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Yamashiro K, Liu J, Matsumoto N, Ikegaya Y. Deep Learning-Based Classification of GAD67-Positive Neurons Without the Immunosignal. Front Neuroanat 2021; 15:643067. [PMID: 33867947 PMCID: PMC8044854 DOI: 10.3389/fnana.2021.643067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/01/2021] [Indexed: 02/02/2023] Open
Abstract
Excitatory neurons and GABAergic interneurons constitute neural circuits and play important roles in information processing. In certain brain regions, such as the neocortex and the hippocampus, there are fewer interneurons than excitatory neurons. Interneurons have been quantified via immunohistochemistry, for example, for GAD67, an isoform of glutamic acid decarboxylase. Additionally, the expression level of other proteins varies among cell types. For example, NeuN, a commonly used marker protein for postmitotic neurons, is expressed differently across brain regions and cell classes. Thus, we asked whether GAD67-immunopositive neurons can be detected using the immunofluorescence signals of NeuN and the fluorescence signals of Nissl substances. To address this question, we stained neurons in layers 2/3 of the primary somatosensory cortex (S1) and the primary motor cortex (M1) of mice and manually labeled the neurons as either cell type using GAD67 immunosignals. We then sought to detect GAD67-positive neurons without GAD67 immunosignals using a custom-made deep learning-based algorithm. Using this deep learning-based model, we succeeded in the binary classification of the neurons using Nissl and NeuN signals without referring to the GAD67 signals. Furthermore, we confirmed that our deep learning-based method surpassed classic machine-learning methods in terms of binary classification performance. Combined with the visualization of the hidden layer of our deep learning algorithm, our model provides a new platform for identifying unbiased criteria for cell-type classification.
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Affiliation(s)
- Kotaro Yamashiro
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Jiayan Liu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Nobuyoshi Matsumoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuji Ikegaya
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.,Institute for AI and Beyond, The University of Tokyo, Tokyo, Japan.,Center for Information and Neural Networks, National Institute of Information and Communications Technology, Osaka, Japan
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2
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Mampay M, Velasco-Estevez M, Rolle SO, Chaney AM, Boutin H, Dev KK, Moeendarbary E, Sheridan GK. Spatiotemporal immunolocalisation of REST in the brain of healthy ageing and Alzheimer's disease rats. FEBS Open Bio 2020; 11:146-163. [PMID: 33185010 PMCID: PMC7780110 DOI: 10.1002/2211-5463.13036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 10/25/2020] [Accepted: 11/04/2020] [Indexed: 12/30/2022] Open
Abstract
In the brain, REST (Repressor Element‐1 Silencing Transcription factor) is a key regulator of neuron cell‐specific gene expression. Nuclear translocation of neuronal REST has been shown to be neuroprotective in a healthy ageing context. In contrast, inability to upregulate nuclear REST is thought to leave ageing neurons vulnerable to neurodegenerative stimuli, such as Alzheimer’s disease (AD) pathology. Hippocampal and cortical neurons are known to be particularly susceptible to AD‐associated neurodegeneration. However, REST expression has not been extensively characterised in the healthy ageing brain. Here, we examined the spatiotemporal immunolocalisation of REST in the brains of healthy ageing wild‐type Fischer‐344 and transgenic Alzheimer’s disease rats (TgF344‐AD). Nuclear expression of REST increased from 6 months to 18 months of age in the hippocampus, frontal cortex and subiculum of wild‐type rats, but not in TgF344‐AD rats. No changes in REST were measured in more posterior cortical regions or in the thalamus. Interestingly, levels of the presynaptic marker synaptophysin, a known gene target of REST, were lower in CA1 hippocampal neurons of 18‐month TgF344‐AD rats compared to 18‐month wild‐types, suggesting that elevated nuclear REST may protect against synapse loss in the CA1 of 18‐month wild‐type rats. High REST expression in ageing wild‐type rats did not, however, protect against axonal loss nor against astroglial reactivity in the hippocampus. Taken together, our data confirm that changes in nuclear REST expression are context‐, age‐ and brain region‐specific. Moreover, key brain structures involved in learning and memory display elevated REST expression in healthy ageing wild‐type rats but not TgF344‐AD rats.
