51
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Xiong L, Xu K, Tian K, Shao Y, Tang L, Gao G, Zhang M, Jiang T, Zhang QC. SCALE method for single-cell ATAC-seq analysis via latent feature extraction. Nat Commun 2019; 10:4576. [PMID: 31594952 PMCID: PMC6783552 DOI: 10.1038/s41467-019-12630-7] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/20/2019] [Indexed: 12/31/2022] Open
Abstract
Single-cell ATAC-seq (scATAC-seq) profiles the chromatin accessibility landscape at single cell level, thus revealing cell-to-cell variability in gene regulation. However, the high dimensionality and sparsity of scATAC-seq data often complicate the analysis. Here, we introduce a method for analyzing scATAC-seq data, called Single-Cell ATAC-seq analysis via Latent feature Extraction (SCALE). SCALE combines a deep generative framework and a probabilistic Gaussian Mixture Model to learn latent features that accurately characterize scATAC-seq data. We validate SCALE on datasets generated on different platforms with different protocols, and having different overall data qualities. SCALE substantially outperforms the other tools in all aspects of scATAC-seq data analysis, including visualization, clustering, and denoising and imputation. Importantly, SCALE also generates interpretable features that directly link to cell populations, and can potentially reveal batch effects in scATAC-seq experiments.
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Affiliation(s)
- Lei Xiong
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Kui Xu
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Kang Tian
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Yanqiu Shao
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Lei Tang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Ge Gao
- Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), Peking University, 100871, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, 100871, Beijing, China
| | - Michael Zhang
- Bioinformatics Division, BNRist, Department of Automation, Tsinghua University, 100084, Beijing, China
- Department of Biological Sciences, Center for Systems Biology, The University of Texas, Dallas 800 West Campbell Road, RL11, Richardson, TX, 75080-3021, USA
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Tao Jiang
- Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA
- Bioinformatics Division, BNRIST; Department of Computer Science and Technology, Tsinghua University, 100084, Beijing, China
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084, Beijing, China.
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52
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Huang ZJ, Paul A. The diversity of GABAergic neurons and neural communication elements. Nat Rev Neurosci 2019; 20:563-572. [PMID: 31222186 PMCID: PMC8796706 DOI: 10.1038/s41583-019-0195-4] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2019] [Indexed: 12/18/2022]
Abstract
The phenotypic diversity of cortical GABAergic neurons is probably necessary for their functional versatility in shaping the spatiotemporal dynamics of neural circuit operations underlying cognition. Deciphering the logic of this diversity requires comprehensive analysis of multi-modal cell features and a framework of neuronal identity that reflects biological mechanisms and principles. Recent high-throughput single-cell analyses have generated unprecedented data sets characterizing the transcriptomes, morphology and electrophysiology of interneurons. We posit that cardinal interneuron types can be defined by their synaptic communication properties, which are encoded in key transcriptional signatures. This conceptual framework integrates multi-modal cell features, captures neuronal input-output properties fundamental to circuit operation and may advance understanding of the appropriate granularity of neuron types, towards a biologically grounded and operationally useful interneuron taxonomy.
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Affiliation(s)
- Z Josh Huang
- Cold Spring Harbor Laboratory, New York, NY, USA.
| | - Anirban Paul
- Cold Spring Harbor Laboratory, New York, NY, USA
- Department of Neural & Behavioral Sciences, Penn State University College of Medicine, Hershey, PA, USA
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53
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Wei CL, Nicolis SK, Zhu Y, Pagin M. Sox2-Dependent 3D Chromatin Interactomes in Transcription, Neural Stem Cell Proliferation and Neurodevelopmental Diseases. J Exp Neurosci 2019; 13:1179069519868224. [PMID: 31431802 PMCID: PMC6686325 DOI: 10.1177/1179069519868224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 07/15/2019] [Indexed: 11/16/2022] Open
Abstract
In our article, we asked whether Sox2, a transcription factor important in brain
development and disease, is involved in gene regulation through its action on
long-range interactions between promoters and distant enhancers. Our findings
highlight that Sox2 shapes a genome-wide network of promoter-enhancer
interactions, acting by direct binding to these elements. Sox2 loss affects the
three-dimensional (3D) genome and decreases the activity of a subset of genes
involved in Sox2-bound interactions. At least one of such downregulated genes,
Socs3, is critical for long-term neural stem cell
maintenance. These results point to the possibility of identifying a
transcriptional network downstream to Sox2, and involved in neural stem cell
maintenance. In addition, interacting Sox2-bound enhancers are often connected
to genes which are relevant, in man, to neurodevelopmental disease; this may
facilitate the detection of functionally relevant mutations in regulatory
elements in man, contributing to neural disease.
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Affiliation(s)
- Chia-Lin Wei
- Department of Genome Technologies, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Silvia K Nicolis
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
| | - Yanfen Zhu
- Department of Genome Technologies, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Miriam Pagin
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
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54
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Sestan N, State MW. Lost in Translation: Traversing the Complex Path from Genomics to Therapeutics in Autism Spectrum Disorder. Neuron 2019; 100:406-423. [PMID: 30359605 DOI: 10.1016/j.neuron.2018.10.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/29/2018] [Accepted: 10/08/2018] [Indexed: 12/24/2022]
Abstract
Recent progress in the genomics of non-syndromic autism spectrum disorder (nsASD) highlights rare, large-effect, germline, heterozygous de novo coding mutations. This distinguishes nsASD from later-onset psychiatric disorders where gene discovery efforts have predominantly yielded common alleles of small effect. These differences point to distinctive opportunities for clarifying the neurobiology of nsASD and developing novel treatments. We argue that the path ahead also presents key challenges, including distinguishing human pathophysiology from the potentially pleiotropic neurobiology mediated by established risk genes. We present our view of some of the conceptual limitations of traditional studies of model organisms, suggest a strategy focused on investigating the convergence of multiple nsASD genes, and propose that the detailed characterization of the molecular and cellular landscapes of developing human brain is essential to illuminate disease mechanisms. Finally, we address how recent advances are leading to novel strategies for therapeutics that target various points along the path from genes to behavior.
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Affiliation(s)
- Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Departments of Genetics, of Psychiatry, and of Comparative Medicine, Program in Cellular Neuroscience, Neurodegeneration and Repair, and Yale Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA.
| | - Matthew W State
- Department of Psychiatry, Langley Porter Psychiatric Institute, Quantitative Biosciences Institute, Institute for Human Genetics, and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA.
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55
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Caporale AL, Gonda CM, Franchini LF. Transcriptional Enhancers in the FOXP2 Locus Underwent Accelerated Evolution in the Human Lineage. Mol Biol Evol 2019; 36:2432-2450. [PMID: 31359064 DOI: 10.1093/molbev/msz173] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 04/26/2019] [Accepted: 07/16/2019] [Indexed: 12/11/2022] Open
Abstract
Unique human features such as complex language are the result of molecular evolutionary changes that modified developmental programs of our brain. The human-specific evolution of the forkhead box P2 (FOXP2) gene coding region has been linked to the emergence of speech and language in the human kind. However, little is known about how the expression of FOXP2 is regulated and if its regulatory machinery evolved in a lineage-specific manner in humans. In order to identify FOXP2 regulatory regions containing human-specific changes we used databases of human accelerated non-coding sequences or HARs. We found that the topologically associating domain (TAD) determined using developing human cerebral cortex containing the FOXP2 locus includes two clusters of 12 HARs, placing the locus occupied by FOXP2 among the top regions showing fast acceleration rates in non-coding regions in the human genome. Using in vivo enhancer assays in zebrafish, we found that at least five FOXP2-HARs behave as transcriptional enhancers throughout different developmental stages. In addition, we found that at least two FOXP2-HARs direct the expression of the reporter gene EGFP to foxP2 expressing regions and cells. Moreover, we uncovered two FOXP2-HARs showing reporter expression gain of function in the nervous system when compared with the chimpanzee ortholog sequences. Our results indicate that regulatory sequences in the FOXP2 locus underwent a human-specific evolutionary process suggesting that the transcriptional machinery controlling this gene could have also evolved differentially in the human lineage.
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Affiliation(s)
- Alfredo Leandro Caporale
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Catalina M Gonda
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Lucía Florencia Franchini
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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56
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Shen T, Ji F, Wang Y, Lei X, Zhang D, Jiao J. Brain-specific deletion of histone variant H2A.z results in cortical neurogenesis defects and neurodevelopmental disorder. Nucleic Acids Res 2019; 46:2290-2307. [PMID: 29294103 PMCID: PMC5861433 DOI: 10.1093/nar/gkx1295] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/19/2017] [Indexed: 12/14/2022] Open
Abstract
Defects in neurogenesis alter brain circuit formations and may lead to neurodevelopmental disorders such as autism and schizophrenia. Histone H2A.z, a variant of histone H2A, plays critical roles in chromatin structure and epigenetic regulation, but its function and mechanism in brain development remain largely unknown. Here, we find that the deletion of H2A.z results in enhanced proliferation of neural progenitors but reduced neuronal differentiation. In addition, neurons in H2A.z knockout mice exhibit abnormal dendrites during brain development. Furthermore, H2A.zcKO mice exhibit serial behavioral deficits, such as decreased exploratory activity and impaired learning and memory. Mechanistically, H2A.z regulates embryonic neurogenesis by targeting Nkx2–4 through interaction with Setd2, thereby promoting H3K36me3 modification to activate the transcription of Nkx2–4. Furthermore, enforced expression of Nkx2–4 can rescue the defective neurogenesis in the H2A.z-knockdown embryonic brain. Together, our findings implicate the epigenetic regulation by H2A.z in embryonic neurogenesis and provide a framework for understanding how disruption in the H2A.z gene may contribute to neurological disorders.
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Affiliation(s)
- Tianjin Shen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fen Ji
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanyuan Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuepei Lei
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongming Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianwei Jiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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57
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Hemming IA, Clément O, Gladwyn-Ng IE, Cullen HD, Ng HL, See HB, Ngo L, Ulgiati D, Pfleger KDG, Agostino M, Heng JIT. Disease-associated missense variants in ZBTB18 disrupt DNA binding and impair the development of neurons within the embryonic cerebral cortex. Hum Mutat 2019; 40:1841-1855. [PMID: 31112317 DOI: 10.1002/humu.23803] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 05/08/2019] [Accepted: 05/19/2019] [Indexed: 12/12/2022]
Abstract
The activities of DNA-binding transcription factors, such as the multi-zinc-finger protein ZBTB18 (also known as RP58, or ZNF238), are essential to coordinate mammalian neurodevelopment, including the birth and radial migration of newborn neurons within the fetal brain. In humans, the majority of disease-associated missense mutations in ZBTB18 lie within the DNA-binding zinc-finger domain and are associated with brain developmental disorder, yet the molecular mechanisms explaining their role in disease remain unclear. To address this, we developed in silico models of ZBTB18, bound to DNA, and discovered that half of the missense variants map to residues (Asn461, Arg464, Glu486) predicted to be essential to sequence-specific DNA contact, whereas others map to residues (Leu434, Tyr447, Arg495) with limited contributions to DNA binding. We studied pathogenic variants to residues with close (N461S) and limited (R495G) DNA contact and found that each bound DNA promiscuously, displayed altered transcriptional regulatory activity in vitro, and influenced the radial migration of newborn neurons in vivo in different ways. Taken together, our results suggest that altered transcriptional regulation could represent an important pathological mechanism for ZBTB18 missense variants in brain developmental disease.
