apelblat D, Roethler O, Bitan L, Keren-Shaul H, Spiegel I. Meso-seq for in-depth transcriptomics in ultra-low amounts of FACS-purified neuronal nuclei. CELL REPORTS METHODS 2022; 2:100259. [PMID: 36046622 PMCID: PMC9421536 DOI: 10.1016/j.crmeth.2022.100259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 05/17/2022] [Accepted: 06/27/2022] [Indexed: 11/25/2022]
Abstract
Profiling of gene expression in sparse populations of genetically defined neurons is essential for dissecting the molecular mechanisms that control the development and plasticity of neural circuits. However, current transcriptomic approaches are ill suited for detailed mechanistic studies in sparse neuronal populations, as they either are technically complex and relatively expensive (e.g., single-cell RNA sequencing [RNA-seq]) or require large amounts of input material (e.g., traditional bulk RNA-seq). Thus, we established Meso-seq, a meso-scale protocol for identifying more than 10,000 robustly expressed genes in as little as 50 FACS-sorted neuronal nuclei. We demonstrate that Meso-seq works well for multiple neuroscience applications, including transcriptomics in antibody-labeled cortical neurons in mice and non-human primates, analyses of experience-regulated gene programs, and RNA-seq from visual cortex neurons labeled ultra-sparsely with viruses. Given its simplicity, robustness, and relatively low costs, Meso-seq is well suited for molecular-mechanistic studies in ultra-sparse neuronal populations in the brain.
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Affiliation(s)
- Daniella Apelblat
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Ori Roethler
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Lidor Bitan
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Hadas Keren-Shaul
- Life Science Core Facility, Weizmann Institute of Science, Rehovot, Israel
- The Nancy & Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Ivo Spiegel
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
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27
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Ramirez M, Badayeva Y, Yeung J, Wu J, Abdalla-Wyse A, Yang E, Trost B, Scherer SW, Goldowitz D. Temporal analysis of enhancers during mouse cerebellar development reveals dynamic and novel regulatory functions. eLife 2022; 11:74207. [PMID: 35942939 PMCID: PMC9398453 DOI: 10.7554/elife.74207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
We have identified active enhancers in the mouse cerebellum at embryonic and postnatal stages which provides a view of novel enhancers active during cerebellar development. The majority of cerebellar enhancers have dynamic activity between embryonic and postnatal development. Cerebellar enhancers were enriched for neural transcription factor binding sites with temporally specific expression. Putative gene targets displayed spatially restricted expression patterns, indicating cell-type specific expression regulation. Functional analysis of target genes indicated that enhancers regulate processes spanning several developmental epochs such as specification, differentiation and maturation. We use these analyses to discover one novel regulator and one novel marker of cerebellar development: Bhlhe22 and Pax3, respectively. We identified an enrichment of de novo mutations and variants associated with autism spectrum disorder in cerebellar enhancers. Furthermore, by comparing our data with relevant brain development ENCODE histone profiles and cerebellar single-cell datasets we have been able to generalize and expand on the presented analyses, respectively. We have made the results of our analyses available online in the Developing Mouse Cerebellum Enhancer Atlas (https://goldowitzlab.shinyapps.io/developing_mouse_cerebellum_enhancer_atlas/), where our dataset can be efficiently queried, curated and exported by the scientific community to facilitate future research efforts. Our study provides a valuable resource for studying the dynamics of gene expression regulation by enhancers in the developing cerebellum and delivers a rich dataset of novel gene-enhancer associations providing a basis for future in-depth studies in the cerebellum.
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Affiliation(s)
- Miguel Ramirez
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Yuliya Badayeva
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Joanna Yeung
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Joshua Wu
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Ayasha Abdalla-Wyse
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Erin Yang
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
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- Department of Molecular Genetics, Hospital for Sick Children, Toronto, Canada
| | - Brett Trost
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Canada
| | - Stephen W Scherer
- Department of Molecular Genetics, Hospital for Sick Children, Toronto, Canada
| | - Daniel Goldowitz
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
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28
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Lu Y, Feng Z, Zhang S, Wang Y. Annotating regulatory elements by heterogeneous network embedding. Bioinformatics 2022; 38:2899-2911. [PMID: 35561169 PMCID: PMC9326849 DOI: 10.1093/bioinformatics/btac185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/05/2022] [Accepted: 03/24/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Regulatory elements (REs), such as enhancers and promoters, are known as regulatory sequences functional in a heterogeneous regulatory network to control gene expression by recruiting transcription regulators and carrying genetic variants in a context specific way. Annotating those REs relies on costly and labor-intensive next-generation sequencing and RNA-guided editing technologies in many cellular contexts. RESULTS We propose a systematic Gene Ontology Annotation method for Regulatory Elements (RE-GOA) by leveraging the powerful word embedding in natural language processing. We first assemble a heterogeneous network by integrating context specific regulations, protein-protein interactions and gene ontology (GO) terms. Then we perform network embedding and associate regulatory elements with GO terms by assessing their similarity in a low dimensional vector space. With three applications, we show that RE-GOA outperforms existing methods in annotating TFs' binding sites from ChIP-seq data, in functional enrichment analysis of differentially accessible peaks from ATAC-seq data, and in revealing genetic correlation among phenotypes from their GWAS summary statistics data. AVAILABILITY AND IMPLEMENTATION The source code and the systematic RE annotation for human and mouse are available at https://github.com/AMSSwanglab/RE-GOA. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yurun Lu
- CEMS, NCMIS, HCMS, MADIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
- School of Mathematics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Zhanying Feng
- CEMS, NCMIS, HCMS, MADIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