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Affiliation(s)
- Myrthe Mampay
- School of Pharmacy and Biomolecular Sciences, University of Brighton, UK
| | - María Velasco-Estevez
- Drug Development, Department of Physiology, School of Medicine, Trinity College Dublin, Ireland
| | - Sara O Rolle
- The Sainsbury Welcome Centre for Neural Circuits and Behaviour, University College London, UK
| | - Aisling M Chaney
- Faculty of Biology, Medicine and Health, School of Health Sciences, Division of Informatics, Imaging and Data Sciences, University of Manchester, UK
| | - Hervé Boutin
- Wolfson Molecular Imaging Centre, University of Manchester, UK.,Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, UK
| | - Kumlesh K Dev
- Drug Development, Department of Physiology, School of Medicine, Trinity College Dublin, Ireland
| | | | - Graham K Sheridan
- School of Life Sciences, Queens Medical Centre, University of Nottingham, UK
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3
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Pai S, Li P, Killinger B, Marshall L, Jia P, Liao J, Petronis A, Szabó PE, Labrie V. Differential methylation of enhancer at IGF2 is associated with abnormal dopamine synthesis in major psychosis. Nat Commun 2019; 10:2046. [PMID: 31053723 PMCID: PMC6499808 DOI: 10.1038/s41467-019-09786-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 03/27/2019] [Indexed: 01/08/2023] Open
Abstract
Impaired neuronal processes, including dopamine imbalance, are central to the pathogenesis of major psychosis, but the molecular origins are unclear. Here we perform a multi-omics study of neurons isolated from the prefrontal cortex in schizophrenia and bipolar disorder (n = 55 cases and 27 controls). DNA methylation, transcriptomic, and genetic-epigenetic interactions in major psychosis converged on pathways of neurodevelopment, synaptic activity, and immune functions. We observe prominent hypomethylation of an enhancer within the insulin-like growth factor 2 (IGF2) gene in major psychosis neurons. Chromatin conformation analysis revealed that this enhancer targets the nearby tyrosine hydroxylase (TH) gene responsible for dopamine synthesis. In patients, we find hypomethylation of the IGF2 enhancer is associated with increased TH protein levels. In mice, Igf2 enhancer deletion disrupts the levels of TH protein and striatal dopamine, and induces transcriptional and proteomic abnormalities affecting neuronal structure and signaling. Our data suggests that epigenetic activation of the enhancer at IGF2 may enhance dopamine synthesis associated with major psychosis.
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Affiliation(s)
- Shraddha Pai
- The Donnelly Centre, University of Toronto, Toronto, M5S 3E1, ON, Canada.
- The Centre for Addiction and Mental Health, Toronto, M5T 1R8, ON, Canada.
| | - Peipei Li
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, 49503, MI, USA
| | - Bryan Killinger
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, 49503, MI, USA
| | - Lee Marshall
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, 49503, MI, USA
| | - Peixin Jia
- Krembil Family Epigenetics Laboratory, Centre for Addiction and Mental Health, Toronto, M5T 1R8, ON, Canada
| | - Ji Liao
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, 49503, MI, USA
| | - Arturas Petronis
- Krembil Family Epigenetics Laboratory, Centre for Addiction and Mental Health, Toronto, M5T 1R8, ON, Canada
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257, Vilnius, Lithuania
| | - Piroska E Szabó
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, 49503, MI, USA
| | - Viviane Labrie
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, 49503, MI, USA.
- Krembil Family Epigenetics Laboratory, Centre for Addiction and Mental Health, Toronto, M5T 1R8, ON, Canada.
- Division of Psychiatry and Behavioral Medicine, College of Human Medicine, Michigan State University, Grand Rapids, 49503, MI, USA.
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4
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Uchigashima M, Cheung A, Suh J, Watanabe M, Futai K. Differential expression of neurexin genes in the mouse brain. J Comp Neurol 2019; 527:1940-1965. [PMID: 30761534 DOI: 10.1002/cne.24664] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/04/2019] [Accepted: 02/01/2019] [Indexed: 01/22/2023]
Abstract
Synapses, highly specialized membrane junctions between neurons, connect presynaptic neurotransmitter release sites and postsynaptic ligand-gated channels. Neurexins (Nrxns), a family of presynaptic adhesion molecules, have been characterized as major regulators of synapse development and function. Via their extracellular domains, Nrxns bind to different postsynaptic proteins, generating highly diverse functional readouts through their postsynaptic binding partners. Not surprisingly given these versatile protein interactions, mutations and deletions of Nrxn genes have been identified in patients with autism spectrum disorders, intellectual disabilities, and schizophrenia. Therefore, elucidating the expression profiles of Nrxns in the brain is of high significance. Here, using chromogenic and fluorescent in situ hybridization, we characterize the expression patterns of Nrxn isoforms throughout the brain. We found that each Nrxn isoform displays a unique expression profile in a region-, cell type-, and sensory system-specific manner. Interestingly, we also found that αNrxn1 and αNrxn2 mRNAs are expressed in non-neuronal cells, including astrocytes and oligodendrocytes. Lastly, we found diverse expression patterns of genes that encode Nrxn binding proteins, such as Neuroligins (Nlgns), Leucine-rich repeat transmembrane neuronal protein (Lrrtms) and Latrophilins (Adgrls), suggesting that Nrxn proteins can mediate numerous combinations of trans-synaptic interactions. Together, our anatomical profiling of Nrxn gene expression reflects the diverse roles of Nrxn molecules.