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Affiliation(s)
- Isabel A Hemming
- Molecular Medicine Division, QEII Medical Centre, The Harry Perkins Institute of Medical Research, Nedlands, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, Australia.,Faculty of Health and Medical Sciences, Medical School, The University of Western Australia, Crawley, Australia
| | - Olivier Clément
- Molecular Medicine Division, QEII Medical Centre, The Harry Perkins Institute of Medical Research, Nedlands, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, Australia.,Faculty of Health and Medical Sciences, Medical School, The University of Western Australia, Crawley, Australia.,School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Australia
| | - Ivan E Gladwyn-Ng
- Molecular Medicine Division, QEII Medical Centre, The Harry Perkins Institute of Medical Research, Nedlands, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, Australia
| | - Hayley D Cullen
- Molecular Medicine Division, QEII Medical Centre, The Harry Perkins Institute of Medical Research, Nedlands, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, Australia.,Faculty of Health and Medical Sciences, Medical School, The University of Western Australia, Crawley, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, Australia
| | - Han Leng Ng
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Australia
| | - Heng B See
- Molecular Medicine Division, QEII Medical Centre, The Harry Perkins Institute of Medical Research, Nedlands, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, Australia
| | - Linh Ngo
- Molecular Medicine Division, QEII Medical Centre, The Harry Perkins Institute of Medical Research, Nedlands, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, Australia
| | - Daniela Ulgiati
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Australia
| | - Kevin D G Pfleger
- Molecular Medicine Division, QEII Medical Centre, The Harry Perkins Institute of Medical Research, Nedlands, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, Australia.,ARC Centre for Personalised Therapeutics Technologies, Melbourne, Australia
| | - Mark Agostino
- Curtin Health Innovation Research Institute, Curtin University, Bentley, Australia.,School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Australia.,Curtin Institute for Computation, Curtin University, Bentley, Australia
| | - Julian I-T Heng
- Curtin Health Innovation Research Institute, Curtin University, Bentley, Australia.,ARC Centre for Personalised Therapeutics Technologies, Melbourne, Australia.,School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Australia
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58
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Wei S, Du H, Li Z, Tao G, Xu Z, Song X, Shang Z, Su Z, Chen H, Wen Y, Liu G, You Y, Zhang Z, Yang Z. Transcription factors
Sp8
and
Sp9
regulate the development of caudal ganglionic eminence‐derived cortical interneurons. J Comp Neurol 2019; 527:2860-2874. [DOI: 10.1002/cne.24712] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/16/2019] [Accepted: 05/03/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Song Wei
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, MOE Frontier Research Center for Brain Science, Department of Neurology, Zhongshan HospitalFudan University Shanghai China
| | - Heng Du
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, MOE Frontier Research Center for Brain Science, Department of Neurology, Zhongshan HospitalFudan University Shanghai China
| | - Zhenmeiyu Li
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, MOE Frontier Research Center for Brain Science, Department of Neurology, Zhongshan HospitalFudan University Shanghai China
| | - Guangxu Tao
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, MOE Frontier Research Center for Brain Science, Department of Neurology, Zhongshan HospitalFudan University Shanghai China
| | - Zhejun Xu
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, MOE Frontier Research Center for Brain Science, Department of Neurology, Zhongshan HospitalFudan University Shanghai China
| | - Xiaolei Song
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, MOE Frontier Research Center for Brain Science, Department of Neurology, Zhongshan HospitalFudan University Shanghai China
| | - Zicong Shang
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, MOE Frontier Research Center for Brain Science, Department of Neurology, Zhongshan HospitalFudan University Shanghai China
| | - Zihao Su
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, MOE Frontier Research Center for Brain Science, Department of Neurology, Zhongshan HospitalFudan University Shanghai China
| | - Haotian Chen
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, MOE Frontier Research Center for Brain Science, Department of Neurology, Zhongshan HospitalFudan University Shanghai China
| | - Yan Wen
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, MOE Frontier Research Center for Brain Science, Department of Neurology, Zhongshan HospitalFudan University Shanghai China
| | - Guoping Liu
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, MOE Frontier Research Center for Brain Science, Department of Neurology, Zhongshan HospitalFudan University Shanghai China
| | - Yan You
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, MOE Frontier Research Center for Brain Science, Department of Neurology, Zhongshan HospitalFudan University Shanghai China
| | - Zhuangzhi Zhang
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, MOE Frontier Research Center for Brain Science, Department of Neurology, Zhongshan HospitalFudan University Shanghai China
| | - Zhengang Yang
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, MOE Frontier Research Center for Brain Science, Department of Neurology, Zhongshan HospitalFudan University Shanghai China
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59
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Egervari G, Kozlenkov A, Dracheva S, Hurd YL. Molecular windows into the human brain for psychiatric disorders. Mol Psychiatry 2019; 24:653-673. [PMID: 29955163 PMCID: PMC6310674 DOI: 10.1038/s41380-018-0125-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 05/14/2018] [Accepted: 06/05/2018] [Indexed: 12/20/2022]
Abstract
Delineating the pathophysiology of psychiatric disorders has been extremely challenging but technological advances in recent decades have facilitated a deeper interrogation of molecular processes in the human brain. Initial candidate gene expression studies of the postmortem brain have evolved into genome wide profiling of the transcriptome and the epigenome, a critical regulator of gene expression. Here, we review the potential and challenges of direct molecular characterization of the postmortem human brain, and provide a brief overview of recent transcriptional and epigenetic studies with respect to neuropsychiatric disorders. Such information can now be leveraged and integrated with the growing number of genome-wide association databases to provide a functional context of trait-associated genetic variants linked to psychiatric illnesses and related phenotypes. While it is clear that the field is still developing and challenges remain to be surmounted, these recent advances nevertheless hold tremendous promise for delineating the neurobiological underpinnings of mental diseases and accelerating the development of novel medication strategies.
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Affiliation(s)
- Gabor Egervari
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Addiction Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA
- Epigenetics Institute and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alexey Kozlenkov
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center, Bronx, NY, USA
| | - Stella Dracheva
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center, Bronx, NY, USA
| | - Yasmin L Hurd
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Addiction Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA.
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60
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Abstract
Nobel laureate Nikolaas Tinbergen provided clear criteria for declaring a neuroscience problem solved, criteria which despite the passage of more than 50 years and vastly expanded neuroscience tool kits remain applicable today. Tinbergen said for neuroscientists to claim that a behavior is understood, they must correspondingly understand its (i) development and its (ii) mechanisms and its (iii) function and its (iv) evolution. Now, all four of these domains represent hotbeds of current experimental work, each using arrays of new techniques which overlap only partly. Thus, as new methodologies come online, from single-nerve-cell RNA sequencing, for example, to smart FISH, large-scale calcium imaging from cortex and deep brain structures, computational ethology, and so on, one person, however smart, cannot master everything. Our response to the likely “fracturing” of neuroscience recognizes the value of ever larger consortia. This response suggests new kinds of problems for (i) funding and (ii) the fair distribution of credit, especially for younger scientists.
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61
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Ayhan F, Konopka G. Regulatory genes and pathways disrupted in autism spectrum disorders. Prog Neuropsychopharmacol Biol Psychiatry 2019; 89:57-64. [PMID: 30165121 PMCID: PMC6249101 DOI: 10.1016/j.pnpbp.2018.08.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/01/2018] [Accepted: 08/21/2018] [Indexed: 02/07/2023]
Abstract
Autism spectrum disorder (ASD) is a highly prevalent and complex genetic disorder. The complex genetic make-up of ASD has been extensively studied and both common and rare genetic variants in up to 1000 genes have been linked to increased ASD risk. While these studies highlight the genetic complexity and begin to provide a window for delineating pathways at risk in ASD, the pathogenicity and specific contribution of many mutations to the disorder are poorly understood. Defining the convergent pathways disrupted by this large number of ASD-associated genetic variants will help to understand disease pathogenesis and direct future therapeutic efforts for the groups of patients with distinct etiologies. Here, we review some of the common regulatory pathways including chromatin remodeling, transcription, and alternative splicing that have emerged as common features from genetic and transcriptomic profiling of ASD. For each category, we focus on one gene (CHD8, FOXP1, and RBFOX1) that is significantly linked to ASD and functionally characterized in recent years. Finally, we discuss genetic and transcriptomic overlap between ASD and other neurodevelopmental disorders.
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Affiliation(s)
- Fatma Ayhan
- Department of Neuroscience, UT Southwestern Medical Center, Dallas 75390-9111, USA
| | - Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, Dallas 75390-9111, USA.
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62
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Sharma N, Pollina EA, Nagy MA, Yap EL, DiBiase FA, Hrvatin S, Hu L, Lin C, Greenberg ME. ARNT2 Tunes Activity-Dependent Gene Expression through NCoR2-Mediated Repression and NPAS4-Mediated Activation. Neuron 2019; 102:390-406.e9. [PMID: 30846309 DOI: 10.1016/j.neuron.2019.02.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 11/20/2018] [Accepted: 02/04/2019] [Indexed: 12/22/2022]
Abstract
Neuronal activity-dependent transcription is tuned to ensure precise gene induction during periods of heightened synaptic activity, allowing for appropriate responses of activated neurons within neural circuits. The consequences of aberrant induction of activity-dependent genes on neuronal physiology are not yet clear. Here, we demonstrate that, in the absence of synaptic excitation, the basic-helix-loop-helix (bHLH)-PAS family transcription factor ARNT2 recruits the NCoR2 co-repressor complex to suppress neuronal activity-dependent regulatory elements and maintain low basal levels of inducible genes. This restricts inhibition of excitatory neurons, maintaining them in a state that is receptive to future sensory stimuli. By contrast, in response to heightened neuronal activity, ARNT2 recruits the neuronal-specific bHLH-PAS factor NPAS4 to activity-dependent regulatory elements to induce transcription and thereby increase somatic inhibitory input. Thus, the interplay of bHLH-PAS complexes at activity-dependent regulatory elements maintains temporal control of activity-dependent gene expression and scales somatic inhibition with circuit activity.
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Affiliation(s)
- Nikhil Sharma
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | | | - M Aurel Nagy
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Ee-Lynn Yap
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Florence A DiBiase
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Sinisa Hrvatin
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Linda Hu
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Cindy Lin
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
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Puelles L, Alonso A, García-Calero E, Martínez-de-la-Torre M. Concentric ring topology of mammalian cortical sectors and relevance for patterning studies. J Comp Neurol 2019; 527:1731-1752. [PMID: 30737959 DOI: 10.1002/cne.24650] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 01/05/2019] [Accepted: 01/28/2019] [Indexed: 01/07/2023]
Abstract
Models aiming to explain causally the evolutionary or ontogenetic emergence of the pallial isocortex and its regional/areal heterogeneity in mammals use simple or complex assumptions about the pallial structure present in basal mammals and nonmammals. The question arises: how complex is the pattern that needs to be accounted for in causal models? This topic is also paramount for comparative purposes, since some topological relationships may be explained as being ancestral, rather than newly emerged. The mouse pallium is apt to be reexamined in this context, due to the breadth of available molecular markers and correlative experimental patterning results. We center the present essay on a recapitulative glance at the classic theory of concentric mammalian allo-, meso-, and neocortex domains. In its simplest terms, this theory postulates a central neocortical island (6 layers) separated by a surrounding mesocortical ring (4-5 layers) from a peripheral allocortical ring (3 layers). These territories show additional partition into regional or areal subdivisions. There are also borderline amygdalar, claustral, and septal areas of the pallium, nuclear in structure. There has been little effort so far to contemplate the full concentric ring model in current "cortex patterning" models. In this essay, we recapitulate the ring idea in mammals (mouse) and consider a potential causal patterning scenario using topologic models. Finally, we briefly explore how far this theory may apply to pallium models proposed recently for sauropsids.
