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Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain. Neuron 2015; 86:1369-84. [PMID: 26087164 PMCID: PMC4499463 DOI: 10.1016/j.neuron.2015.05.018] [Citation(s) in RCA: 485] [Impact Index Per Article: 53.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 04/14/2015] [Accepted: 05/07/2015] [Indexed: 12/20/2022]
Abstract
Neuronal diversity is essential for mammalian brain function but poses a challenge to molecular profiling. To address the need for tools that facilitate cell-type-specific epigenomic studies, we developed the first affinity purification approach to isolate nuclei from genetically defined cell types in a mammal. We combine this technique with next-generation sequencing to show that three subtypes of neocortical neurons have highly distinctive epigenomic landscapes. Over 200,000 regions differ in chromatin accessibility and DNA methylation signatures characteristic of gene regulatory regions. By footprinting and motif analyses, these regions are predicted to bind distinct cohorts of neuron subtype-specific transcription factors. Neuronal epigenomes reflect both past and present gene expression, with DNA hyper-methylation at developmentally critical genes appearing as a novel epigenomic signature in mature neurons. Taken together, our findings link the functional and transcriptional complexity of neurons to their underlying epigenomic diversity.
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DeRosa BA, Belle KC, Thomas BJ, Cukier HN, Pericak-Vance MA, Vance JM, Dykxhoorn DM. hVGAT-mCherry: A novel molecular tool for analysis of GABAergic neurons derived from human pluripotent stem cells. Mol Cell Neurosci 2015; 68:244-57. [PMID: 26284979 PMCID: PMC4593758 DOI: 10.1016/j.mcn.2015.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 07/30/2015] [Accepted: 08/10/2015] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND GABAergic synaptic transmission is known to play a critical role in the assembly of neuronal circuits during development and is responsible for maintaining the balance between excitatory and inhibitory signaling in the brain during maturation into adulthood. Importantly, defects in GABAergic neuronal function and signaling have been linked to a number of neurological diseases, including autism spectrum disorders, schizophrenia, and epilepsy. With patient-specific induced pluripotent stem cell (iPSC)-based models of neurological disease, it is now possible to investigate the disease mechanisms that underlie deficits in GABAergic function in affected human neurons. To that end, tools that enable the labeling and purification of viable GABAergic neurons from human pluripotent stem cells would be of great value. RESULTS To address the need for tools that facilitate the identification and isolation of viable GABAergic neurons from the in vitro differentiation of iPSC lines, a cell type-specific promoter-driven fluorescent reporter construct was developed that utilizes the human vesicular GABA transporter (hVGAT) promoter to drive the expression of mCherry specifically in VGAT-expressing neurons. The transduction of iPSC-derived forebrain neuronal cultures with the hVGAT promoter-mCherry lentiviral reporter construct specifically labeled GABAergic neurons. Immunocytochemical analysis of hVGAT-mCherry expression cells showed significant co-labeling with the GABAergic neuronal markers for endogenous VGAT, GABA, and GAD67. Expression of mCherry from the VGAT promoter showed expression in several cortical interneuron subtypes to similar levels. In addition, an effective and reproducible protocol was developed to facilitate the fluorescent activated cell sorting (FACS)-mediated purification of high yields of viable VGAT-positive cells. CONCLUSIONS These studies demonstrate the utility of the hVGAT-mCherry reporter construct as an effective tool for studying GABAergic neurons differentiated in vitro from human pluripotent stem cells. This approach could provide a means of obtaining large quantities of viable GABAergic neurons derived from disease-specific hiPSCs that could be used for functional assays or high-throughput screening of small molecule libraries.
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Affiliation(s)
- Brooke A DeRosa
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, United States; John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States.
| | - Kinsley C Belle
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, United States; John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States.
| | - Blake J Thomas
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, United States; John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States.
| | - Holly N Cukier
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, United States; John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States.
| | - Margaret A Pericak-Vance
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, United States; John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States.
| | - Jeffery M Vance
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, United States; John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States.
| | - Derek M Dykxhoorn
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, United States; John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, United States.