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Affiliation(s)
- Motokazu Uchigashima
- Department of Neurobiology, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts.,Department of Anatomy, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido, Japan
| | - Amy Cheung
- Department of Neurobiology, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Julie Suh
- Department of Neurobiology, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Masahiko Watanabe
- Department of Anatomy, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido, Japan
| | - Kensuke Futai
- Department of Neurobiology, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts
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Bakshi S, McKee C, Walker K, Brown C, Chaudhry GR. Toxicity of JQ1 in neuronal derivatives of human umbilical cord mesenchymal stem cells. Oncotarget 2018; 9:33853-33864. [PMID: 30333915 PMCID: PMC6173460 DOI: 10.18632/oncotarget.26127] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 09/01/2018] [Indexed: 12/13/2022] Open
Abstract
Bromodomain and extra-terminal domain (BET) proteins regulate the transcription of many genes including c-MYC, a proto-oncogene, which is upregulated in many types of cancers. The thienodiazepine class of BET inhibitors, such as JQ1, inhibits growth of cancer cells and triggers apoptosis. However, the effects of BET inhibitors on normal cells and mesenchymal stem cells (MSCs), which are important in routine maintenance or regeneration of damaged cells and tissues, are poorly investigated. Previously, we have shown that JQ1 causes human umbilical cord MSCs to undergo cell cycle arrest and neural differentiation. In this study, we determined that JQ1 is more deleterious to neuronal derivatives (NDs) than adipogenic, chondrogenic or osteogenic derivatives of MSCs. NDs treated with JQ1 showed a significant decrease in cell proliferation, viability, and neuronal markers. JQ1 caused cell death through the intrinsic apoptotic pathway in NDs as determined by activation of Caspase 9 and increased expression of Cytochrome C. A comparative analysis showed differential action of JQ1 on MSCs and NDs. The results showed selective neuronal toxicity of JQ1 in NDs but not in the undifferentiated MSCs. These findings suggest a more careful examination of the selection and use of BET inhibitors as therapeutic agents, as they may cause unwanted damage to non-target cells and tissues.
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Affiliation(s)
- Shreeya Bakshi
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA.,OU-WB Institute for Stem Cell and Regenerative Medicine, Oakland University, Rochester, MI 48309, USA
| | - Christina McKee
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA.,OU-WB Institute for Stem Cell and Regenerative Medicine, Oakland University, Rochester, MI 48309, USA
| | - Keegan Walker
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA.,OU-WB Institute for Stem Cell and Regenerative Medicine, Oakland University, Rochester, MI 48309, USA
| | - Christina Brown
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA.,OU-WB Institute for Stem Cell and Regenerative Medicine, Oakland University, Rochester, MI 48309, USA
| | - G Rasul Chaudhry
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA.,OU-WB Institute for Stem Cell and Regenerative Medicine, Oakland University, Rochester, MI 48309, USA
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6
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de-la-Cruz M, Millán-Aldaco D, Soriano-Nava DM, Drucker-Colín R, Murillo-Rodríguez E. The artificial sweetener Splenda intake promotes changes in expression of c-Fos and NeuN in hypothalamus and hippocampus of rats. Brain Res 2018; 1700:181-189. [PMID: 30201258 DOI: 10.1016/j.brainres.2018.