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Affiliation(s)
- Luis Puelles
- Department of Human Anatomy and IMIB-Arrixaca Institute, School of Medicine, University of Murcia, Murcia, Spain
| | - Antonia Alonso
- Department of Human Anatomy and IMIB-Arrixaca Institute, School of Medicine, University of Murcia, Murcia, Spain
| | - Elena García-Calero
- Department of Human Anatomy and IMIB-Arrixaca Institute, School of Medicine, University of Murcia, Murcia, Spain
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64
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Wang ZT, Tan CC, Tan L, Yu JT. Systems biology and gene networks in Alzheimer’s disease. Neurosci Biobehav Rev 2019; 96:31-44. [DOI: 10.1016/j.neubiorev.2018.11.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 11/18/2018] [Accepted: 11/18/2018] [Indexed: 12/25/2022]
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Li M, Santpere G, Imamura Kawasawa Y, Evgrafov OV, Gulden FO, Pochareddy S, Sunkin SM, Li Z, Shin Y, Zhu Y, Sousa AMM, Werling DM, Kitchen RR, Kang HJ, Pletikos M, Choi J, Muchnik S, Xu X, Wang D, Lorente-Galdos B, Liu S, Giusti-Rodríguez P, Won H, de Leeuw CA, Pardiñas AF, Hu M, Jin F, Li Y, Owen MJ, O'Donovan MC, Walters JTR, Posthuma D, Reimers MA, Levitt P, Weinberger DR, Hyde TM, Kleinman JE, Geschwind DH, Hawrylycz MJ, State MW, Sanders SJ, Sullivan PF, Gerstein MB, Lein ES, Knowles JA, Sestan N. Integrative functional genomic analysis of human brain development and neuropsychiatric risks. Science 2018; 362:eaat7615. [PMID: 30545854 PMCID: PMC6413317 DOI: 10.1126/science.aat7615] [Citation(s) in RCA: 421] [Impact Index Per Article: 70.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 11/15/2018] [Indexed: 12/14/2022]
Abstract
To broaden our understanding of human neurodevelopment, we profiled transcriptomic and epigenomic landscapes across brain regions and/or cell types for the entire span of prenatal and postnatal development. Integrative analysis revealed temporal, regional, sex, and cell type-specific dynamics. We observed a global transcriptomic cup-shaped pattern, characterized by a late fetal transition associated with sharply decreased regional differences and changes in cellular composition and maturation, followed by a reversal in childhood-adolescence, and accompanied by epigenomic reorganizations. Analysis of gene coexpression modules revealed relationships with epigenomic regulation and neurodevelopmental processes. Genes with genetic associations to brain-based traits and neuropsychiatric disorders (including MEF2C, SATB2, SOX5, TCF4, and TSHZ3) converged in a small number of modules and distinct cell types, revealing insights into neurodevelopment and the genomic basis of neuropsychiatric risks.
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66
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Transcriptional control of long-range cortical projections. Curr Opin Neurobiol 2018; 53:57-65. [DOI: 10.1016/j.conb.2018.05.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/23/2018] [Indexed: 12/11/2022]
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67
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Xu X, Stoyanova EI, Lemiesz AE, Xing J, Mash DC, Heintz N. Species and cell-type properties of classically defined human and rodent neurons and glia. eLife 2018; 7:e37551. [PMID: 30320555 PMCID: PMC6188473 DOI: 10.7554/elife.37551] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 09/18/2018] [Indexed: 11/13/2022] Open
Abstract
Determination of the molecular properties of genetically targeted cell types has led to fundamental insights into mouse brain function and dysfunction. Here, we report an efficient strategy for precise exploration of gene expression and epigenetic events in specific cell types in a range of species, including postmortem human brain. We demonstrate that classically defined, homologous neuronal and glial cell types differ between rodent and human by the expression of hundreds of orthologous, cell specific genes. Confirmation that these genes are differentially active was obtained using epigenetic mapping and immunofluorescence localization. Studies of sixteen human postmortem brains revealed gender specific transcriptional differences, cell-specific molecular responses to aging, and the induction of a shared, robust response to an unknown external event evident in three donor samples. Our data establish a comprehensive approach for analysis of molecular events associated with specific circuits and cell types in a wide variety of human conditions.
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Affiliation(s)
- Xiao Xu
- Laboratory of Molecular BiologyHoward Hughes Medical Institute, The Rockefeller UniversityNew YorkUnited States
| | - Elitsa I Stoyanova
- Laboratory of Molecular BiologyHoward Hughes Medical Institute, The Rockefeller UniversityNew YorkUnited States
| | - Agata E Lemiesz
- Laboratory of Molecular BiologyHoward Hughes Medical Institute, The Rockefeller UniversityNew YorkUnited States
| | - Jie Xing
- Laboratory of Molecular BiologyHoward Hughes Medical Institute, The Rockefeller UniversityNew YorkUnited States
| | - Deborah C Mash
- Miller School of MedicineUniversity of MiamiMiamiUnited States
| | - Nathaniel Heintz
- Laboratory of Molecular BiologyHoward Hughes Medical Institute, The Rockefeller UniversityNew YorkUnited States
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68
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Genomic analysis of transcriptional networks directing progression of cell states during MGE development. Neural Dev 2018; 13:21. [PMID: 30217225 PMCID: PMC6138899 DOI: 10.1186/s13064-018-0119-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/27/2018] [Indexed: 01/01/2023] Open
Abstract
Background Homeodomain (HD) transcription factor (TF) NKX2–1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8. NKX2–1 defines MGE regional identity in large part through transcriptional repression, while specification and maturation of GABAergic and cholinergic fates is mediated in part by transcriptional activation via TFs such as LHX6 and LHX8. Here we analyze the signaling and TF pathways, downstream of NKX2–1, required for GABAergic and cholinergic neuron fate maturation. Methods Differential ChIP-seq analysis was used to identify regulatory elements (REs) where chromatin state was sensitive to change in the Nkx2–1cKO MGE at embryonic day (E) 13.5. TF motifs in the REs were identified using RSAT. CRISPR-mediated genome editing was used to generate enhancer knockouts. Differential gene expression in these knockouts was analyzed through RT-qPCR and in situ hybridization. Functional analysis of motifs within hs623 was analyzed via site directed mutagenesis and reporter assays in primary MGE cultures. Results We identified 4782 activating REs (aREs) and 6391 repressing REs (rREs) in the Nkx2–1 conditional knockout (Nkx2–1cKO) MGE. aREs are associated with basic-Helix-Loop-Helix (bHLH) TFs. Deletion of hs623, an intragenic Tcf12 aRE, caused a reduction of Tcf12 expression in the sub-ventricular zone (SVZ) and mantle zone (MZ) of the MGE. Mutation of LHX, SOX and octamers, within hs623, caused a reduction of hs623 activity in MGE primary cultures. Conclusions Tcf12 expression in the SVZ of the MGE is mediated through aRE hs623. The activity of hs623 is dependent on LHX6, SOX and octamers. Thus, maintaining the expression of Tcf12 in the SVZ involves on TF pathways parallel and genetically downstream of NKX2–1. Electronic supplementary material The online version of this article (10.1186/s13064-018-0119-4) contains supplementary material, which is available to authorized users.
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Elsen GE, Bedogni F, Hodge RD, Bammler TK, MacDonald JW, Lindtner S, Rubenstein JLR, Hevner RF. The Epigenetic Factor Landscape of Developing Neocortex Is Regulated by Transcription Factors Pax6→ Tbr2→ Tbr1. Front Neurosci 2018; 12:571. [PMID: 30186101 PMCID: PMC6113890 DOI: 10.3389/fnins.2018.00571] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 07/30/2018] [Indexed: 12/12/2022] Open
Abstract
Epigenetic factors (EFs) regulate multiple aspects of cerebral cortex development, including proliferation, differentiation, laminar fate, and regional identity. The same neurodevelopmental processes are also regulated by transcription factors (TFs), notably the Pax6→ Tbr2→ Tbr1 cascade expressed sequentially in radial glial progenitors (RGPs), intermediate progenitors, and postmitotic projection neurons, respectively. Here, we studied the EF landscape and its regulation in embryonic mouse neocortex. Microarray and in situ hybridization assays revealed that many EF genes are expressed in specific cortical cell types, such as intermediate progenitors, or in rostrocaudal gradients. Furthermore, many EF genes are directly bound and transcriptionally regulated by Pax6, Tbr2, or Tbr1, as determined by chromatin immunoprecipitation-sequencing and gene expression analysis of TF mutant cortices. Our analysis demonstrated that Pax6, Tbr2, and Tbr1 form a direct feedforward genetic cascade, with direct feedback repression. Results also revealed that each TF regulates multiple EF genes that control DNA methylation, histone marks, chromatin remodeling, and non-coding RNA. For example, Tbr1 activates Rybp and Auts2 to promote the formation of non-canonical Polycomb repressive complex 1 (PRC1). Also, Pax6, Tbr2, and Tbr1 collectively drive massive changes in the subunit isoform composition of BAF chromatin remodeling complexes during differentiation: for example, a novel switch from Bcl7c (Baf40c) to Bcl7a (Baf40a), the latter directly activated by Tbr2. Of 11 subunits predominantly in neuronal BAF, 7 were transcriptionally activated by Pax6, Tbr2, or Tbr1. Using EFs, Pax6→ Tbr2→ Tbr1 effect persistent changes of gene expression in cell lineages, to propagate features such as regional and laminar identity from progenitors to neurons.