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A neural basis for melanocortin-4 receptor-regulated appetite. Nat Neurosci 2015; 18:863-71. [PMID: 25915476 PMCID: PMC4446192 DOI: 10.1038/nn.4011] [Citation(s) in RCA: 291] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 03/30/2015] [Indexed: 12/14/2022]
Abstract
Pro-opiomelanocortin (POMC)- and agouti-related peptide (AgRP)-expressing neurons are oppositely regulated by caloric depletion and co-ordinately stimulate and inhibit homeostatic satiety, respectively. This bimodality is principally underscored by the antagonistic actions of these ligands at downstream melanocortin-4 receptors (MC4R) within the paraventricular nucleus of the hypothalamus. Although this population is critical to energy balance the underlying neural circuitry remains unknown. Enabled by mice expressing Cre-recombinase in MC4R neurons, we demonstrate bidirectional control of feeding following real-time activation and inhibition of PVHMC4R neurons and further identify these cells as a functional exponent of ARCAgRP neuron-driven hunger. Moreover, we reveal this function to be mediated by a PVHMC4R→lateral parabrachial nucleus (LPBN) pathway. Activation of this circuit encodes positive valence, but only in calorically depleted mice. Thus, the satiating and appetitive nature of PVHMC4R→LPBN neurons supports the principles of drive reduction and highlights this circuit as a promising target for anti-obesity drug development.
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Kobayashi Y, Ye Z, Hensch TK. Clock genes control cortical critical period timing. Neuron 2015; 86:264-75. [PMID: 25801703 PMCID: PMC4392344 DOI: 10.1016/j.neuron.2015.02.036] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Revised: 01/25/2015] [Accepted: 02/18/2015] [Indexed: 01/05/2023]
Abstract
Circadian rhythms control a variety of physiological processes, but whether they may also time brain development remains largely unknown. Here, we show that circadian clock genes control the onset of critical period plasticity in the neocortex. Within visual cortex of Clock-deficient mice, the emergence of circadian gene expression was dampened, and the maturation of inhibitory parvalbumin (PV) cell networks slowed. Loss of visual acuity in response to brief monocular deprivation was concomitantly delayed and rescued by direct enhancement of GABAergic transmission. Conditional deletion of Clock or Bmal1 only within PV cells recapitulated the results of total Clock-deficient mice. Unique downstream gene sets controlling synaptic events and cellular homeostasis for proper maturation and maintenance were found to be mis-regulated by Clock deletion specifically within PV cells. These data demonstrate a developmental role for circadian clock genes outside the suprachiasmatic nucleus, which may contribute mis-timed brain plasticity in associated mental disorders.
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Affiliation(s)
- Yohei Kobayashi
- Center for Brain Science, Department of Molecular Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA; F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Zhanlei Ye
- Center for Brain Science, Department of Molecular Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Takao K Hensch
- Center for Brain Science, Department of Molecular Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA; F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA.
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Khuansuwan S, Gamse JT. Identification of differentially expressed genes during development of the zebrafish pineal complex using RNA sequencing. Dev Biol 2014; 395:144-53. [PMID: 25173875 DOI: 10.1016/j.ydbio.2014.08.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/17/2014] [Accepted: 08/17/2014] [Indexed: 02/03/2023]
Abstract
We describe a method for isolating RNA suitable for high-throughput RNA sequencing (RNA-seq) from small numbers of fluorescently labeled cells isolated from live zebrafish (Danio rerio) embryos without using costly, commercially available columns. This method ensures high cell viability after dissociation and suspension of cells and gives a very high yield of intact RNA. We demonstrate the utility of our new protocol by isolating RNA from fluorescence activated cell sorted (FAC sorted) pineal complex neurons in wild-type and tbx2b knockdown embryos at 24 hours post-fertilization. Tbx2b is a transcription factor required for pineal complex formation. We describe a bioinformatics pipeline used to analyze differential expression following high-throughput sequencing and demonstrate the validity of our results using in situ hybridization of differentially expressed transcripts. This protocol brings modern transcriptome analysis to the study of small cell populations in zebrafish.