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 08/16/2018] [Accepted: 09/04/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND Obesity is the result of the interaction of multiple variables, including the excessive increase of sugar-sweetened beverages consumption. Diets aimed to treat obesity have suggested the use of artificial sweeteners. However, recent evidence has shown several health deficits after intake of artificial sweeteners, including effects in neuronal activity. Therefore, the influence of artificial sweeteners consumption such as Splenda, on the expression of c-Fos and neuronal nuclear protein (NeuN) in hypothalamus and hippocampus remains to be determined. OBJECTIVES We investigated the effects on c-Fos or NeuN expression in hypothalamus and hippocampus of Splenda-treated rats. METHODS Splenda was diluted in water (25, 75 or 250 mg/100 mL) and orally given to rats during 2 weeks ad libitum. Next, animals were sacrificed by decapitation and brains were collected for analysis of c-Fos or NeuN immunoreactivity. RESULTS Consumption of Splenda provoked an inverted U-shaped dose-effect in c-Fos expression in ventromedial hypothalamic nucleus while similar findings were observed in dentate gyrus of hippocampus. In addition, NeuN immunoreactivity was enhanced in ventromedial hypothalamic nucleus at 25 or 75 mg/100 mL of Splenda intake whereas an opposite effect was observed at 250 mg/100 mL of artificial sweetener consumption. Lastly, NeuN positive neurons were increased in CA2/CA3 fields of hippocampus from Splenda-treated rats (25, 75 or 250 mg/100 mL). CONCLUSION Consuming Splenda induced effects in neuronal biomarkers expression. To our knowledge, this study is the first description of the impact of intake Splenda on c-Fos and NeuN immunoreactivity in hypothalamus and hippocampus in rats.
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Affiliation(s)
- Miriel de-la-Cruz
- Laboratorio de Neurociencias Moleculares e Integrativas, Escuela de Medicina, División Ciencias de la Salud, Universidad Anáhuac Mayab, Mérida, Yucatán, Mexico; Intercontinental Neuroscience Research Group
| | - Diana Millán-Aldaco
- Depto. de Neuropatología Molecular, División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, México, Mexico
| | - Daniela Marcia Soriano-Nava
- Laboratorio de Neurociencias Moleculares e Integrativas, Escuela de Medicina, División Ciencias de la Salud, Universidad Anáhuac Mayab, Mérida, Yucatán, Mexico; Intercontinental Neuroscience Research Group
| | - René Drucker-Colín
- Depto. de Neuropatología Molecular, División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, México, Mexico
| | - Eric Murillo-Rodríguez
- Laboratorio de Neurociencias Moleculares e Integrativas, Escuela de Medicina, División Ciencias de la Salud, Universidad Anáhuac Mayab, Mérida, Yucatán, Mexico; Intercontinental Neuroscience Research Group.
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7
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García-Cabezas MÁ, Barbas H, Zikopoulos B. Parallel Development of Chromatin Patterns, Neuron Morphology, and Connections: Potential for Disruption in Autism. Front Neuroanat 2018; 12:70. [PMID: 30174592 PMCID: PMC6107687 DOI: 10.3389/fnana.2018.00070] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/30/2018] [Indexed: 12/27/2022] Open
Abstract
The phenotype of neurons and their connections depend on complex genetic and epigenetic processes that regulate the expression of genes in the nucleus during development and throughout life. Here we examined the distribution of nuclear chromatin patters in relation to the epigenetic landscape, phenotype and connections of neurons with a focus on the primate cerebral cortex. We show that nuclear patterns of chromatin in cortical neurons are related to neuron size and cortical connections. Moreover, we point to evidence that reveals an orderly sequence of events during development, linking chromatin and gene expression patterns, neuron morphology, function, and connections across cortical areas and layers. Based on this synthesis, we posit that systematic studies of changes in chromatin patterns and epigenetic marks across cortical areas will provide novel insights on the development and evolution of cortical networks, and their disruption in connectivity disorders of developmental origin, like autism. Achieving this requires embedding and interpreting genetic, transcriptional, and epigenetic studies within a framework that takes into consideration distinct types of neurons, local circuit interactions, and interareal pathways. These features vary systematically across cortical areas in parallel with laminar structure and are differentially affected in disorders. Finally, based on evidence that autism-associated genetic polymorphisms are especially prominent in excitatory neurons and connectivity disruption affects mostly limbic cortices, we employ this systematic approach to propose novel, targeted studies of projection neurons in limbic areas to elucidate the emergence and time-course of developmental disruptions in autism.