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Affiliation(s)
- Gina E. Elsen
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Francesco Bedogni
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Rebecca D. Hodge
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Theo K. Bammler
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
| | - James W. MacDonald
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
| | - Susan Lindtner
- Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, CA, United States
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, United States
| | - John L. R. Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, CA, United States
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, United States
| | - Robert F. Hevner
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, United States
- Department of Neurological Surgery, School of Medicine, University of Washington, Seattle, WA, United States
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Human-Specific NOTCH2NL Genes Expand Cortical Neurogenesis through Delta/Notch Regulation. Cell 2018; 173:1370-1384.e16. [PMID: 29856955 PMCID: PMC6092419 DOI: 10.1016/j.cell.2018.03.067] [Citation(s) in RCA: 241] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/16/2018] [Accepted: 03/26/2018] [Indexed: 12/03/2022]
Abstract
The cerebral cortex underwent rapid expansion and increased complexity during recent hominid evolution. Gene duplications constitute a major evolutionary force, but their impact on human brain development remains unclear. Using tailored RNA sequencing (RNA-seq), we profiled the spatial and temporal expression of hominid-specific duplicated (HS) genes in the human fetal cortex and identified a repertoire of 35 HS genes displaying robust and dynamic patterns during cortical neurogenesis. Among them NOTCH2NL, human-specific paralogs of the NOTCH2 receptor, stood out for their ability to promote cortical progenitor maintenance. NOTCH2NL promote the clonal expansion of human cortical progenitors, ultimately leading to higher neuronal output. At the molecular level, NOTCH2NL function by activating the Notch pathway through inhibition of cis Delta/Notch interactions. Our study uncovers a large repertoire of recently evolved genes active during human corticogenesis and reveals how human-specific NOTCH paralogs may have contributed to the expansion of the human cortex. Identification of >35 HS protein-coding genes expressed during human corticogenesis NOTCH2NL human-specific paralogs of NOTCH2 expressed in human cortical progenitors NOTCH2NL genes expand human cortical progenitors and their neuronal output NOTCH2NL promotes Notch signaling through cis-inhibition of Delta/Notch interactions
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WT1-Expressing Interneurons Regulate Left-Right Alternation during Mammalian Locomotor Activity. J Neurosci 2018; 38:5666-5676. [PMID: 29789381 DOI: 10.1523/jneurosci.0328-18.2018] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 04/12/2018] [Accepted: 05/12/2018] [Indexed: 12/31/2022] Open
Abstract
The basic pattern of activity underlying stepping in mammals is generated by a neural network located in the caudal spinal cord. Within this network, the specific circuitry coordinating left-right alternation has been shown to involve several groups of molecularly defined interneurons. Here we characterize a population of spinal neurons that express the Wilms' tumor 1 (WT1) gene and investigate their role during locomotor activity in mice of both sexes. We demonstrate that WT1-expressing cells are located in the ventromedial region of the spinal cord of mice and are also present in the human spinal cord. In the mouse, these cells are inhibitory, project axons to the contralateral spinal cord, terminate in close proximity to other commissural interneuron subtypes, and are essential for appropriate left-right alternation during locomotion. In addition to identifying WT1-expressing interneurons as a key component of the locomotor circuitry, this study provides insight into the manner in which several populations of molecularly defined interneurons are interconnected to generate coordinated motor activity on either side of the body during stepping.SIGNIFICANCE STATEMENT In this study, we characterize WT1-expressing spinal interneurons in mice and demonstrate that they are commissurally projecting and inhibitory. Silencing of this neuronal population during a locomotor task results in a complete breakdown of left-right alternation, whereas flexor-extensor alternation was not significantly affected. Axons of WT1 neurons are shown to terminate nearby commissural interneurons, which coordinate motoneuron activity during locomotion, and presumably regulate their activity. Finally, the WT1 gene is shown to be present in the spinal cord of humans, raising the possibility of functional homology between these species. This study not only identifies a key component of the locomotor circuitry but also begins to unravel the connectivity among the growing number of molecularly defined interneurons that comprise this neural network.
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Manoli DS, Tollkuhn J. Gene regulatory mechanisms underlying sex differences in brain development and psychiatric disease. Ann N Y Acad Sci 2018; 1420:26-45. [PMID: 29363776 PMCID: PMC5991992 DOI: 10.1111/nyas.13564] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 10/26/2017] [Accepted: 11/01/2017] [Indexed: 12/12/2022]
Abstract
The sexual differentiation of the mammalian nervous system requires the precise coordination of the temporal and spatial regulation of gene expression in diverse cell types. Sex hormones act at multiple developmental time points to specify sex-typical differentiation during embryonic and early development and to coordinate subsequent responses to gonadal hormones later in life by establishing sex-typical patterns of epigenetic modifications across the genome. Thus, mutations associated with neuropsychiatric conditions may result in sexually dimorphic symptoms by acting on different neural substrates or chromatin landscapes in males and females. Finally, as stress hormone signaling may directly alter the molecular machinery that interacts with sex hormone receptors to regulate gene expression, the contribution of chronic stress to the pathogenesis or presentation of mental illness may be additionally different between the sexes. Here, we review the mechanisms that contribute to sexual differentiation in the mammalian nervous system and consider some of the implications of these processes for sex differences in neuropsychiatric conditions.
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Affiliation(s)
- Devanand S. Manoli
- Department of Psychiatry and Weill Institute for Neuroscience, University of California, San Francisco, San Francisco, California
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73
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Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Nat Neurosci 2018; 21:432-439. [PMID: 29434377 DOI: 10.1038/s41593-018-0079-3] [Citation(s) in RCA: 195] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/27/2017] [Indexed: 01/23/2023]
Abstract
Analysis of chromatin accessibility can reveal transcriptional regulatory sequences, but heterogeneity of primary tissues poses a significant challenge in mapping the precise chromatin landscape in specific cell types. Here we report single-nucleus ATAC-seq, a combinatorial barcoding-assisted single-cell assay for transposase-accessible chromatin that is optimized for use on flash-frozen primary tissue samples. We apply this technique to the mouse forebrain through eight developmental stages. Through analysis of more than 15,000 nuclei, we identify 20 distinct cell populations corresponding to major neuronal and non-neuronal cell types. We further define cell-type-specific transcriptional regulatory sequences, infer potential master transcriptional regulators and delineate developmental changes in forebrain cellular composition. Our results provide insight into the molecular and cellular dynamics that underlie forebrain development in the mouse and establish technical and analytical frameworks that are broadly applicable to other heterogeneous tissues.
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de la Torre-Ubieta L, Stein JL, Won H, Opland CK, Liang D, Lu D, Geschwind DH. The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis. Cell 2018; 172:289-304.e18. [PMID: 29307494 PMCID: PMC5924568 DOI: 10.1016/j.cell.2017.12.014] [Citation(s) in RCA: 200] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 09/14/2017] [Accepted: 12/07/2017] [Indexed: 01/19/2023]
Abstract
Non-coding regions comprise most of the human genome and harbor a significant fraction of risk alleles for neuropsychiatric diseases, yet their functions remain poorly defined. We created a high-resolution map of non-coding elements involved in human cortical neurogenesis by contrasting chromatin accessibility and gene expression in the germinal zone and cortical plate of the developing cerebral cortex. We link distal regulatory elements (DREs) to their cognate gene(s) together with chromatin interaction data and show that target genes of human-gained enhancers (HGEs) regulate cortical neurogenesis and are enriched in outer radial glia, a cell type linked to human cortical evolution. We experimentally validate the regulatory effects of predicted enhancers for FGFR2 and EOMES. We observe that common genetic variants associated with educational attainment, risk for neuropsychiatric disease, and intracranial volume are enriched within regulatory elements involved in cortical neurogenesis, demonstrating the importance of this early developmental process for adult human cognitive function.
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Affiliation(s)
- Luis de la Torre-Ubieta
- Neurogenetics Program, Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jason L Stein
- Neurogenetics Program, Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Hyejung Won
- Neurogenetics Program, Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Carli K Opland
- Neurogenetics Program, Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dan Liang
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Daning Lu
- Neurogenetics Program, Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel H Geschwind
- Neurogenetics Program, Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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75
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de Juan Romero C, Borrell V. Genetic maps and patterns of cerebral cortex folding. Curr Opin Cell Biol 2017; 49:31-37. [PMID: 29227862 DOI: 10.1016/j.ceb.2017.11.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 11/17/2017] [Accepted: 11/26/2017] [Indexed: 01/24/2023]
Abstract
Folding of the cerebral cortex during brain development is a complex process that depends on the orchestrated action of a number of factors, including generation and proliferation of basal progenitor cells, and the radial migration of neurons. Patterns of primary cortical folding are stereotyped between individuals and across phylogeny, reflecting a strong genetic regulation of the underlying cellular mechanisms. Here we summarize recent findings on cellular and genetic mechanisms regulating this fascinating process that underlies expansion and functional complexification of the mammalian cerebral cortex.
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Affiliation(s)
- Camino de Juan Romero
- Instituto de Neurociencias, Agencia Estatal Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, 03550 Sant Joan d'Alacant, Spain
| | - Víctor Borrell
- Instituto de Neurociencias, Agencia Estatal Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, 03550 Sant Joan d'Alacant, Spain.
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76
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Hardingham GE, Pruunsild P, Greenberg ME, Bading H. Lineage divergence of activity-driven transcription and evolution of cognitive ability. Nat Rev Neurosci 2017; 19:9-15. [PMID: 29167525 DOI: 10.1038/nrn.2017.138] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Excitation-transcription coupling shapes network formation during brain development and controls neuronal survival, synaptic function and cognitive skills in the adult. New studies have uncovered differences in the transcriptional responses to synaptic activity between humans and mice. These differences are caused both by the emergence of lineage-specific activity-regulated genes and by the acquisition of signal-responsive DNA elements in gene regulatory regions that determine whether a gene can be transcriptionally induced by synaptic activity or alter the extent of its inducibility. Such evolutionary divergence may have contributed to lineage-related advancements in cognitive abilities.
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Affiliation(s)
- Giles E Hardingham
- UK Dementia Research Institute at The University of Edinburgh, Edinburgh Medical School, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Priit Pruunsild
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, 69120 Heidelberg, Germany
| | - Michael E Greenberg
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hilmar Bading
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, 69120 Heidelberg, Germany
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Benabdallah NS, Gautier P, Hekimoglu-Balkan B, Lettice LA, Bhatia S, Bickmore WA. SBE6: a novel long-range enhancer involved in driving sonic hedgehog expression in neural progenitor cells. Open Biol 2017; 6:rsob.160197. [PMID: 27852806 PMCID: PMC5133441 DOI: 10.1098/rsob.160197] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 10/20/2016] [Indexed: 12/14/2022] Open
Abstract
The expression of genes with key roles in development is under very tight spatial and temporal control, mediated by enhancers. A classic example of this is the sonic hedgehog gene (Shh), which plays a pivotal role in the proliferation, differentiation and survival of neural progenitor cells both in vivo and in vitro. Shh expression in the brain is tightly controlled by several known enhancers that have been identified through genetic, genomic and functional assays. Using chromatin profiling during the differentiation of embryonic stem cells to neural progenitor cells, here we report the identification of a novel long-range enhancer for Shh—Shh-brain-enhancer-6 (SBE6)—that is located 100 kb upstream of Shh and that is required for the proper induction of Shh expression during this differentiation programme. This element is capable of driving expression in the vertebrate brain. Our study illustrates how a chromatin-focused approach, coupled to in vivo testing, can be used to identify new cell-type specific cis-regulatory elements, and points to yet further complexity in the control of Shh expression during embryonic brain development.
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Affiliation(s)
- Nezha S Benabdallah
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK.,Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Philippe Gautier
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Betul Hekimoglu-Balkan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Laura A Lettice
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Shipra Bhatia
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
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78
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Ecker JR, Geschwind DH, Kriegstein AR, Ngai J, Osten P, Polioudakis D, Regev A, Sestan N, Wickersham IR, Zeng H. The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas. Neuron 2017; 96:542-557. [PMID: 29096072 PMCID: PMC5689454 DOI: 10.1016/j.neuron.2017.10.007] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/01/2017] [Accepted: 10/03/2017] [Indexed: 10/25/2022]
Abstract
A comprehensive characterization of neuronal cell types, their distributions, and patterns of connectivity is critical for understanding the properties of neural circuits and how they generate behaviors. Here we review the experiences of the BRAIN Initiative Cell Census Consortium, ten pilot projects funded by the U.S. BRAIN Initiative, in developing, validating, and scaling up emerging genomic and anatomical mapping technologies for creating a complete inventory of neuronal cell types and their connections in multiple species and during development. These projects lay the foundation for a larger and longer-term effort to generate whole-brain cell atlases in species including mice and humans.