- School of Mathematics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Songmao Zhang
- CEMS, NCMIS, HCMS, MADIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
| | - Yong Wang
- To whom correspondence should be addressed. or
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29
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Warren TL, Lambert JT, Nord AS. AAV Deployment of Enhancer-Based Expression Constructs In Vivo in Mouse Brain. J Vis Exp 2022:10.3791/62650. [PMID: 35435902 PMCID: PMC10010840 DOI: 10.3791/62650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Enhancers are binding platforms for a diverse array of transcription factors that drive specific expression patterns of tissue- and cell-type-specific genes. Multiple means of assessing non-coding DNA and various chromatin states have proven useful in predicting the presence of enhancer sequences in the genome, but validating the activity of these sequences and finding the organs and developmental stages they are active in is a labor-intensive process. Recent advances in adeno-associated virus (AAV) vectors have enabled the widespread delivery of transgenes to mouse tissues, enabling in vivo enhancer testing without necessitating a transgenic animal. This protocol shows how a reporter construct that expresses EGFP under the control of a minimal promoter, which does not drive significant expression on its own, can be used to study the activity patterns of candidate enhancer sequences in the mouse brain. An AAV-packaged reporter construct is delivered to the mouse brain and incubated for 1-4 weeks, after which the animal is sacrificed, and brain sections are observed under a microscope. EGFP appears in cells in which the tested enhancer is sufficient to initiate gene expression, pinpointing the location and developmental stage in which the enhancer is active in the brain. Standard cloning methods, low-cost AAV packaging, and expanding AAV serotypes and methods for in vivo delivery and standard imaging readout make this an accessible approach for the study of how gene expression is regulated in the brain.
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Affiliation(s)
- Tracy L Warren
- Department of Psychiatry and Behavioral Sciences, University of California, Davis; Department of Neurobiology, Physiology and Behavior, University of California, Davis
| | - Jason T Lambert
- Department of Psychiatry and Behavioral Sciences, University of California, Davis; Department of Neurobiology, Physiology and Behavior, University of California, Davis;
| | - Alex S Nord
- Department of Psychiatry and Behavioral Sciences, University of California, Davis; Department of Neurobiology, Physiology and Behavior, University of California, Davis;
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30
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Kyzar EJ, Bohnsack JP, Pandey SC. Current and Future Perspectives of Noncoding RNAs in Brain Function and Neuropsychiatric Disease. Biol Psychiatry 2022; 91:183-193. [PMID: 34742545 PMCID: PMC8959010 DOI: 10.1016/j.biopsych.2021.08.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 08/05/2021] [Accepted: 08/12/2021] [Indexed: 02/07/2023]
Abstract
Noncoding RNAs (ncRNAs) represent the majority of the transcriptome and play important roles in regulating neuronal functions. ncRNAs are exceptionally diverse in both structure and function and include enhancer RNAs, long ncRNAs, and microRNAs, all of which demonstrate specific temporal and regional expression in the brain. Here, we review recent studies demonstrating that ncRNAs modulate chromatin structure, act as chaperone molecules, and contribute to synaptic remodeling and behavior. In addition, we discuss ncRNA function within the context of neuropsychiatric diseases, particularly focusing on addiction and schizophrenia, and the recent methodological developments that allow for better understanding of ncRNA function in the brain. Overall, ncRNAs represent an underrecognized molecular contributor to complex neuronal processes underlying neuropsychiatric disorders.
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Affiliation(s)
- Evan J Kyzar
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois; Department of Psychiatry, Columbia University Irving Medical Center, New York State Psychiatric Institute, New York, New York
| | - John Peyton Bohnsack
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois
| | - Subhash C Pandey
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois; Jesse Brown Veterans Affairs Medical Center, University of Illinois at Chicago, Chicago, Illinois; Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, Illinois.
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31
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de la Torre-Ubieta L. Defining the evolutionary and gene regulatory logic of vertebrate neuronal diversity. Neuron 2022; 110:3-5. [PMID: 34990577 DOI: 10.1016/j.neuron.2021.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
How is the exquisite cellular complexity of the vertebrate brain achieved? In this issue of Neuron, Closser et al. (2022) reveal that an expanded neuronal gene regulatory landscape may drive evolutionary cellular diversification by providing complex context and cell-specific control of effector genes.
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Affiliation(s)
- Luis de la Torre-Ubieta
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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32
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Sousa E, Flames N. Transcriptional regulation of neuronal identity. Eur J Neurosci 2021; 55:645-660. [PMID: 34862697 PMCID: PMC9306894 DOI: 10.1111/ejn.15551] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 11/29/2022]
Abstract
Neuronal diversity is an intrinsic feature of the nervous system. Transcription factors (TFs) are key regulators in the establishment of different neuronal identities; how are the actions of different TFs coordinated to orchestrate this diversity? Are there common features shared among the different neuron types of an organism or even among different animal groups? In this review, we provide a brief overview on common traits emerging on the transcriptional regulation of neuron type diversification with a special focus on the comparison between mouse and Caenorhabditis elegans model systems. In the first part, we describe general concepts on neuronal identity and transcriptional regulation of gene expression. In the second part of the review, TFs are classified in different categories according to their key roles at specific steps along the protracted process of neuronal specification and differentiation. The same TF categories can be identified both in mammals and nematodes. Importantly, TFs are very pleiotropic: Depending on the neuron type or the time in development, the same TF can fulfil functions belonging to different categories. Finally, we describe the key role of transcriptional repression at all steps controlling neuronal diversity and propose that acquisition of neuronal identities could be considered a metastable process.