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Affiliation(s)
- Miguel Á García-Cabezas
- Neural Systems Laboratory, Department of Health Sciences, Boston University, Boston, MA, United States
| | - Helen Barbas
- Neural Systems Laboratory, Department of Health Sciences, Boston University, Boston, MA, United States.,Graduate Program in Neuroscience, Boston University, Boston, MA, United States
| | - Basilis Zikopoulos
- Graduate Program in Neuroscience, Boston University, Boston, MA, United States.,Human Systems Neuroscience Laboratory, Department of Health Sciences, Boston University, Boston, MA, United States
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8
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Lu Z, Hofmeister BT, Vollmers C, DuBois RM, Schmitz RJ. Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes. Nucleic Acids Res 2017; 45:e41. [PMID: 27903897 PMCID: PMC5389718 DOI: 10.1093/nar/gkw1179] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/15/2016] [Indexed: 12/27/2022] Open
Abstract
Chromatin structure plays a pivotal role in facilitating proper control of gene expression. Transcription factor (TF) binding of cis-elements is often associated with accessible chromatin regions. Therefore, the ability to identify these accessible regions throughout plant genomes will advance understanding of the relationship between TF binding, chromatin status and the regulation of gene expression. Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) is a recently developed technique used to map open chromatin zones in animal genomes. However, in plants, the existence of cell walls, subcellular organelles and the lack of stable cell lines have prevented routine application of this technique. Here, we describe an assay combining ATAC-seq with fluorescence-activated nuclei sorting (FANS) to identify and map open chromatin and TF-binding sites in plant genomes. FANS-ATAC-seq compares favorably with published DNaseI sequencing (DNase-seq) results and it requires less than 50 000 nuclei for accurate identification of accessible genomic regions. Summary: Application of ATAC-seq to sorted nuclei identifies accessible regions genome-wide.
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Affiliation(s)
- Zefu Lu
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | | | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Rebecca M DuBois
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
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9
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Mizutani R, Saiga R, Ohtsuka M, Miura H, Hoshino M, Takeuchi A, Uesugi K. Three-dimensional X-ray visualization of axonal tracts in mouse brain hemisphere. Sci Rep 2016; 6:35061. [PMID: 27725699 PMCID: PMC5057144 DOI: 10.1038/srep35061] [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: 04/21/2016] [Accepted: 09/23/2016] [Indexed: 11/09/2022] Open
Abstract
Neurons transmit active potentials through axons, which are essential for the brain to function. In this study, the axonal networks of the murine brain were visualized with X-ray tomographic microscopy, also known as X-ray microtomography or micro-CT. Murine brain samples were freeze-dried to reconstitute the intrinsic contrast of tissue constituents and subjected to X-ray visualization. A whole brain hemisphere visualized by absorption contrast illustrated three-dimensional structures including those of the striatum, corpus callosum, and anterior commissure. Axonal tracts observed in the striatum start from the basal surface of the cerebral cortex and end at various positions in the basal ganglia. The distribution of X-ray attenuation coefficients indicated that differences in water and phospholipid content between the myelin sheath and surrounding tissue constituents account for the observed contrast. A rod-shaped cutout of brain tissue was also analyzed with a phase retrieval method, wherein tissue microstructures could be resolved with up to 2.7 μm resolution. Structures of axonal networks of the striatum were reconstructed by tracing axonal tracts. Such an analysis should be able to delineate the functional relationships of the brain regions involved in the observed network.