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Affiliation(s)
- Joseph R Ecker
- Genomic Analysis Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Arnold R Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John Ngai
- Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, QB3 Functional Genomics Laboratory, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Pavel Osten
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Damon Polioudakis
- Program in Neurogenetics, Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Department of Biology, Koch Institute of Integrative Cancer Research, and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Nenad Sestan
- Departments of Neuroscience, Genetics, Psychiatry and Comparative Medicine, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale Child Study Center, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Ian R Wickersham
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
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79
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Floruta CM, Du R, Kang H, Stein JL, Weick JP. Default Patterning Produces Pan-cortical Glutamatergic and CGE/LGE-like GABAergic Neurons from Human Pluripotent Stem Cells. Stem Cell Reports 2017; 9:1463-1476. [PMID: 29107596 PMCID: PMC5831028 DOI: 10.1016/j.stemcr.2017.09.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 09/25/2017] [Accepted: 09/26/2017] [Indexed: 10/25/2022] Open
Abstract
Default differentiation of human pluripotent stem cells has been promoted as a model of cortical development. In this study, a developmental transcriptome analysis of default-differentiated hPSNs revealed a gene expression program resembling in vivo CGE/LGE subpallial domains and GABAergic signaling. A combination of bioinformatic, functional, and immunocytochemical analysis further revealed that hPSNs consist of both cortical glutamatergic and CGE-like GABAergic neurons. This study provides a comprehensive characterization of the heterogeneous group of neurons produced by default differentiation and insight into future directed differentiation strategies.
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Affiliation(s)
- Crina M. Floruta
- Department of Neurosciences, University of New Mexico-Health Science Center, Albuquerque, NM 87131, USA
| | - Ruofei Du
- UNM Comprehensive Cancer Center, University of New Mexico-Health Science Center, Albuquerque, NM 87131, USA
| | - Huining Kang
- UNM Comprehensive Cancer Center, University of New Mexico-Health Science Center, Albuquerque, NM 87131, USA,Department of Internal Medicine, University of New Mexico-Health Science Center, Albuquerque, NM 87131, USA
| | - Jason L. Stein
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA,UNC Neuroscience Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Jason P. Weick
- Department of Neurosciences, University of New Mexico-Health Science Center, Albuquerque, NM 87131, USA,Corresponding author
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80
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Desfilis E, Abellán A, Sentandreu V, Medina L. Expression of regulatory genes in the embryonic brain of a lizard and implications for understanding pallial organization and evolution. J Comp Neurol 2017; 526:166-202. [PMID: 28891227 PMCID: PMC5765483 DOI: 10.1002/cne.24329] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/13/2017] [Accepted: 09/01/2017] [Indexed: 02/03/2023]
Abstract
The comparison of gene expression patterns in the embryonic brain of mouse and chicken is being essential for understanding pallial organization. However, the scarcity of gene expression data in reptiles, crucial for understanding evolution, makes it difficult to identify homologues of pallial divisions in different amniotes. We cloned and analyzed the expression of the genes Emx1, Lhx2, Lhx9, and Tbr1 in the embryonic telencephalon of the lacertid lizard Psammodromus algirus. The comparative expression patterns of these genes, critical for pallial development, are better understood when using a recently proposed six‐part model of pallial divisions. The lizard medial pallium, expressing all genes, includes the medial and dorsomedial cortices, and the majority of the dorsal cortex, except the region of the lateral cortical superposition. The latter is rich in Lhx9 expression, being excluded as a candidate of dorsal or lateral pallia, and may belong to a distinct dorsolateral pallium, which extends from rostral to caudal levels. Thus, the neocortex homolog cannot be found in the classical reptilian dorsal cortex, but perhaps in a small Emx1‐expressing/Lhx9‐negative area at the front of the telencephalon, resembling the avian hyperpallium. The ventral pallium, expressing Lhx9, but not Emx1, gives rise to the dorsal ventricular ridge and appears comparable to the avian nidopallium. We also identified a distinct ventrocaudal pallial sector comparable to the avian arcopallium and to part of the mammalian pallial amygdala. These data open new venues for understanding the organization and evolution of the pallium.
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Affiliation(s)
- Ester Desfilis
- Laboratory of Evolutionary and Developmental Neurobiology, Department of Experimental Medicine, Faculty of Medicine, University of Lleida, Lleida Institute for Biomedical Research Dr. Pifarré Foundation (IRBLleida), 25198, Lleida, Spain
| | - Antonio Abellán
- Laboratory of Evolutionary and Developmental Neurobiology, Department of Experimental Medicine, Faculty of Medicine, University of Lleida, Lleida Institute for Biomedical Research Dr. Pifarré Foundation (IRBLleida), 25198, Lleida, Spain
| | - Vicente Sentandreu
- Servicio Central de Apoyo a la Investigación Experimental (SCSIE), Sección de Genómica, University of València, 46100, València, Spain
| | - Loreta Medina
- Laboratory of Evolutionary and Developmental Neurobiology, Department of Experimental Medicine, Faculty of Medicine, University of Lleida, Lleida Institute for Biomedical Research Dr. Pifarré Foundation (IRBLleida), 25198, Lleida, Spain
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81
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Sandberg M, Flandin P, Silberberg S, Su-Feher L, Price JD, Hu JS, Kim C, Visel A, Nord AS, Rubenstein JLR. Transcriptional Networks Controlled by NKX2-1 in the Development of Forebrain GABAergic Neurons. Neuron 2017; 91:1260-1275. [PMID: 27657450 DOI: 10.1016/j.neuron.2016.08.020] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 07/01/2016] [Accepted: 08/08/2016] [Indexed: 12/31/2022]
Abstract
The embryonic basal ganglia generates multiple projection neurons and interneuron subtypes from distinct progenitor domains. Combinatorial interactions of transcription factors and chromatin are thought to regulate gene expression. In the medial ganglionic eminence, the NKX2-1 transcription factor controls regional identity and, with LHX6, is necessary to specify pallidal projection neurons and forebrain interneurons. Here, we dissected the molecular functions of NKX2-1 by defining its chromosomal binding, regulation of gene expression, and epigenetic state. NKX2-1 binding at distal regulatory elements led to a repressed epigenetic state and transcriptional repression in the ventricular zone. Conversely, NKX2-1 is required to establish a permissive chromatin state and transcriptional activation in the sub-ventricular and mantle zones. Moreover, combinatorial binding of NKX2-1 and LHX6 promotes transcriptionally permissive chromatin and activates genes expressed in cortical migrating interneurons. Our integrated approach provides a foundation for elucidating transcriptional networks guiding the development of the MGE and its descendants.
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Affiliation(s)
- Magnus Sandberg
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Pierre Flandin
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Shanni Silberberg
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Linda Su-Feher
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95817, USA; Department of Neurobiology, Physiology, and Behavior, University of California, Davis, Davis, CA 95616, USA
| | - James D Price
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jia Sheng Hu
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Carol Kim
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Axel Visel
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Alex S Nord
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95817, USA; Department of Neurobiology, Physiology, and Behavior, University of California, Davis, Davis, CA 95616, USA.
| | - John L R Rubenstein
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA.
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82
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Subpallial Enhancer Transgenic Lines: a Data and Tool Resource to Study Transcriptional Regulation of GABAergic Cell Fate. Neuron 2017; 92:59-74. [PMID: 27710791 DOI: 10.1016/j.neuron.2016.09.027] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 04/22/2016] [Accepted: 09/02/2016] [Indexed: 01/08/2023]
Abstract
Elucidating the transcriptional circuitry controlling forebrain development requires an understanding of enhancer activity and regulation. We generated stable transgenic mouse lines that express CreERT2 and GFP from ten different enhancer elements with activity in distinct domains within the embryonic basal ganglia. We used these unique tools to generate a comprehensive regional fate map of the mouse subpallium, including sources for specific subtypes of amygdala neurons. We then focused on deciphering transcriptional mechanisms that control enhancer activity. Using machine-learning computations, in vivo chromosomal occupancy of 13 transcription factors that regulate subpallial patterning and differentiation and analysis of enhancer activity in Dlx1/2 and Lhx6 mutants, we elucidated novel molecular mechanisms that regulate region-specific enhancer activity in the developing brain. Thus, these subpallial enhancer transgenic lines are data and tool resources to study transcriptional regulation of GABAergic cell fate.
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83
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Temporal Control of Mammalian Cortical Neurogenesis by m 6A Methylation. Cell 2017; 171:877-889.e17. [PMID: 28965759 DOI: 10.1016/j.cell.2017.09.003] [Citation(s) in RCA: 498] [Impact Index Per Article: 71.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 08/09/2017] [Accepted: 08/30/2017] [Indexed: 10/18/2022]
Abstract
N6-methyladenosine (m6A), installed by the Mettl3/Mettl14 methyltransferase complex, is the most prevalent internal mRNA modification. Whether m6A regulates mammalian brain development is unknown. Here, we show that m6A depletion by Mettl14 knockout in embryonic mouse brains prolongs the cell cycle of radial glia cells and extends cortical neurogenesis into postnatal stages. m6A depletion by Mettl3 knockdown also leads to a prolonged cell cycle and maintenance of radial glia cells. m6A sequencing of embryonic mouse cortex reveals enrichment of mRNAs related to transcription factors, neurogenesis, the cell cycle, and neuronal differentiation, and m6A tagging promotes their decay. Further analysis uncovers previously unappreciated transcriptional prepatterning in cortical neural stem cells. m6A signaling also regulates human cortical neurogenesis in forebrain organoids. Comparison of m6A-mRNA landscapes between mouse and human cortical neurogenesis reveals enrichment of human-specific m6A tagging of transcripts related to brain-disorder risk genes. Our study identifies an epitranscriptomic mechanism in heightened transcriptional coordination during mammalian cortical neurogenesis.
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84
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Paul A, Crow M, Raudales R, He M, Gillis J, Huang ZJ. Transcriptional Architecture of Synaptic Communication Delineates GABAergic Neuron Identity. Cell 2017; 171:522-539.e20. [PMID: 28942923 DOI: 10.1016/j.cell.2017.08.032] [Citation(s) in RCA: 276] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 05/04/2017] [Accepted: 08/16/2017] [Indexed: 01/07/2023]
Abstract
Understanding the organizational logic of neural circuits requires deciphering the biological basis of neuronal diversity and identity, but there is no consensus on how neuron types should be defined. We analyzed single-cell transcriptomes of a set of anatomically and physiologically characterized cortical GABAergic neurons and conducted a computational genomic screen for transcriptional profiles that distinguish them from one another. We discovered that cardinal GABAergic neuron types are delineated by a transcriptional architecture that encodes their synaptic communication patterns. This architecture comprises 6 categories of ∼40 gene families, including cell-adhesion molecules, transmitter-modulator receptors, ion channels, signaling proteins, neuropeptides and vesicular release components, and transcription factors. Combinatorial expression of select members across families shapes a multi-layered molecular scaffold along the cell membrane that may customize synaptic connectivity patterns and input-output signaling properties. This molecular genetic framework of neuronal identity integrates cell phenotypes along multiple axes and provides a foundation for discovering and classifying neuron types.