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Affiliation(s)
- Erick Sousa
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
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33
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Chen D, McManus CE, Radmanesh B, Matzat LH, Lei EP. Temporal inhibition of chromatin looping and enhancer accessibility during neuronal remodeling. Nat Commun 2021; 12:6366. [PMID: 34737269 PMCID: PMC8568962 DOI: 10.1038/s41467-021-26628-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/14/2021] [Indexed: 11/24/2022] Open
Abstract
During development, looping of an enhancer to a promoter is frequently observed in conjunction with temporal and tissue-specific transcriptional activation. The chromatin insulator-associated protein Alan Shepard (Shep) promotes Drosophila post-mitotic neuronal remodeling by repressing transcription of master developmental regulators, such as brain tumor (brat), specifically in maturing neurons. Since insulator proteins can promote looping, we hypothesized that Shep antagonizes brat promoter interaction with an as yet unidentified enhancer. Using chromatin conformation capture and reporter assays, we identified two enhancer regions that increase in looping frequency with the brat promoter specifically in pupal brains after Shep depletion. The brat promoters and enhancers function independently of Shep, ruling out direct repression of these elements. Moreover, ATAC-seq in isolated neurons demonstrates that Shep restricts chromatin accessibility of a key brat enhancer as well as other enhancers genome-wide in remodeling pupal but not larval neurons. These enhancers are enriched for chromatin targets of Shep and are located at Shep-inhibited genes, suggesting direct Shep inhibition of enhancer accessibility and gene expression during neuronal remodeling. Our results provide evidence for temporal regulation of chromatin looping and enhancer accessibility during neuronal maturation.
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Affiliation(s)
- Dahong Chen
- Nuclear Organization and Gene Expression Section, Bethesda, MD, USA
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Catherine E McManus
- Nuclear Organization and Gene Expression Section, Bethesda, MD, USA
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Behram Radmanesh
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, USA
| | - Leah H Matzat
- Nuclear Organization and Gene Expression Section, Bethesda, MD, USA
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, USA
| | - Elissa P Lei
- Nuclear Organization and Gene Expression Section, Bethesda, MD, USA.
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA.
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34
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Yousefi S, Deng R, Lanko K, Salsench EM, Nikoncuk A, van der Linde HC, Perenthaler E, van Ham TJ, Mulugeta E, Barakat TS. Comprehensive multi-omics integration identifies differentially active enhancers during human brain development with clinical relevance. Genome Med 2021; 13:162. [PMID: 34663447 PMCID: PMC8524963 DOI: 10.1186/s13073-021-00980-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/29/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Non-coding regulatory elements (NCREs), such as enhancers, play a crucial role in gene regulation, and genetic aberrations in NCREs can lead to human disease, including brain disorders. The human brain is a complex organ that is susceptible to numerous disorders; many of these are caused by genetic changes, but a multitude remain currently unexplained. Understanding NCREs acting during brain development has the potential to shed light on previously unrecognized genetic causes of human brain disease. Despite immense community-wide efforts to understand the role of the non-coding genome and NCREs, annotating functional NCREs remains challenging. METHODS Here we performed an integrative computational analysis of virtually all currently available epigenome data sets related to human fetal brain. RESULTS Our in-depth analysis unravels 39,709 differentially active enhancers (DAEs) that show dynamic epigenomic rearrangement during early stages of human brain development, indicating likely biological function. Many of these DAEs are linked to clinically relevant genes, and functional validation of selected DAEs in cell models and zebrafish confirms their role in gene regulation. Compared to enhancers without dynamic epigenomic rearrangement, DAEs are subjected to higher sequence constraints in humans, have distinct sequence characteristics and are bound by a distinct transcription factor landscape. DAEs are enriched for GWAS loci for brain-related traits and for genetic variation found in individuals with neurodevelopmental disorders, including autism. CONCLUSION This compendium of high-confidence enhancers will assist in deciphering the mechanism behind developmental genetics of human brain and will be relevant to uncover missing heritability in human genetic brain disorders.
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Affiliation(s)
- Soheil Yousefi
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Ruizhi Deng
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Kristina Lanko
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Eva Medico Salsench
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Anita Nikoncuk
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Herma C. van der Linde
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Elena Perenthaler
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Tjakko J. van Ham
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Eskeatnaf Mulugeta
- Department of Cell Biology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
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35
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de la Fuente Revenga M, Zhu B, Guevara CA, Naler LB, Saunders JM, Zhou Z, Toneatti R, Sierra S, Wolstenholme JT, Beardsley PM, Huntley GW, Lu C, González-Maeso J. Prolonged epigenomic and synaptic plasticity alterations following single exposure to a psychedelic in mice. Cell Rep 2021; 37:109836. [PMID: 34686347 PMCID: PMC8582597 DOI: 10.1016/j.celrep.2021.109836] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 07/21/2021] [Accepted: 09/24/2021] [Indexed: 12/20/2022] Open
Abstract
Clinical evidence suggests that rapid and sustained antidepressant action can be attained with a single exposure to psychedelics. However, the biological substrates and key mediators of psychedelics' enduring action remain unknown. Here, we show that a single administration of the psychedelic DOI produces fast-acting effects on frontal cortex dendritic spine structure and acceleration of fear extinction via the 5-HT2A receptor. Additionally, a single dose of DOI leads to changes in chromatin organization, particularly at enhancer regions of genes involved in synaptic assembly that stretch for days after the psychedelic exposure. These DOI-induced alterations in the neuronal epigenome overlap with genetic loci associated with schizophrenia, depression, and attention deficit hyperactivity disorder. Together, these data support that epigenomic-driven changes in synaptic plasticity sustain psychedelics' long-lasting antidepressant action but also warn about potential substrate overlap with genetic risks for certain psychiatric conditions.
