1
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Stankiewicz AM, Jaszczyk A, Goscik J, Juszczak GR. Stress and the brain transcriptome: Identifying commonalities and clusters in standardized data from published experiments. Prog Neuropsychopharmacol Biol Psychiatry 2022; 119:110558. [PMID: 35405299 DOI: 10.1016/j.pnpbp.2022.110558] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 03/17/2022] [Accepted: 04/04/2022] [Indexed: 12/28/2022]
Abstract
Interpretation of transcriptomic experiments is hindered by many problems including false positives/negatives inherent to big-data methods and changes in gene nomenclature. To find the most consistent effect of stress on brain transcriptome, we retrieved data from 79 studies applying animal models and 3 human studies investigating post-traumatic stress disorder (PTSD). The analyzed data were obtained either with microarrays or RNA sequencing applied to samples collected from more than 1887 laboratory animals and from 121 human subjects. Based on the initial database containing a quarter million differential expression effect sizes representing transcripts in three species, we identified the most frequently reported genes in 223 stress-control comparisons. Additionally, the analysis considers sex, individual vulnerability and contribution of glucocorticoids. We also found an overlap between gene expression in PTSD patients and animals which indicates relevance of laboratory models for human stress response. Our analysis points to genes that, as far as we know, were not specifically tested for their role in stress response (Pllp, Arrdc2, Midn, Mfsd2a, Ccn1, Htra1, Csrnp1, Tenm4, Tnfrsf25, Sema3b, Fmo2, Adamts4, Gjb1, Errfi1, Fgf18, Galnt6, Slc25a42, Ifi30, Slc4a1, Cemip, Klf10, Tom1, Dcdc2c, Fancd2, Luzp2, Trpm1, Abcc12, Osbpl1a, Ptp4a2). Provided transcriptomic resource will be useful for guiding the new research.
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Affiliation(s)
- Adrian M Stankiewicz
- Department of Molecular Biology, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzebiec, Poland
| | - Aneta Jaszczyk
- Department of Animal Behavior and Welfare, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzebiec, Poland
| | - Joanna Goscik
- Faculty of Computer Science, Bialystok University of Technology, Bialystok, Poland
| | - Grzegorz R Juszczak
- Department of Animal Behavior and Welfare, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzebiec, Poland.
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2
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Català-Solsona J, Miñano-Molina AJ, Rodríguez-Álvarez J. Nr4a2 Transcription Factor in Hippocampal Synaptic Plasticity, Memory and Cognitive Dysfunction: A Perspective Review. Front Mol Neurosci 2021; 14:786226. [PMID: 34880728 PMCID: PMC8645690 DOI: 10.3389/fnmol.2021.786226] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/27/2021] [Indexed: 12/26/2022] Open
Abstract
Long-lasting changes of synaptic efficacy are largely mediated by activity-induced gene transcription and are essential for neuronal plasticity and memory. In this scenario, transcription factors have emerged as pivotal players underlying synaptic plasticity and the modification of neural networks required for memory formation and consolidation. Hippocampal synaptic dysfunction is widely accepted to underlie the cognitive decline observed in some neurodegenerative disorders including Alzheimer’s disease. Therefore, understanding the molecular pathways regulating gene expression profiles may help to identify new synaptic therapeutic targets. The nuclear receptor 4A subfamily (Nr4a) of transcription factors has been involved in a variety of physiological processes within the hippocampus, ranging from inflammation to neuroprotection. Recent studies have also pointed out a role for the activity-dependent nuclear receptor subfamily 4, group A, member 2 (Nr4a2/Nurr1) in hippocampal synaptic plasticity and cognitive functions, although the underlying molecular mechanisms are still poorly understood. In this review, we highlight the specific effects of Nr4a2 in hippocampal synaptic plasticity and memory formation and we discuss whether the dysregulation of this transcription factor could contribute to hippocampal synaptic dysfunction, altogether suggesting the possibility that Nr4a2 may emerge as a novel synaptic therapeutic target in brain pathologies associated to cognitive dysfunctions.