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Affiliation(s)
- Anirban Paul
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Megan Crow
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ricardo Raudales
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Program in Neuroscience, Stony Brook University, Stony Brook, NY 11790, USA
| | - Miao He
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jesse Gillis
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Z Josh Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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85
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Turrero García M, Harwell CC. Radial glia in the ventral telencephalon. FEBS Lett 2017; 591:3942-3959. [PMID: 28862741 DOI: 10.1002/1873-3468.12829] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 12/31/2022]
Abstract
The ventral telencephalon is the developmental origin of the basal ganglia and the source of neuronal and glial cells that integrate into developing circuits in other areas of the brain. Radial glia in the embryonic subpallium give rise to an enormous diversity of mature cell types, either directly or through other transit-amplifying progenitors. Here, we review current knowledge about these subpallial neural stem cells and their progeny, focusing on the period of neurogenesis. We describe their cell biological features and the extrinsic and intrinsic molecular codes that guide their fate specification in defined temporal and spatial sequences. We also discuss the role of clonal lineage in the organization and specification of mature neurons.
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Affiliation(s)
| | - Corey C Harwell
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
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86
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Suppli NP, Bukh JD, Moffitt TE, Caspi A, Johansen C, Tjønneland A, Kessing LV, Dalton SO. Genetic variants in 5-HTTLPR, BDNF, HTR1A, COMT, and FKBP5 and risk for treated depression after cancer diagnosis. Depress Anxiety 2017; 34:845-855. [PMID: 28590587 PMCID: PMC5933050 DOI: 10.1002/da.22660] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 05/02/2017] [Accepted: 05/09/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The role of gene-environment interactions in the pathogenesis of depression is unclear. Previous studies addressed vulnerability for depression after childhood adversity and stressful life events among carriers of numerous specific genetic variants; however, the importance of individual genetic variants, the environmental exposures with which they interact, and the magnitude of the risk conveyed by these interactions remain elusive. METHODS We included 7,320 people with a first primary cancer identified in the prospective Diet, Cancer and Health study in an exposed-only cohort study. The mean age of the individuals was 68 years (5th, 95th percentiles: 58, 78) at cancer diagnosis. Using Cox regression models and cumulative incidence plots, we analyzed the associations between genetic variants in 5-HTTLPR, BDNF, HTR1A, COMT, and FKBP5 and use of antidepressants as well as hospital contact for depression after diagnosis of cancer. RESULTS Overall, we observed no statistically significant associations, with nonsignificant hazard ratio estimates for use of antidepressants of 0.95-1.07. CONCLUSIONS This study of elderly people indicates that it is unlikely that the investigated genetic variants are clinically relevantly associated with depression after diagnosis of cancer. The mechanisms for gene-environment interactions in younger individuals are probably different, and we advise caution in extrapolating our results to early life stress. However, conclusion from the present study might be generalizable to elderly persons exposed to other stressful life events.
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Affiliation(s)
- Nis P. Suppli
- Survivorship, Danish Cancer Society Research Center, Copenhagen, Denmark,Psychiatric Center Copenhagen, University of Copenhagen, Copenhagen, Denmark
| | - Jens D. Bukh
- Psychiatric Center Copenhagen, University of Copenhagen, Copenhagen, Denmark
| | - Terrie E. Moffitt
- Department of Psychology and Neuroscience, Duke University, NC, USA,Department of Psychiatry and Behavioral Sciences, Duke University, NC, USA,Center for Genomic and Computational Biology, Duke University, NC, USA,Social, Genetic, and Developmental Psychiatry Research Center, Institute of Psychiatry, King’s College London, London, UK
| | - Avshalom Caspi
- Department of Psychology and Neuroscience, Duke University, NC, USA,Department of Psychiatry and Behavioral Sciences, Duke University, NC, USA,Center for Genomic and Computational Biology, Duke University, NC, USA,Social, Genetic, and Developmental Psychiatry Research Center, Institute of Psychiatry, King’s College London, London, UK
| | - Christoffer Johansen
- Survivorship, Danish Cancer Society Research Center, Copenhagen, Denmark,Department of Oncology, Finsencentret, Rigshospitalet, Copenhagen, Denmark
| | - Anne Tjønneland
- Diet, Genes and Environment, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Lars V. Kessing
- Psychiatric Center Copenhagen, University of Copenhagen, Copenhagen, Denmark
| | - Susanne O. Dalton
- Survivorship, Danish Cancer Society Research Center, Copenhagen, Denmark
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87
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Solek CM, Feng S, Perin S, Weinschutz Mendes H, Ekker M. Lineage tracing of dlx1a/2a and dlx5a/6a expressing cells in the developing zebrafish brain. Dev Biol 2017; 427:131-147. [PMID: 28479339 DOI: 10.1016/j.ydbio.2017.04.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 04/28/2017] [Accepted: 04/29/2017] [Indexed: 02/06/2023]
Abstract
Lineage tracing of specific populations of progenitor cells provides crucial information about developmental programs. Four members of the Dlx homeobox gene family, Dlx1,2, 5 and 6, are involved in the specification of γ-aminobutyric acid (GABA)ergic neurons in the vertebrate forebrain. Orthologous genes in mammals and teleost show similarities in expression patterns and transcriptional regulation mechanisms. We have used lineage tracing to permanently label dlx-expressing cells in the zebrafish and have characterized the progeny of these cells in the larva and in the juvenile and adult brain. We have found that dlx1a/2a and dlx5a/6a expressing progenitors give rise, for the most part, to small populations of cells which constitute only a small proportion of GABAergic cells in the adult brain tissue. Moreover, some of the cells do not acquire a neuronal phenotype suggesting that, regardless of the time a cell expresses dlx genes in the brain, it can potentially give rise to cells other than neurons. In some instances, labeling larval dlx5a/6a-expressing cells, but not dlx1a/2a-expressing cells, results in massively expanding, widespread clonal expansion throughout the adult brain. Our data provide a detailed lineage analysis of the dlx1a/2a and dlx5a/6a expressing progenitors in the zebrafish brain and lays the foundation for further characterization of the role of these transcription factors beyond the specification of GABAergic neurons.
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Affiliation(s)
- Cynthia M Solek
- CAREG, Department of Biology, University of Ottawa, 20 Marie-Curie Private, Ottawa, ON, Canada K1N 6N5; Montreal Neurological Institute, McGill University, 3801 University Street, Montreal, QC, Canada H3A 2B4
| | - Shengrui Feng
- CAREG, Department of Biology, University of Ottawa, 20 Marie-Curie Private, Ottawa, ON, Canada K1N 6N5; Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto, ON, Canada M5G 2M9
| | - Sofia Perin
- CAREG, Department of Biology, University of Ottawa, 20 Marie-Curie Private, Ottawa, ON, Canada K1N 6N5
| | - Hellen Weinschutz Mendes
- CAREG, Department of Biology, University of Ottawa, 20 Marie-Curie Private, Ottawa, ON, Canada K1N 6N5
| | - Marc Ekker
- CAREG, Department of Biology, University of Ottawa, 20 Marie-Curie Private, Ottawa, ON, Canada K1N 6N5.
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88
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Zhang M, Chen D, Xia J, Han W, Cui X, Neuenkirchen N, Hermes G, Sestan N, Lin H. Post-transcriptional regulation of mouse neurogenesis by Pumilio proteins. Genes Dev 2017; 31:1354-1369. [PMID: 28794184 PMCID: PMC5580656 DOI: 10.1101/gad.298752.117] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 07/14/2017] [Indexed: 12/19/2022]
Abstract
Despite extensive studies on mammalian neurogenesis, its post-transcriptional regulation remains under-explored. Here we report that neural-specific inactivation of two murine post-transcriptional regulators, Pumilio 1 (Pum1) and Pum2, severely reduced the number of neural stem cells (NSCs) in the postnatal dentate gyrus (DG), drastically increased perinatal apoptosis, altered DG cell composition, and impaired learning and memory. Consistently, the mutant DG neurospheres generated fewer NSCs with defects in proliferation, survival, and differentiation, supporting a major role of Pum1 and Pum2 in hippocampal neurogenesis and function. Cross-linking immunoprecipitation revealed that Pum1 and Pum2 bind to thousands of mRNAs, with at least 694 common targets in multiple neurogenic pathways. Depleting Pum1 and/or Pum2 did not change the abundance of most target mRNAs but up-regulated their proteins, indicating that Pum1 and Pum2 regulate the translation of their target mRNAs. Moreover, Pum1 and Pum2 display RNA-dependent interaction with fragile X mental retardation protein (FMRP) and bind to one another's mRNA. This indicates that Pum proteins might form collaborative networks with FMRP and possibly other post-transcriptional regulators to regulate neurogenesis.
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Affiliation(s)
- Meng Zhang
- Yale Stem Cell Center, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Dong Chen
- Yale Stem Cell Center, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, USA
| | - Jing Xia
- Yale Stem Cell Center, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Wenqi Han
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Xiekui Cui
- Yale Stem Cell Center, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Nils Neuenkirchen
- Yale Stem Cell Center, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Gretchen Hermes
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut 06511, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut 06510, USA
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut 06511, USA
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Section of Comparative Medicine, Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Yale Child Study Center, Yale School of Medicine, New Haven, Connecticut 06519, USA
| | - Haifan Lin
- Yale Stem Cell Center, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Obstetrics and Gynecology, Yale School of Medicine, New Haven, Connecticut 06520, USA
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89
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Fujita Y, Masuda K, Bando M, Nakato R, Katou Y, Tanaka T, Nakayama M, Takao K, Miyakawa T, Tanaka T, Ago Y, Hashimoto H, Shirahige K, Yamashita T. Decreased cohesin in the brain leads to defective synapse development and anxiety-related behavior. J Exp Med 2017; 214:1431-1452. [PMID: 28408410 PMCID: PMC5413336 DOI: 10.1084/jem.20161517] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/14/2017] [Accepted: 03/03/2017] [Indexed: 11/21/2022] Open
Abstract
Abnormal epigenetic regulation can cause the nervous system to develop abnormally. Here, we sought to understand the mechanism by which this occurs by investigating the protein complex cohesin, which is considered to regulate gene expression and, when defective, is associated with higher-level brain dysfunction and the developmental disorder Cornelia de Lange syndrome (CdLS). We generated conditional Smc3-knockout mice and observed greater dendritic complexity and larger numbers of immature synapses in the cerebral cortex of Smc3+/- mice. Smc3+/- mice also exhibited more anxiety-related behavior, which is a symptom of CdLS. Further, a gene ontology analysis after RNA-sequencing suggested the enrichment of immune processes, particularly the response to interferons, in the Smc3+/- mice. Indeed, fewer synapses formed in their cortical neurons, and this phenotype was rescued by STAT1 knockdown. Thus, low levels of cohesin expression in the developing brain lead to changes in gene expression that in turn lead to a specific and abnormal neuronal and behavioral phenotype.