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Affiliation(s)
- Ryuta Mizutani
- Department of Applied Biochemistry, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan
| | - Rino Saiga
- Department of Applied Biochemistry, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan
| | - Masato Ohtsuka
- Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
| | - Hiromi Miura
- Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
| | - Masato Hoshino
- Japan Synchrotron Radiation Research Institute (JASRI/SPring-8), Sayo, Hyogo 679-5198, Japan
| | - Akihisa Takeuchi
- Japan Synchrotron Radiation Research Institute (JASRI/SPring-8), Sayo, Hyogo 679-5198, Japan
| | - Kentaro Uesugi
- Japan Synchrotron Radiation Research Institute (JASRI/SPring-8), Sayo, Hyogo 679-5198, Japan
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10
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Ambati S, Yu P, McKinney EC, Kandasamy MK, Hartzell D, Baile CA, Meagher RB. Adipocyte nuclei captured from VAT and SAT. BMC OBESITY 2016; 3:35. [PMID: 27462403 PMCID: PMC4949929 DOI: 10.1186/s40608-016-0112-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 06/16/2016] [Indexed: 12/11/2022]
Abstract
Background Obesity-related comorbidities are thought to result from the reprogramming of the epigenome in numerous tissues and cell types, and in particular, mature adipocytes within visceral and subcutaneous adipose tissue, VAT and SAT. The cell-type specific chromatin remodeling of mature adipocytes within VAT and SAT is poorly understood, in part, because of the difficulties of isolating and manipulating large fragile mature adipocyte cells from adipose tissues. Methods We constructed MA-INTACT (Mature Adipocyte-Isolation of Nuclei TAgged in specific Cell Types) mice using the adiponectin (ADIPOQ) promoter (ADNp) to tag the surface of mature adipocyte nuclei with a reporter protein. The SUN1mRFP1Flag reporter is comprised of a fragment of the nuclear transmembrane protein SUN1, the fluorescent protein mRFP1, and three copies of the Flag epitope tag. Results Mature adipocyte nuclei were rapidly and efficiently immuno-captured from VAT and SAT (MVA and MSA nuclei, respectively), of MA-INTACT mice. MVA and MSA nuclei contained 1,000 to 10,000-fold higher levels of adipocyte-specific transcripts, ADIPOQ, PPARg2, EDNRB, and LEP, relative to uncaptured nuclei, while the latter expressed higher levels of leukocyte and endothelial cell markers IKZF1, RETN, SERPINF1, SERPINE1, ILF3, and TNFA. MVA and MSA nuclei differentially expressed several factors linked to adipogenesis or obesity-related health risks including CEBPA, KLF2, RETN, SERPINE1, and TNFA. The various nuclear populations dramatically differentially expressed transcripts encoding chromatin remodeler proteins regulating DNA cytosine methylation and hydroxymethylation (TETs, DNMTs, TDG, GADD45s) and nucleosomal histone modification (ARID1A, KAT2B, KDM4A, PRMT1, PRMT5, PAXIP1). Remarkably, MSA and MVA nuclei expressed 200 to 1000-fold higher levels of thermogenic marker transcripts PRDM16 and UCP1. Conclusions The MA-INTACT mouse enables a simple way to perform cell-type specific analysis of highly purified mature adipocyte nuclei from VAT and SAT and increases the statistical significance of data collected on adipocytes. Isolated VAT and SAT adipocyte nuclei expressed distinct patterns of transcripts encoding chromatin remodeling factors and proteins relevant to diabetes, cardiovascular disease, and thermogenesis. The MA-INTACT mouse is an useful model to test the impact of caloric intake, dietary nutrients, exercise, and pharmaceuticals on the epigenome-induced health risks of obesity. Electronic supplementary material The online version of this article (doi:10.1186/s40608-016-0112-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Suresh Ambati
- Department of Genetics, University of Georgia, Athens, GA USA
| | - Ping Yu
- Department of Genetics, University of Georgia, Athens, GA USA
| | | | | | - Diane Hartzell
- Department of Foods and Nutrition, University of Georgia, Athens, GA USA ; Department of Animal and Dairy Science, University of Georgia, Athens, GA USA
| | - Clifton A Baile
- Department of Foods and Nutrition, University of Georgia, Athens, GA USA ; Department of Animal and Dairy Science, University of Georgia, Athens, GA USA
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11
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Yu P, Ji L, Lee KJ, Yu M, He C, Ambati S, McKinney EC, Jackson C, Baile CA, Schmitz RJ, Meagher RB. Subsets of Visceral Adipose Tissue Nuclei with Distinct Levels of 5-Hydroxymethylcytosine. PLoS One 2016; 11:e0154949. [PMID: 27171244 PMCID: PMC4865362 DOI: 10.1371/journal.pone.0154949] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/21/2016] [Indexed: 12/11/2022] Open
Abstract
The reprogramming of cellular memory in specific cell types, and in visceral adipocytes in particular, appears to be a fundamental aspect of obesity and its related negative health outcomes. We explored the hypothesis that adipose tissue contains epigenetically distinct subpopulations of adipocytes that are differentially potentiated to record cellular memories of their environment. Adipocytes are large, fragile, and technically difficult to efficiently isolate and fractionate. We developed fluorescence nuclear cytometry (FNC) and fluorescence activated nuclear sorting (FANS) of cellular nuclei from visceral adipose tissue (VAT) using the levels of the pan-adipocyte protein, peroxisome proliferator-activated receptor gamma-2 (PPARg2), to distinguish classes of PPARg2-Positive (PPARg2-Pos) adipocyte nuclei from PPARg2-Negative (PPARg2-Neg) leukocyte and endothelial cell nuclei. PPARg2-Pos nuclei were 10-fold enriched for most adipocyte marker transcripts relative to PPARg2-Neg nuclei. PPARg2-Pos nuclei showed 2- to 50-fold higher levels of transcripts encoding most of the chromatin-remodeling factors assayed, which regulate the methylation of histones and DNA cytosine (e.g., DNMT1, TET1, TET2, KDM4A, KMT2C, SETDB1, PAXIP1, ARID1A, JMJD6, CARM1, and PRMT5). PPARg2-Pos nuclei were large with decondensed chromatin. TAB-seq demonstrated 5-hydroxymethylcytosine (5hmC) levels were remarkably dynamic in gene bodies of various classes of VAT nuclei, dropping 3.8-fold from the highest quintile of expressed genes to the lowest. In short, VAT-derived adipocytes appear to be more actively remodeling their chromatin than non-adipocytes.