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Affiliation(s)
- Sataree Khuansuwan
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Joshua T Gamse
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
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Li X, Baker-Andresen D, Zhao Q, Marshall V, Bredy TW. Methyl CpG Binding Domain Ultra-Sequencing: a novel method for identifying inter-individual and cell-type-specific variation in DNA methylation. GENES BRAIN AND BEHAVIOR 2014; 13:721-31. [DOI: 10.1111/gbb.12150] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 05/06/2014] [Accepted: 06/11/2014] [Indexed: 12/16/2022]
Affiliation(s)
- X. Li
- Psychiatric Epigenomics Laboratory, Queensland Brain Institute; The University of Queensland; Brisbane
| | - D. Baker-Andresen
- Psychiatric Epigenomics Laboratory, Queensland Brain Institute; The University of Queensland; Brisbane
| | - Q. Zhao
- Psychiatric Epigenomics Laboratory, Queensland Brain Institute; The University of Queensland; Brisbane
| | - V. Marshall
- Psychiatric Epigenomics Laboratory, Queensland Brain Institute; The University of Queensland; Brisbane
- Murdoch Children's Research Institute (MCRI); Royal Children's Hospital; Melbourne Australia
| | - T. W. Bredy
- Psychiatric Epigenomics Laboratory, Queensland Brain Institute; The University of Queensland; Brisbane
- Center for Neurobiology of Learning & Memory; University of California Irvine; Irvine CA USA
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Qu B, Gu Y, Shen J, Qin J, Bao J, Hu Y, Zeng W, Dong W. Trehalose maintains vitality of mouse epididymal epithelial cells and mediates gene transfer. PLoS One 2014; 9:e92483. [PMID: 24651491 PMCID: PMC3961358 DOI: 10.1371/journal.pone.0092483] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 02/24/2014] [Indexed: 11/20/2022] Open
Abstract
In the present study, trehalose was utilized to improve primary culture of mouse epididymal epithelial cells in vitro, and to enhance naked DNA delivery in epididymis in vivo. During the six-day culture, the proliferation activity of the cells in the medium with addition of trehalose was higher than that of those cells cultured in absence of trehalose (p<0.01). To determine the optimal concentration for cell proliferation, a series of trehalose concentrations (0, 60, 120, 180 mM) were tested, and the result indicated that the cell in the medium with 120 mM trehalose showed the highest proliferation potential. The epididymis epithelial cells were cultured in the medium containing 120 mM trehalose upon 16th passage, and they continued expressing markers of epididymal epithelial cell, such as rE-RABP, AR and ER-beta. Our study also indicated that trehalose concentrations of 120–240 mM, especially 180 mM, could effectively enhance DNA delivery into the mouse epididymis epithelial cell in vitro. Moreover, trehalose could induce in vivo expression of exogenous DNA in epididymal epithelial cells and help to internalize plasmid into sperm,which did not influence motility of sperm when the mixture of trehalose (180 mM) and DNA was injected into epididymal lumen through efferent tubule. This study suggested that trehalose, as an effective and safer reagent, could be employed potentially to maintain vitality of mouse epididymal epthetial cells during long-term culture in vitro and to mediate in vitro and in vivo gene transfer.
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Affiliation(s)
- Bin Qu
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, P. R. China
| | - Yihua Gu
- Shanghai Institute of Planned Parenthood Research, Shanghai, P. R. China
| | - Jian Shen
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, P. R. China
| | - Jinzhou Qin
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, P. R. China
| | - Jianqiang Bao
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America
| | - Yuan Hu
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, P. R. China
| | - Wenxian Zeng
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, P. R. China
| | - Wuzi Dong
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, P. R. China
- * E-mail:
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