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MESH Headings
- Amphetamines/pharmacology
- Animals
- Behavior, Animal/drug effects
- Dendritic Spines/drug effects
- Dendritic Spines/metabolism
- Epigenesis, Genetic/drug effects
- Epigenome/drug effects
- Epigenomics
- Extinction, Psychological/drug effects
- Fear/drug effects
- Frontal Lobe/drug effects
- Frontal Lobe/metabolism
- Hallucinogens/pharmacology
- Male
- Mice, 129 Strain
- Mice, Inbred C57BL
- Mice, Knockout
- Neuronal Plasticity/drug effects
- Receptor, Serotonin, 5-HT2A/drug effects
- Receptor, Serotonin, 5-HT2A/genetics
- Receptor, Serotonin, 5-HT2A/metabolism
- Serotonin 5-HT2 Receptor Agonists/pharmacology
- Synapses/drug effects
- Synapses/metabolism
- Time Factors
- Mice
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Affiliation(s)
- Mario de la Fuente Revenga
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA; Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Bohan Zhu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Christopher A Guevara
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lynette B Naler
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Justin M Saunders
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Zirui Zhou
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Rudy Toneatti
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Salvador Sierra
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Jennifer T Wolstenholme
- Department of Pharmacology and Toxicology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Patrick M Beardsley
- Department of Pharmacology and Toxicology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA; Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - George W Huntley
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Javier González-Maeso
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA.
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36
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Abstract
Nuclei are central hubs for information processing in eukaryotic cells. The need to fit large genomes into small nuclei imposes severe restrictions on genome organization and the mechanisms that drive genome-wide regulatory processes. How a disordered polymer such as chromatin, which has vast heterogeneity in its DNA and histone modification profiles, folds into discernibly consistent patterns is a fundamental question in biology. Outstanding questions include how genomes are spatially and temporally organized to regulate cellular processes with high precision and whether genome organization is causally linked to transcription regulation. The advent of next-generation sequencing, super-resolution imaging, multiplexed fluorescent in situ hybridization, and single-molecule imaging in individual living cells has caused a resurgence in efforts to understand the spatiotemporal organization of the genome. In this review, we discuss structural and mechanistic properties of genome organization at different length scales and examine changes in higher-order chromatin organization during important developmental transitions.
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Affiliation(s)
- Rajarshi P Ghosh
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA; ,
| | - Barbara J Meyer
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA; ,
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37
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Ludwig MQ, Todorov PV, Egerod KL, Olson DP, Pers TH. Single-Cell Mapping of GLP-1 and GIP Receptor Expression in the Dorsal Vagal Complex. Diabetes 2021; 70:1945-1955. [PMID: 34176785 PMCID: PMC8576419 DOI: 10.2337/dbi21-0003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/08/2021] [Indexed: 11/13/2022]
Abstract
The dorsal vagal complex (DVC) in the hindbrain, composed of the area postrema, nucleus of the solitary tract, and dorsal motor nucleus of the vagus, plays a critical role in modulating satiety. The incretins glucagon-like peptide 1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP) act directly in the brain to modulate feeding, and receptors for both are expressed in the DVC. Given the impressive clinical responses to pharmacologic manipulation of incretin signaling, understanding the central mechanisms by which incretins alter metabolism and energy balance is of critical importance. Here, we review recent single-cell approaches used to detect molecular signatures of GLP-1 and GIP receptor-expressing cells in the DVC. In addition, we discuss how current advancements in single-cell transcriptomics, epigenetics, spatial transcriptomics, and circuit mapping techniques have the potential to further characterize incretin receptor circuits in the hindbrain.
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Affiliation(s)
- Mette Q Ludwig
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Petar V Todorov
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Kristoffer L Egerod
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - David P Olson
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI
- Division of Pediatric Endocrinology, Department of Pediatrics, Michigan Medicine, Ann Arbor, MI
| | - Tune H Pers
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
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38
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Sarropoulos I, Sepp M, Frömel R, Leiss K, Trost N, Leushkin E, Okonechnikov K, Joshi P, Giere P, Kutscher LM, Cardoso-Moreira M, Pfister SM, Kaessmann H. Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells. Science 2021; 373:eabg4696. [PMID: 34446581 PMCID: PMC7611596 DOI: 10.1126/science.abg4696] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 07/14/2021] [Indexed: 12/13/2022]
Abstract
Organ development is orchestrated by cell- and time-specific gene regulatory networks. In this study, we investigated the regulatory basis of mouse cerebellum development from early neurogenesis to adulthood. By acquiring snATAC-seq (single-nucleus assay for transposase accessible chromatin using sequencing) profiles for ~90,000 cells spanning 11 stages, we mapped cerebellar cell types and identified candidate cis-regulatory elements (CREs). We detected extensive spatiotemporal heterogeneity among progenitor cells and a gradual divergence in the regulatory programs of cerebellar neurons during differentiation. Comparisons to vertebrate genomes and snATAC-seq profiles for ∼20,000 cerebellar cells from the marsupial opossum revealed a shared decrease in CRE conservation during development and differentiation as well as differences in constraint between cell types. Our work delineates the developmental and evolutionary dynamics of gene regulation in cerebellar cells and provides insights into mammalian organ development.