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Affiliation(s)
- Ping Yu
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America
| | - Kevin J. Lee
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America
- GRU-UGA Medical Partnership, University of Georgia Health Sciences Campus, Prince Avenue, Athens, GA, 30602, United States of America
| | - Miao Yu
- Department of Chemistry, University of Chicago, 5735 S Ellis Ave, Chicago, IL, 60637 USA
| | - Chuan He
- Department of Chemistry, University of Chicago, 5735 S Ellis Ave, Chicago, IL, 60637 USA
| | - Suresh Ambati
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America
| | - Elizabeth C. McKinney
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America
| | - Crystal Jackson
- Abeome Corporation, Athens, GA, 111 Riverbend Road, 30602, United States of America
| | - Clifton A. Baile
- Department of Foods and Nutrition, University of Georgia, 305 Sanford Dr, Athens, GA, 30602, United States of America
| | - Robert J. Schmitz
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America
| | - Richard B. Meagher
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America
- * E-mail:
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12
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Kami K, Taguchi S, Tajima F, Senba E. Histone Acetylation in Microglia Contributes to Exercise-Induced Hypoalgesia in Neuropathic Pain Model Mice. THE JOURNAL OF PAIN 2016; 17:588-99. [PMID: 26844418 DOI: 10.1016/j.jpain.2016.01.471] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 12/20/2015] [Accepted: 01/11/2016] [Indexed: 02/06/2023]
Abstract
UNLABELLED Physical exercise can attenuate neuropathic pain (NPP), but the exact mechanism underlying exercise-induced hypoalgesia (EIH) remains unclear. Recent studies have shown that histone hyperacetylation via pharmacological inhibition of histone deacetylases in the spinal cord attenuates NPP, and that histone acetylation may lead to the production of analgesic factors including interleukin 10. We intended to clarify whether histone acetylation in microglia in the spinal dorsal horn contributes to EIH in NPP model mice. C57BL/6J mice underwent partial sciatic nerve ligation (PSL) and PSL- and sham-runner mice ran on a treadmill at a speed of 7 m/min for 60 min/d, 5 days per week, from 2 days after the surgery. PSL-sedentary mice developed mechanical allodynia and heat hyperalgesia, but such behaviors were significantly attenuated in PSL-runner mice. In immunofluorescence analysis, PSL surgery markedly increased the number of histone deacetylase 1-positive/CD11b-positive microglia in the ipsilateral superficial dorsal horn, and they were significantly decreased by treadmill-running. Moreover, the number of microglia with nuclear expression of acetylated H3K9 in the ipsilateral superficial dorsal horn was maintained at low levels in PSL-sedentary mice, but running exercise significantly increased them. Therefore, we conclude that the epigenetic modification that causes hyperacetylation of H3K9 in activated microglia may play a role in producing EIH. PERSPECTIVE This article presents the importance of epigenetic modification in microglia in producing EIH. The current research is not only helpful for developing novel nonpharmacological therapy for NPP, but will also enhance our understanding of the mechanisms and availability of exercise in our daily life.