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Affiliation(s)
- Yuki Fujita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Koji Masuda
- Research Center for Epigenetic Disease, Institute for Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Masashige Bando
- Research Center for Epigenetic Disease, Institute for Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Ryuichiro Nakato
- Research Center for Epigenetic Disease, Institute for Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Yuki Katou
- Research Center for Epigenetic Disease, Institute for Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Takashi Tanaka
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Masahiro Nakayama
- Department of Pathology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka 594-1101, Japan
| | - Keizo Takao
- Life Science Research Center, University of Toyama, Toyama 930-0194, Japan
| | - Tsuyoshi Miyakawa
- Life Science Research Center, University of Toyama, Toyama 930-0194, Japan
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Aichi 470-1192, Japan
| | - Tatsunori Tanaka
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | - Yukio Ago
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | - Hitoshi Hashimoto
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
- Division of Bioscience, Institute for Datability Science, Osaka University, Osaka 565-0871, Japan
- iPS Cell-based Research Project on Brain Neuropharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
- Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Osaka 565-0871, Japan
| | - Katsuhiko Shirahige
- Research Center for Epigenetic Disease, Institute for Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Toshihide Yamashita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
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NEUROD2 Regulates Stim1 Expression and Store-Operated Calcium Entry in Cortical Neurons. eNeuro 2017; 4:eN-NWR-0255-16. [PMID: 28303257 PMCID: PMC5343279 DOI: 10.1523/eneuro.0255-16.2017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 01/18/2017] [Accepted: 01/25/2017] [Indexed: 12/26/2022] Open
Abstract
Calcium signaling controls many key processes in neurons, including gene expression, axon guidance, and synaptic plasticity. In contrast to calcium influx through voltage- or neurotransmitter-gated channels, regulatory pathways that control store-operated calcium entry (SOCE) in neurons are poorly understood. Here, we report a transcriptional control of Stim1 (stromal interaction molecule 1) gene, which is a major sensor of endoplasmic reticulum (ER) calcium levels and a regulator of SOCE. By using a genome-wide chromatin immunoprecipitation and sequencing approach in mice, we find that NEUROD2, a neurogenic transcription factor, binds to an intronic element within the Stim1 gene. We show that NEUROD2 limits Stim1 expression in cortical neurons and consequently fine-tunes the SOCE response upon depletion of ER calcium. Our findings reveal a novel mechanism that regulates neuronal calcium homeostasis during cortical development.
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91
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Yang X, Feng S, Tang K. COUP-TF Genes, Human Diseases, and the Development of the Central Nervous System in Murine Models. Curr Top Dev Biol 2017; 125:275-301. [PMID: 28527575 DOI: 10.1016/bs.ctdb.2016.12.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
COUP-TFI and -TFII are members of the steroid/thyroid nuclear receptor superfamily. Recent clinical studies reveal that COUP-TFI gene mutations are associated with Bosch-Boonstra-Schaaf optic atrophy syndrome displaying symptoms of optic atrophy, intellectual disability, hypotonia, seizure, autism spectrum disorders, oromotor dysfunction, thin corpus callosum, or hearing defects, and COUP-TFII gene mutations lead to congenital heart defects and/or congenital diaphragmatic hernia with developmental delay and mental defects. In this review, we first describe the functions of COUP-TF genes in the morphogenesis of mouse forebrain including cerebral cortex, hippocampus, amygdala complex, hypothalamus, and cortical interneuron. Then, we address their roles in the development of cerebellum, glial cells, neural crest cells, and adult neuronal stem cells. Clearly, the investigations on the functions of COUP-TF genes in the developing mouse central nervous system will benefit not only the understanding of neurodevelopment, but also the etiology of human mental diseases.
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Affiliation(s)
- Xiong Yang
- Institute of Life Science, Nanchang University, Nanchang, Jiangxi, China
| | - Su Feng
- Institute of Life Science, Nanchang University, Nanchang, Jiangxi, China
| | - Ke Tang
- Institute of Life Science, Nanchang University, Nanchang, Jiangxi, China.
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92
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Dimidschstein J, Chen Q, Tremblay R, Rogers SL, Saldi GA, Guo L, Xu C, Liu R, Lu C, Chu J, Avery MC, Rashid SM, Baek M, Jacob AL, Smith GB, Wilson DE, Kosche G, Kruglikov I, Rusielewicz T, Kotak VC, Mowery TM, Anderson SA, Callaway EM, Dasen JS, Fitzpatrick D, Fossati V, Long MA, Noggle S, Reynolds JH, Sanes DH, Rudy B, Feng G, Fishell G. A viral strategy for targeting and manipulating interneurons across vertebrate species. Nat Neurosci 2016; 19:1743-1749. [PMID: 27798629 PMCID: PMC5348112 DOI: 10.1038/nn.4430] [Citation(s) in RCA: 306] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 09/27/2016] [Indexed: 12/11/2022]
Abstract
A fundamental impediment to understanding the brain is the availability of inexpensive and robust methods for targeting and manipulating specific neuronal populations. The need to overcome this barrier is pressing because there are considerable anatomical, physiological, cognitive and behavioral differences between mice and higher mammalian species in which it is difficult to specifically target and manipulate genetically defined functional cell types. In particular, it is unclear the degree to which insights from mouse models can shed light on the neural mechanisms that mediate cognitive functions in higher species, including humans. Here we describe a novel recombinant adeno-associated virus that restricts gene expression to GABAergic interneurons within the telencephalon. We demonstrate that the viral expression is specific and robust, allowing for morphological visualization, activity monitoring and functional manipulation of interneurons in both mice and non-genetically tractable species, thus opening the possibility to study GABAergic function in virtually any vertebrate species.
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Affiliation(s)
- J Dimidschstein
- NYU Neuroscience Institute and the Department of Neuroscience and Physiology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
- Center for Genomics & Systems Biology, New York University, Abu Dhabi, UAE
| | - Q Chen
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - R Tremblay
- NYU Neuroscience Institute and the Department of Neuroscience and Physiology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - SL Rogers
- NYU Neuroscience Institute and the Department of Neuroscience and Physiology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - GA Saldi
- NYU Neuroscience Institute and the Department of Neuroscience and Physiology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - L Guo
- NYU Neuroscience Institute and the Department of Neuroscience and Physiology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
- Center for Genomics & Systems Biology, New York University, Abu Dhabi, UAE
| | - C Xu
- NYU Neuroscience Institute and the Department of Neuroscience and Physiology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
- Center for Genomics & Systems Biology, New York University, Abu Dhabi, UAE
| | - R Liu
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - C Lu
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - J Chu
- Department of Psychiatry, Children’s Hospital of Philadelphia and UPenn School of Medicine, Philadelphia, PA 19104, USA
| | - MC Avery
- Systems Neurobiology Laboratories, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - SM Rashid
- Systems Neurobiology Laboratories, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - M Baek
- NYU Neuroscience Institute and the Department of Neuroscience and Physiology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - AL Jacob
- Department of Functional Architecture and Development of Cerebral Cortex, Max Planck Florida Institute for Neuroscience, Jupiter, FL 33458, USA
| | - GB Smith
- Department of Functional Architecture and Development of Cerebral Cortex, Max Planck Florida Institute for Neuroscience, Jupiter, FL 33458, USA
| | - DE Wilson
- Department of Functional Architecture and Development of Cerebral Cortex, Max Planck Florida Institute for Neuroscience, Jupiter, FL 33458, USA
| | - G Kosche
- NYU Neuroscience Institute and the Department of Otolaryngology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - I Kruglikov
- New York Stem Cell Foundation, New York, NY10023, USA
| | - T Rusielewicz
- New York Stem Cell Foundation, New York, NY10023, USA
| | - VC Kotak
- NYU Center for Neural Science, New York University, New York, NY 10003, USA
| | - TM Mowery
- NYU Center for Neural Science, New York University, New York, NY 10003, USA
| | - SA Anderson
- Department of Psychiatry, Children’s Hospital of Philadelphia and UPenn School of Medicine, Philadelphia, PA 19104, USA
| | - EM Callaway
- Systems Neurobiology Laboratories, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - JS Dasen
- NYU Neuroscience Institute and the Department of Neuroscience and Physiology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - D Fitzpatrick
- Department of Functional Architecture and Development of Cerebral Cortex, Max Planck Florida Institute for Neuroscience, Jupiter, FL 33458, USA
| | - V Fossati
- New York Stem Cell Foundation, New York, NY10023, USA
| | - MA Long
- NYU Neuroscience Institute and the Department of Otolaryngology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - S Noggle
- New York Stem Cell Foundation, New York, NY10023, USA
| | - JH Reynolds
- Systems Neurobiology Laboratories, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - DH Sanes
- NYU Center for Neural Science, New York University, New York, NY 10003, USA
| | - B Rudy
- NYU Neuroscience Institute and the Department of Neuroscience and Physiology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - G Feng
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - G Fishell
- NYU Neuroscience Institute and the Department of Neuroscience and Physiology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
- Center for Genomics & Systems Biology, New York University, Abu Dhabi, UAE
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93
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Cortical interneuron specification: the juncture of genes, time and geometry. Curr Opin Neurobiol 2016; 42:17-24. [PMID: 27889625 DOI: 10.1016/j.conb.2016.10.003] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/20/2016] [Accepted: 10/28/2016] [Indexed: 01/23/2023]
Abstract
A fundamental question in developmental neuroscience is how hundreds of diverse cell types are generated to form specialized brain regions. The ganglionic eminences (GEs) are embryonic brain structures located in the ventral telencephalon that produce many inhibitory GABA (γ-Aminobutyric acid)-ergic cell types, including long-range projection neurons and local interneurons (INs), which disperse widely throughout the brain. While much has been discovered about the origin and wiring of these cells, a major question remains: how do neurons originating in the GEs become specified during development as one differentiated subtype versus another? This review will cover recent work that has advanced our knowledge of the mechanisms governing cortical interneuron subtype specification, particularly progenitors' spatial origin, birthdates, lineage, and mode of division.