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Affiliation(s)
- Ioannis Sarropoulos
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany.
| | - Mari Sepp
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany.
| | - Robert Frömel
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Kevin Leiss
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Nils Trost
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Evgeny Leushkin
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center (KiTZ) Heidelberg, Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), and German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Piyush Joshi
- Hopp Children's Cancer Center (KiTZ) Heidelberg, Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), and German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Peter Giere
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Lena M Kutscher
- Hopp Children's Cancer Center (KiTZ) Heidelberg, Developmental Origins of Pediatric Cancer Group, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Margarida Cardoso-Moreira
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
- Evolutionary Developmental Biology Laboratory, Francis Crick Institute, London NW1 1AT, UK
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ) Heidelberg, Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), and German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany.
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany.
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39
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Kim B, Luo Y, Zhan X, Zhang Z, Shi X, Yi J, Xuan Z, Wu J. Neuronal activity-induced BRG1 phosphorylation regulates enhancer activation. Cell Rep 2021; 36:109357. [PMID: 34260936 PMCID: PMC8315893 DOI: 10.1016/j.celrep.2021.109357] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/16/2021] [Accepted: 06/17/2021] [Indexed: 11/30/2022] Open
Abstract
Neuronal activity-induced enhancers drive gene activation. We demonstrate that BRG1, the core subunit of SWI/SNF-like BAF ATP-dependent chromatin remodeling complexes, regulates neuronal activity-induced enhancers. Upon stimulation, BRG1 is recruited to enhancers in an H3K27Ac-dependent manner. BRG1 regulates enhancer basal activities and inducibility by affecting cohesin binding, enhancer-promoter looping, RNA polymerase II recruitment, and enhancer RNA expression. We identify a serine phosphorylation site in BRG1 that is induced by neuronal stimulations and is sensitive to CaMKII inhibition. BRG1 phosphorylation affects its interaction with several transcription co-factors, including the NuRD repressor complex and cohesin, possibly modulating BRG1-mediated transcription outcomes. Using mice with knockin mutations, we show that non-phosphorylatable BRG1 fails to efficiently induce activity-dependent genes, whereas phosphomimic BRG1 increases enhancer activity and inducibility. These mutant mice display anxiety-like phenotypes and altered responses to stress. Therefore, we reveal a mechanism connecting neuronal signaling to enhancer activities through BRG1 phosphorylation.
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Affiliation(s)
- BongWoo Kim
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yi Luo
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zilai Zhang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xuanming Shi
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiaqing Yi
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhenyu Xuan
- Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Jiang Wu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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40
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McKinney RM, Valdez R, Ben-Shahar Y. The genetic architecture of larval aggregation behavior in Drosophila. J Neurogenet 2021; 35:274-284. [PMID: 33629904 DOI: 10.1080/01677063.2021.1887174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Many insect species exhibit basal social behaviors such as aggregation, which play important roles in their feeding and mating ecologies. However, the evolutionary, genetic, and physiological mechanisms that regulate insect aggregation remain unknown for most species. Here, we used natural populations of Drosophila melanogaster to identify the genetic architecture that drives larval aggregation feeding behavior. By using quantitative and reverse genetic approaches, we have identified a complex neurogenetic network that plays a role in regulating the decision of larvae to feed in either solitude or as a group. Results from single gene, RNAi-knockdown experiments show that several of the identified genes represent key nodes in the genetic network that determines the level of aggregation while feeding. Furthermore, we show that a single non-coding variant in the gene CG14205, a putative acyltransferase, is associated with both decreased mRNA expression and increased aggregate formation, which suggests that it has a specific role in inhibiting aggregation behavior. Our results identify, for the first time, the genetic components which interact to regulate naturally occurring levels of aggregation in D. melanogaster larvae.
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Affiliation(s)
- Ross M McKinney
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Ryan Valdez
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Yehuda Ben-Shahar
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
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41
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Tuvikene J, Esvald EE, Rähni A, Uustalu K, Zhuravskaya A, Avarlaid A, Makeyev EV, Timmusk T. Intronic enhancer region governs transcript-specific Bdnf expression in rodent neurons. eLife 2021; 10:65161. [PMID: 33560226 PMCID: PMC7891933 DOI: 10.7554/elife.65161] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/08/2021] [Indexed: 12/14/2022] Open
Abstract
Brain-derived neurotrophic factor (BDNF) controls the survival, growth, and function of neurons both during the development and in the adult nervous system. Bdnf is transcribed from several distinct promoters generating transcripts with alternative 5' exons. Bdnf transcripts initiated at the first cluster of exons have been associated with the regulation of body weight and various aspects of social behavior, but the mechanisms driving the expression of these transcripts have remained poorly understood. Here, we identify an evolutionarily conserved intronic enhancer region inside the Bdnf gene that regulates both basal and stimulus-dependent expression of the Bdnf transcripts starting from the first cluster of 5' exons in mouse and rat neurons. We further uncover a functional E-box element in the enhancer region, linking the expression of Bdnf and various pro-neural basic helix–loop–helix transcription factors. Collectively, our results shed new light on the cell-type- and stimulus-specific regulation of the important neurotrophic factor BDNF.