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Affiliation(s)
- Katsuya Kami
- Department of Rehabilitation Medicine, Wakayama Medical University, Wakayama, Japan.
| | - Satoru Taguchi
- Department of Rehabilitation Medicine, Wakayama Medical University, Wakayama, Japan
| | - Fumihiro Tajima
- Department of Rehabilitation Medicine, Wakayama Medical University, Wakayama, Japan
| | - Emiko Senba
- Department of Rehabilitation Medicine, Wakayama Medical University, Wakayama, Japan; Department of Physical Therapy, Osaka Yukioka College of Health Science, Osaka, Japan
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Cunningham CB, Ji L, Wiberg RAW, Shelton J, McKinney EC, Parker DJ, Meagher RB, Benowitz KM, Roy-Zokan EM, Ritchie MG, Brown SJ, Schmitz RJ, Moore AJ. The Genome and Methylome of a Beetle with Complex Social Behavior, Nicrophorus vespilloides (Coleoptera: Silphidae). Genome Biol Evol 2015; 7:3383-96. [PMID: 26454014 PMCID: PMC4700941 DOI: 10.1093/gbe/evv194] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2015] [Indexed: 12/22/2022] Open
Abstract
Testing for conserved and novel mechanisms underlying phenotypic evolution requires a diversity of genomes available for comparison spanning multiple independent lineages. For example, complex social behavior in insects has been investigated primarily with eusocial lineages, nearly all of which are Hymenoptera. If conserved genomic influences on sociality do exist, we need data from a wider range of taxa that also vary in their levels of sociality. Here, we present the assembled and annotated genome of the subsocial beetle Nicrophorus vespilloides, a species long used to investigate evolutionary questions of complex social behavior. We used this genome to address two questions. First, do aspects of life history, such as using a carcass to breed, predict overlap in gene models more strongly than phylogeny? We found that the overlap in gene models was similar between N. vespilloides and all other insect groups regardless of life history. Second, like other insects with highly developed social behavior but unlike other beetles, does N. vespilloides have DNA methylation? We found strong evidence for an active DNA methylation system. The distribution of methylation was similar to other insects with exons having the most methylated CpGs. Methylation status appears highly conserved; 85% of the methylated genes in N. vespilloides are also methylated in the hymentopteran Nasonia vitripennis. The addition of this genome adds a coleopteran resource to answer questions about the evolution and mechanistic basis of sociality and to address questions about the potential role of methylation in social behavior.
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Affiliation(s)
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia
| | - R Axel W Wiberg
- Centre for Biological Diversity, School of Biology, University of St. Andrews, Fife, United Kingdom
| | - Jennifer Shelton
- Division of Biology & Bioinformatics Center & Arthropod Genomics Center, Kansas State University
| | | | - Darren J Parker
- Centre for Biological Diversity, School of Biology, University of St. Andrews, Fife, United Kingdom
| | | | | | | | - Michael G Ritchie
- Centre for Biological Diversity, School of Biology, University of St. Andrews, Fife, United Kingdom
| | - Susan J Brown
- Division of Biology & Bioinformatics Center & Arthropod Genomics Center, Kansas State University
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'Memory and molecular turnover,' 30 years after inception. Epigenetics Chromatin 2014; 7:37. [PMID: 25525471 PMCID: PMC4269865 DOI: 10.1186/1756-8935-7-37] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 11/28/2014] [Indexed: 12/28/2022] Open
Abstract
In 1984 Sir Francis Crick hypothesized that memory is recorded in the brain as reversible modifications to DNA and protein, but acknowledged that most biomolecules turn over too rapidly to account for long-term memories. To accommodate this possible paradox he modeled an enzymatic mechanism to maintain modifications on hemi-modified multimeric symmetrical molecules. While studies on the turnover of chromatin modifications that may be involved in memory are in their infancy, an exploration of his model in the light of modern epigenetics produced somewhat surprising results. The molecular turnover rates for two classes of chromatin modifications believed to record and store durable memories were approximated from experiments using diverse approaches and were found to be remarkably short. The half-lives of DNA cytosine methylation and post-translationally modified nucleosomal histones are measured in hours and minutes, respectively, for a subset of sites on chromatin controlling gene expression. It appears likely that the turnover of DNA methylation in the brain and in neurons, in particular, is even more rapid than in other cell types and organs, perhaps accommodating neuronal plasticity, learning, and memory. The machinery responsible for the rapid turnover of DNA methylation and nucleosomal histone modifications is highly complex, partially redundant, and appears to act in a sequence specific manner. Molecular symmetry plays an important part in maintaining site-specific turnover, but its particular role in memory maintenance is unknown. Elucidating Crick’s paradox, the contradiction between rapid molecular turnover of modified biomolecules and long-term memory storage, appears fundamental to understanding cognitive function and neurodegenerative disease.
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