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94
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Gandal MJ, Leppa V, Won H, Parikshak NN, Geschwind DH. The road to precision psychiatry: translating genetics into disease mechanisms. Nat Neurosci 2016; 19:1397-1407. [DOI: 10.1038/nn.4409] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/08/2016] [Indexed: 12/13/2022]
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Larsen ZH, Chander P, Joyner JA, Floruta CM, Demeter TL, Weick JP. Effects of Ethanol on Cellular Composition and Network Excitability of Human Pluripotent Stem Cell-Derived Neurons. Alcohol Clin Exp Res 2016; 40:2339-2350. [PMID: 27717039 DOI: 10.1111/acer.13218] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 08/12/2016] [Indexed: 11/30/2022]
Abstract
BACKGROUND Prenatal alcohol exposure (PAE) in animal models results in excitatory-inhibitory (E/I) imbalance in neocortex due to alterations in the GABAergic interneuron (IN) differentiation and migration. Thus, E/I imbalance is a potential cause for intellectual disability in individuals with fetal alcohol spectrum disorder (FASD), but whether ethanol (EtOH) changes glutamatergic and GABAergic IN specification during human development remains unknown. Here, we created a human cellular model of PAE/FASD and tested the hypothesis that EtOH exposure during differentiation of human pluripotent stem cell-derived neurons (hPSNs) would cause the aberrant production of glutamatergic and GABAergic neurons, resulting in E/I imbalance. METHODS We applied 50 mM EtOH daily to differentiating hPSNs for 50 days to model chronic first-trimester exposure. We used quantitative polymerase chain reaction, immunocytochemical, and electrophysiological analysis to examine the effects of EtOH on hPSN specification and functional E/I balance. RESULTS We found that EtOH did not alter neural induction nor general forebrain patterning and had no effect on the expression of markers of excitatory cortical pyramidal neurons. In contrast, our data revealed highly significant changes to levels of transcripts involved with IN precursor development (e.g., GSX2, DLX1/2/5/6, NR2F2) as well as mature IN specification (e.g., SST, NPY). Interestingly, EtOH did not affect the number of GABAergic neurons generated nor the frequency or amplitude of miniature excitatory and inhibitory postsynaptic currents. CONCLUSIONS Similar to in vivo rodent studies, EtOH significantly and specifically altered the expression of genes involved with IN specification from hPSNs, but did not cause imbalances of synaptic excitation-inhibition. Thus, our findings corroborate previous studies pointing to aberrant neuronal differentiation as an underlying mechanism of intellectual disability in FASD. However, in contrast to rodent binge models, our chronic exposure model suggests possible compensatory mechanisms that may cause more subtle defects of network processing rather than gross alterations in total E/I balance.
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Affiliation(s)
- Zoe H Larsen
- Department of Neurosciences, University of New Mexico-Health Science Center, Albuquerque, New Mexico
| | - Praveen Chander
- Department of Neurosciences, University of New Mexico-Health Science Center, Albuquerque, New Mexico
| | - Jason A Joyner
- Department of Neurosciences, University of New Mexico-Health Science Center, Albuquerque, New Mexico
| | - Crina M Floruta
- Department of Neurosciences, University of New Mexico-Health Science Center, Albuquerque, New Mexico
| | - Tess L Demeter
- Department of Neurosciences, University of New Mexico-Health Science Center, Albuquerque, New Mexico
| | - Jason P Weick
- Department of Neurosciences, University of New Mexico-Health Science Center, Albuquerque, New Mexico.
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96
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Fujiwara N, Cave JW. Partial Conservation between Mice and Humans in Olfactory Bulb Interneuron Transcription Factor Codes. Front Neurosci 2016; 10:337. [PMID: 27489533 PMCID: PMC4951497 DOI: 10.3389/fnins.2016.00337] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/04/2016] [Indexed: 11/13/2022] Open
Abstract
The mammalian main olfactory bulb (OB) has a large population of GABAergic inhibitory interneurons that contains several subtypes defined by the co-expression other neurotransmitters and calcium binding proteins. The three most commonly studied OB interneuron subtypes co-express either Calretinin, Calbindin, or Tyrosine hydroxylase (Th). Combinations of transcription factors used to specify the phenotype of progenitors are referred to as transcription factor codes, and the current understanding of transcription factor codes that specify OB inhibitory neuron phenotypes are largely based on studies in mice. The conservation of these transcription factor codes in the human OB, however, has not been investigated. The aim of this study was to establish whether transcription factor codes in OB interneurons are conserved between mice and humans. This study compared the co-expression of Foxp2, Meis2, Pax6, and Sp8 transcription factors with Calretinin, Calbindin, or Th in human and mouse OB interneurons. This analysis found strong conservation of Calretinin co-expression with Sp8 and Meis2 as well as Th co-expression with Pax6 and Meis2. This analysis also showed that selective Foxp2 co-expression with Calbindin was conserved between mice and humans, which suggests Foxp2 is a novel determinant of the OB Calbindin interneuron phenotype. Together, the findings in this study provide insight into the conservation of transcription codes for OB interneuron phenotypes between humans and mice, as well as reveal some important differences between the species. This advance in our understanding of transcription factor codes in OB interneurons provides an important complement to the codes that have been established for other regions within the mammalian central nervous system, such as the cortex and spinal cord.
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Affiliation(s)
- Nana Fujiwara
- Burke Medical Research Institute White Plains, NY, USA
| | - John W Cave
- Burke Medical Research InstituteWhite Plains, NY, USA; The Feil Family Brain and Mind Research Institute, Weill Cornell MedicineNew York, NY, USA
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97
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Vogel Ciernia A, LaSalle J. The landscape of DNA methylation amid a perfect storm of autism aetiologies. Nat Rev Neurosci 2016; 17:411-23. [PMID: 27150399 PMCID: PMC4966286 DOI: 10.1038/nrn.2016.41] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Increasing evidence points to a complex interplay between genes and the environment in autism spectrum disorder (ASD), including rare de novo mutations in chromatin genes such as methyl-CpG binding protein 2 (MECP2) in Rett syndrome. Epigenetic mechanisms such as DNA methylation act at this interface, reflecting the plasticity in metabolic and neurodevelopmentally regulated gene pathways. Genome-wide studies of gene sequences, gene pathways and DNA methylation are providing valuable mechanistic insights into ASD. The dynamic developmental landscape of DNA methylation is vulnerable to numerous genetic and environmental insults: therefore, understanding pathways that are central to this 'perfect storm' will be crucial to improving the diagnosis and treatment of ASD.
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Affiliation(s)
- Annie Vogel Ciernia
- Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, California 95616, USA
| | - Janine LaSalle
- Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, California 95616, USA
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98
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Silbereis JC, Pochareddy S, Zhu Y, Li M, Sestan N. The Cellular and Molecular Landscapes of the Developing Human Central Nervous System. Neuron 2016; 89:248-68. [PMID: 26796689 DOI: 10.1016/j.neuron.2015.12.008] [Citation(s) in RCA: 440] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The human CNS follows a pattern of development typical of all mammals, but certain neurodevelopmental features are highly derived. Building the human CNS requires the precise orchestration and coordination of myriad molecular and cellular processes across a staggering array of cell types and over a long period of time. Dysregulation of these processes affects the structure and function of the CNS and can lead to neurological or psychiatric disorders. Recent technological advances and increased focus on human neurodevelopment have enabled a more comprehensive characterization of the human CNS and its development in both health and disease. The aim of this review is to highlight recent advancements in our understanding of the molecular and cellular landscapes of the developing human CNS, with focus on the cerebral neocortex, and the insights these findings provide into human neural evolution, function, and dysfunction.
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Affiliation(s)
- John C Silbereis
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sirisha Pochareddy
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Ying Zhu
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Mingfeng Li
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Department of Genetics and Department of Psychiatry, Yale School of Medicine, New Haven, CT 06510, USA; Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, CT 06510, USA; Section of Comparative Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Yale Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA; Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA.
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99
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Shima Y, Sugino K, Hempel CM, Shima M, Taneja P, Bullis JB, Mehta S, Lois C, Nelson SB. A Mammalian enhancer trap resource for discovering and manipulating neuronal cell types. eLife 2016; 5:e13503. [PMID: 26999799 PMCID: PMC4846381 DOI: 10.7554/elife.13503] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/18/2016] [Indexed: 12/16/2022] Open
Abstract
There is a continuing need for driver strains to enable cell-type-specific manipulation in the nervous system. Each cell type expresses a unique set of genes, and recapitulating expression of marker genes by BAC transgenesis or knock-in has generated useful transgenic mouse lines. However, since genes are often expressed in many cell types, many of these lines have relatively broad expression patterns. We report an alternative transgenic approach capturing distal enhancers for more focused expression. We identified an enhancer trap probe often producing restricted reporter expression and developed efficient enhancer trap screening with the PiggyBac transposon. We established more than 200 lines and found many lines that label small subsets of neurons in brain substructures, including known and novel cell types. Images and other information about each line are available online (enhancertrap.bio.brandeis.edu). DOI:http://dx.doi.org/10.7554/eLife.13503.001 Scientists can track and even alter the activity of different kinds of neurons, as well as the connections between neurons, by manipulating their genes. However, most genes are active in many different kinds of cells in many different places in the brain, making it difficult to track or target only a particular neuron or brain area. Enhancers are sections of DNA that can regulate the activity of nearby genes so that they are only active in very specific cell types, and an “enhancer trap” is a genetic approach that essentially hijacks enhancers to express artificial genes in those same cell types. The technique relies on inserting a genetic marker, which can be easily tracked, into random locations in the genome. If this marker then interacts with an enhancer, it is activated and the effect of the enhancer on gene expression can be assessed. This method has been used in fruit flies and fish to identify enhancers that specifically restrict gene expression to a small subset of cells. Now, Shima et al. show that enhancer traps can be used successfully in mammals too. The experiments produced over 200 different strains of mice, many with the fluorescent marker only in specific brain areas or in specific kinds of brain cells. Some of the types of brain cells uncovered by these experiments are new, and the labelling of specific brain cells and brain areas in different strains makes these mice a useful resource for future work. Furthermore, it will be relatively straightforward to produce many more strains of these mice, because it would simply involve crossbreeding mice. It is likely that some of these to-be-discovered strains will be useful tools for research as well. DOI:http://dx.doi.org/10.7554/eLife.13503.002
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Affiliation(s)
- Yasuyuki Shima
- Department of Biology and National Center for Behavioral Genomics, Brandeis University, Waltham, United States
| | - Ken Sugino
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Chris Martin Hempel
- Department of Biology and National Center for Behavioral Genomics, Brandeis University, Waltham, United States
| | - Masami Shima
- Department of Biology and National Center for Behavioral Genomics, Brandeis University, Waltham, United States
| | - Praveen Taneja
- Department of Biology and National Center for Behavioral Genomics, Brandeis University, Waltham, United States
| | - James B Bullis
- Department of Biology and National Center for Behavioral Genomics, Brandeis University, Waltham, United States
| | - Sonam Mehta
- Department of Biology and National Center for Behavioral Genomics, Brandeis University, Waltham, United States
| | - Carlos Lois
- Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, United States
| | - Sacha B Nelson
- Department of Biology and National Center for Behavioral Genomics, Brandeis University, Waltham, United States
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100
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A transducible nuclear/nucleolar protein, mLLP, regulates neuronal morphogenesis and synaptic transmission. Sci Rep 2016; 6:22892. [PMID: 26961175 PMCID: PMC4790632 DOI: 10.1038/srep22892] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/23/2016] [Indexed: 12/03/2022] Open
Abstract
Cell-permeable proteins are emerging as unconventional regulators of signal transduction and providing a potential for therapeutic applications. However, only a few of them are identified and studied in detail. We identify a novel cell-permeable protein, mouse LLP homolog (mLLP), and uncover its roles in regulating neural development. We found that mLLP is strongly expressed in developing nervous system and that mLLP knockdown or overexpression during maturation of cultured neurons affected the neuronal growth and synaptic transmission. Interestingly, extracellular addition of mLLP protein enhanced dendritic arborization, demonstrating the non-cell-autonomous effect of mLLP. Moreover, mLLP interacts with CCCTC-binding factor (CTCF) as well as transcriptional machineries and modulates gene expression involved in neuronal growth. Together, these results illustrate the characteristics and roles of previously unknown cell-permeable protein mLLP in modulating neural development.
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