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Affiliation(s)
- Jürgen Tuvikene
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia.,Protobios LLC, Tallinn, Estonia
| | - Eli-Eelika Esvald
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia.,Protobios LLC, Tallinn, Estonia
| | - Annika Rähni
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Kaie Uustalu
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Anna Zhuravskaya
- Centre for Developmental Neurobiology, King's College London, London, United Kingdom
| | - Annela Avarlaid
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology, King's College London, London, United Kingdom
| | - Tõnis Timmusk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia.,Protobios LLC, Tallinn, Estonia
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42
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Armand EJ, Li J, Xie F, Luo C, Mukamel EA. Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes. Neuron 2021; 109:11-26. [PMID: 33412093 PMCID: PMC7808568 DOI: 10.1016/j.neuron.2020.12.010] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/17/2020] [Accepted: 12/08/2020] [Indexed: 12/21/2022]
Abstract
Single-cell sequencing technologies, including transcriptomic and epigenomic assays, are transforming our understanding of the cellular building blocks of neural circuits. By directly measuring multiple molecular signatures in thousands to millions of individual cells, single-cell sequencing methods can comprehensively characterize the diversity of brain cell types. These measurements uncover gene regulatory mechanisms that shape cellular identity and provide insight into developmental and evolutionary relationships between brain cell populations. Single-cell sequencing data can aid the design of tools for targeted functional studies of brain circuit components, linking molecular signatures with anatomy, connectivity, morphology, and physiology. Here, we discuss the fundamental principles of single-cell transcriptome and epigenome sequencing, integrative computational analysis of the data, and key applications in neuroscience.
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Affiliation(s)
- Ethan J Armand
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92037, USA
| | - Junhao Li
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92037, USA
| | - Fangming Xie
- Department of Physics, University of California, San Diego, La Jolla, CA 92037, USA
| | - Chongyuan Luo
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Eran A Mukamel
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92037, USA.
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43
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Lambert JT, Su-Feher L, Cichewicz K, Warren TL, Zdilar I, Wang Y, Lim KJ, Haigh JL, Morse SJ, Canales CP, Stradleigh TW, Castillo Palacios E, Haghani V, Moss SD, Parolini H, Quintero D, Shrestha D, Vogt D, Byrne LC, Nord AS. Parallel functional testing identifies enhancers active in early postnatal mouse brain. eLife 2021; 10:69479. [PMID: 34605404 PMCID: PMC8577842 DOI: 10.7554/elife.69479] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/02/2021] [Indexed: 01/07/2023] Open
Abstract
Enhancers are cis-regulatory elements that play critical regulatory roles in modulating developmental transcription programs and driving cell-type-specific and context-dependent gene expression in the brain. The development of massively parallel reporter assays (MPRAs) has enabled high-throughput functional screening of candidate DNA sequences for enhancer activity. Tissue-specific screening of in vivo enhancer function at scale has the potential to greatly expand our understanding of the role of non-coding sequences in development, evolution, and disease. Here, we adapted a self-transcribing regulatory element MPRA strategy for delivery to early postnatal mouse brain via recombinant adeno-associated virus (rAAV). We identified and validated putative enhancers capable of driving reporter gene expression in mouse forebrain, including regulatory elements within an intronic CACNA1C linkage disequilibrium block associated with risk in neuropsychiatric disorder genetic studies. Paired screening and single enhancer in vivo functional testing, as we show here, represents a powerful approach towards characterizing regulatory activity of enhancers and understanding how enhancer sequences organize gene expression in the brain.
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Affiliation(s)
- Jason T Lambert
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Linda Su-Feher
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Karol Cichewicz
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Tracy L Warren
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Iva Zdilar
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Yurong Wang
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Kenneth J Lim
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Jessica L Haigh
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Sarah J Morse
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Cesar P Canales
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Tyler W Stradleigh
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Erika Castillo Palacios
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Viktoria Haghani
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Spencer D Moss
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Hannah Parolini
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Diana Quintero
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Diwash Shrestha
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Daniel Vogt
- Department of Pediatrics and Human Development, Grand Rapids Research Center, Michigan State UniversityGrand RapidsUnited States
| | - Leah C Byrne
- Helen Wills Neuroscience Institute, University of California, BerkeleyBerkeleyUnited States,Departments of Ophthalmology and Neurobiology, University of PittsburghPittsburghUnited States
| | - Alex S Nord
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
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44
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Spiegel I. Experience-regulated molecular mechanisms in cortical GABAergic interneurons: from cellular functions to control over circuit plasticity. Curr Opin Neurobiol 2020; 67:145-154. [PMID: 33316573 DOI: 10.1016/j.conb.2020.11.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 11/10/2020] [Accepted: 11/15/2020] [Indexed: 01/30/2023]
Abstract
Experience-induced changes in GABAergic interneurons (INs) are thought to control the plasticity of neural circuits in the developing and adult cortex. However, it remains poorly understood how experience and the ensuing neuronal activity alter the properties and connectivity of specific IN subtypes and how these cellular changes, in turn, control the plasticity of cortical circuits. Here, I discuss recent experimental and theoretical studies that point to specific experience-induced changes in select IN subtypes as central regulators of plasticity in the cortex. In particular, I focus on the recent identification of several experience-regulated secreted molecules that modulate specific sets of synapses in IN subtypes. I argue that elucidating these molecular mechanisms will allow us to test experimentally the predictions made by theoretical models about the plasticity functions of specific IN subtypes.
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Affiliation(s)
- Ivo Spiegel
- Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel.
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45
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Christian DL, Wu DY, Martin JR, Moore JR, Liu YR, Clemens AW, Nettles SA, Kirkland NM, Papouin T, Hill CA, Wozniak DF, Dougherty JD, Gabel HW. DNMT3A Haploinsufficiency Results in Behavioral Deficits and Global Epigenomic Dysregulation Shared across Neurodevelopmental Disorders. Cell Rep 2020; 33:108416. [PMID: 33238114 PMCID: PMC7716597 DOI: 10.1016/j.celrep.2020.108416] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 09/17/2020] [Accepted: 10/29/2020] [Indexed: 12/19/2022] Open
Abstract
Mutations in DNA methyltransferase 3A (DNMT3A) have been detected in autism and related disorders, but how these mutations disrupt nervous system function is unknown. Here, we define the effects of DNMT3A mutations associated with neurodevelopmental disease. We show that diverse mutations affect different aspects of protein activity but lead to shared deficiencies in neuronal DNA methylation. Heterozygous DNMT3A knockout mice mimicking DNMT3A disruption in disease display growth and behavioral alterations consistent with human phenotypes. Strikingly, in these mice, we detect global disruption of neuron-enriched non-CG DNA methylation, a binding site for the Rett syndrome protein MeCP2. Loss of this methylation leads to enhancer and gene dysregulation that overlaps with models of Rett syndrome and autism. These findings define the effects of DNMT3A haploinsufficiency in the brain and uncover disruption of the non-CG methylation pathway as a convergence point across neurodevelopmental disorders.
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Affiliation(s)
- Diana L Christian
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Dennis Y Wu
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Jenna R Martin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - J Russell Moore
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Yiran R Liu
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Adam W Clemens
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Sabin A Nettles
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Nicole M Kirkland
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Thomas Papouin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Cheryl A Hill
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - David F Wozniak
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110-1093, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110-1093, USA; Taylor Family Institute for Innovative Psychiatric Research, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Joseph D Dougherty
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110-1093, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA.
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46
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Alcalà-Vida R, Awada A, Boutillier AL, Merienne K. Epigenetic mechanisms underlying enhancer modulation of neuronal identity, neuronal activity and neurodegeneration. Neurobiol Dis 2020; 147:105155. [PMID: 33127472 DOI: 10.1016/j.nbd.2020.105155] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 02/08/2023] Open
Abstract
Neurodegenerative diseases, including Huntington's disease (HD) and Alzheimer's disease (AD), are progressive conditions characterized by selective, disease-dependent loss of neuronal regions and/or subpopulations. Neuronal loss is preceded by a long period of neuronal dysfunction, during which glial cells also undergo major changes, including neuroinflammatory response. Those dramatic changes affecting both neuronal and glial cells associate with epigenetic and transcriptional dysregulations, characterized by defined cell-type-specific signatures. Notably, increasing studies support the view that altered regulation of transcriptional enhancers, which are distal regulatory regions of the genome capable of modulating the activity of promoters through chromatin looping, play a critical role in transcriptional dysregulation in HD and AD. We review current knowledge on enhancers in HD and AD, and highlight challenging issues to better decipher the epigenetic code of neurodegenerative diseases.
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Affiliation(s)
- Rafael Alcalà-Vida
- LNCA, University of Strasbourg, France; CNRS UMR 7364, Strasbourg, France
| | - Ali Awada
- LNCA, University of Strasbourg, France; CNRS UMR 7364, Strasbourg, France
| | | | - Karine Merienne
- LNCA, University of Strasbourg, France; CNRS UMR 7364, Strasbourg, France.
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47
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Arzate-Mejía RG, Lottenbach Z, Schindler V, Jawaid A, Mansuy IM. Long-Term Impact of Social Isolation and Molecular Underpinnings. Front Genet 2020; 11:589621. [PMID: 33193727 PMCID: PMC7649797 DOI: 10.3389/fgene.2020.589621] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/28/2020] [Indexed: 11/17/2022] Open
Abstract
Prolonged periods of social isolation can have detrimental effects on the physiology and behavior of exposed individuals in humans and animal models. This involves complex molecular mechanisms across tissues in the body which remain partly identified. This review discusses the biology of social isolation and describes the acute and lasting effects of prolonged periods of social isolation with a focus on the molecular events leading to behavioral alterations. We highlight the role of epigenetic mechanisms and non-coding RNA in the control of gene expression as a response to social isolation, and the consequences for behavior. Considering the use of strict quarantine during epidemics, like currently with COVID-19, we provide a cautionary tale on the indiscriminate implementation of such form of social isolation and its potential damaging and lasting effects in mental health.
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Affiliation(s)
- Rodrigo G Arzate-Mejía
- Laboratory of Neuroepigenetics, Medical Faculty of the University of Zurich and Department of Health Science and Technology of the Swiss Federal Institute of Technology, Neuroscience Center Zurich, Zurich, Switzerland
| | | | | | - Ali Jawaid
- Laboratory of Neuroepigenetics, Medical Faculty of the University of Zurich and Department of Health Science and Technology of the Swiss Federal Institute of Technology, Neuroscience Center Zurich, Zurich, Switzerland
| | - Isabelle M Mansuy
- Laboratory of Neuroepigenetics, Medical Faculty of the University of Zurich and Department of Health Science and Technology of the Swiss Federal Institute of Technology, Neuroscience Center Zurich, Zurich, Switzerland
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48
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Interpreting the impact of noncoding structural variation in neurodevelopmental disorders. Genet Med 2020; 23:34-46. [PMID: 32973355 PMCID: PMC7790743 DOI: 10.1038/s41436-020-00974-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/03/2020] [Accepted: 09/14/2020] [Indexed: 12/21/2022] Open
Abstract
The emergence of novel sequencing technologies has greatly improved the identification of structural variation, revealing that a human genome harbors tens of thousands of structural variants (SVs). Since these SVs primarily impact noncoding DNA sequences, the next challenge is one of interpretation, not least to improve our understanding of human disease etiology. However, this task is severely complicated by the intricacy of the gene regulatory landscapes embedded within these noncoding regions, their incomplete annotation, as well as their dependence on the three-dimensional (3D) conformation of the genome. Also in the context of neurodevelopmental disorders (NDDs), reports of putatively causal, noncoding SVs are accumulating and understanding their impact on transcriptional regulation is presenting itself as the next step toward improved genetic diagnosis.
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49
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Miesfeld JB, Ghiasvand NM, Marsh-Armstrong B, Marsh-Armstrong N, Miller EB, Zhang P, Manna SK, Zawadzki RJ, Brown NL, Glaser T. The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development. Proc Natl Acad Sci U S A 2020; 117:21690-21700. [PMID: 32817515 PMCID: PMC7474671 DOI: 10.1073/pnas.2006888117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The retinal ganglion cell (RGC) competence factor ATOH7 is dynamically expressed during retinal histogenesis. ATOH7 transcription is controlled by a promoter-adjacent primary enhancer and a remote shadow enhancer (SE). Deletion of the ATOH7 human SE causes nonsyndromic congenital retinal nonattachment (NCRNA) disease, characterized by optic nerve aplasia and total blindness. We used genome editing to model NCRNA in mice. Deletion of the murine SE reduces Atoh7 messenger RNA (mRNA) fivefold but does not recapitulate optic nerve loss; however, SEdel/knockout (KO) trans heterozygotes have thin optic nerves. By analyzing Atoh7 mRNA and protein levels, RGC development and survival, and chromatin landscape effects, we show that the SE ensures robust Atoh7 transcriptional output. Combining SE deletion and KO and wild-type alleles in a genotypic series, we determined the amount of Atoh7 needed to produce a normal complement of adult RGCs, and the secondary consequences of graded reductions in Atoh7 dosage. Together, these data reveal the workings of an evolutionary fail-safe, a duplicate enhancer mechanism that is hard-wired in the machinery of vertebrate retinal ganglion cell genesis.
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Affiliation(s)
- Joel B Miesfeld
- Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Davis, CA 95616
| | - Noor M Ghiasvand
- Department of Biology, Grand Valley State University, Allendale, MI 49401
- Functional Neurosurgery Research Center, Shohada Tajrish Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Brennan Marsh-Armstrong
- Department of Ophthalmology and Vision Science, University of California Davis School of Medicine, Sacramento, CA 95817
| | - Nicholas Marsh-Armstrong
- Department of Ophthalmology and Vision Science, University of California Davis School of Medicine, Sacramento, CA 95817
| | - Eric B Miller
- Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Davis, CA 95616
| | - Pengfei Zhang
- Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Davis, CA 95616
| | - Suman K Manna
- Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Davis, CA 95616
| | - Robert J Zawadzki
- Department of Ophthalmology and Vision Science, University of California Davis School of Medicine, Sacramento, CA 95817
| | - Nadean L Brown
- Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Davis, CA 95616
| | - Tom Glaser
- Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Davis, CA 95616;
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50
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Inglis GAS, Zhou Y, Patterson DG, Scharer CD, Han Y, Boss JM, Wen Z, Escayg A. Transcriptomic and epigenomic dynamics associated with development of human iPSC-derived GABAergic interneurons. Hum Mol Genet 2020; 29:2579-2595. [PMID: 32794569 PMCID: PMC7471504 DOI: 10.1093/hmg/ddaa150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/09/2020] [Accepted: 07/11/2020] [Indexed: 12/13/2022] Open
Abstract
GABAergic interneurons (GINs) are a heterogeneous population of inhibitory neurons that collectively contribute to the maintenance of normal neuronal excitability and network activity. Identification of the genetic regulatory elements and transcription factors that contribute toward GIN function may provide new insight into the pathways underlying proper GIN activity while also indicating potential therapeutic targets for GIN-associated disorders, such as schizophrenia and epilepsy. In this study, we examined the temporal changes in gene expression and chromatin accessibility during GIN development by performing transcriptomic and epigenomic analyses on human induced pluripotent stem cell-derived neurons at 22, 50 and 78 days (D) post-differentiation. We observed 13 221 differentially accessible regions (DARs) of chromatin that associate with temporal changes in gene expression at D78 and D50, relative to D22. We also classified families of transcription factors that are increasingly enriched at DARs during differentiation, indicating regulatory networks that likely drive GIN development. Collectively, these data provide a resource for examining the molecular networks regulating GIN functionality.
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Affiliation(s)
- George Andrew S Inglis
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ying Zhou
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30329, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Dillon G Patterson
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yanfei Han
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30329, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Zhexing Wen
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30329, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andrew Escayg
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
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