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Affiliation(s)
- Judit Català-Solsona
- Departament de Bioquímica i Biologia Molecular, Institut de Neurociències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Alfredo J Miñano-Molina
- Departament de Bioquímica i Biologia Molecular, Institut de Neurociències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - José Rodríguez-Álvarez
- Departament de Bioquímica i Biologia Molecular, Institut de Neurociències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.,Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, NY, United States
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3
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Devulapalli R, Jones N, Farrell K, Musaus M, Kugler H, McFadden T, Orsi SA, Martin K, Nelsen J, Navabpour S, O'Donnell M, McCoig E, Jarome TJ. Males and females differ in the regulation and engagement of, but not requirement for, protein degradation in the amygdala during fear memory formation. Neurobiol Learn Mem 2021; 180:107404. [PMID: 33609735 DOI: 10.1016/j.nlm.2021.107404] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/28/2021] [Accepted: 02/10/2021] [Indexed: 02/07/2023]
Abstract
Over the last decade, strong evidence has emerged that protein degradation mediated by the ubiquitin-proteasome system is critical for fear memory formation in the amygdala. However, this work has been done primarily in males, leaving unanswered questions about whether females also require protein degradation during fear memory formation. Here, we found that male and female rats differed in their engagement and regulation of, but not need for, protein degradation in the amygdala during fear memory formation. Male, but not female, rats had increased protein degradation in the nuclei of amygdala cells after fear conditioning. Conversely, females had elevated baseline levels of overall ubiquitin-proteasome activity in amygdala nuclei. Gene expression and DNA methylation analyses identified that females had increased baseline expression of the ubiquitin coding gene Uba52, which had increased DNA 5-hydroxymethylation (5hmc) in its promoter region, indicating a euchromatin state necessary for increased levels of ubiquitin in females. Consistent with this, persistent CRISPR-dCas9 mediated silencing of Uba52 and proteasome subunit Psmd14 in the amygdala reduced baseline protein degradation levels and impaired fear memory in male and female rats, while enhancing baseline protein degradation in the amygdala of both sexes promoted fear memory formation. These results suggest that while both males and females require protein degradation in the amygdala for fear memory formation, they differ in their baseline regulation and engagement of this process following learning. These results have important implications for understanding the etiology of sex-related differences in fear memory formation.
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Affiliation(s)
- Rishi Devulapalli
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Natalie Jones
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Kayla Farrell
- Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Madeline Musaus
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Hannah Kugler
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Taylor McFadden
- Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Sabrina A Orsi
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Kiley Martin
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Jacob Nelsen
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Shaghayegh Navabpour
- Fralin Biomedical Research Institute, Translational Biology, Medicine and Health, Virginia Polytechnic Institute and State University, Roanoke, VA, USA
| | - Madison O'Donnell
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Emmarose McCoig
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Timothy J Jarome
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA; Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA; Fralin Biomedical Research Institute, Translational Biology, Medicine and Health, Virginia Polytechnic Institute and State University, Roanoke, VA, USA.
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4
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Upton DH, Popovic K, Fulton R, Kassiou M. Anaesthetic-dependent changes in gene expression following acute and chronic exposure in the rodent brain. Sci Rep 2020; 10:9366. [PMID: 32518252 PMCID: PMC7283325 DOI: 10.1038/s41598-020-66122-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 05/13/2020] [Indexed: 11/09/2022] Open
Abstract
Anaesthesia has been predicted to affect gene expression of the memory-related regions of the brain including the primary visual cortex. It is also believed that anaesthesia causes inflammation of neural tissues, increasing elderly patients' chances of developing precursor lesions that lead to Alzheimer's disease and other neurodegeneration related diseases. We have analyzed the expression of over 22,000 genes and 129,800 transcripts using oligonucleotide microarrays to examine the brain expression profiles in Sprague Dawley rats following exposure to acute or chronic doses of the anaesthetics isoflurane, ketamine and propofol. Here we report for the first time molecular and genomic data on the effect on the rodent brain of chronic and acute exposure to isoflurane, ketamine and propofol. Our screen identified multiple genes that responded to all three anaesthetics. Although some of the genes were previously known to be anaesthesia responsive, we have for the most part identified novel genes involved in the acute and chronic rodent brain response to different anaesthesia treatments. The latter may be useful candidate genes in the search to elucidate the molecular pathways mediating anaesthetic effects in the brain and may allow us to identify mechanisms by which anaesthetics could impact on neurodegeneration.
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Affiliation(s)
- Dannielle H Upton
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Kata Popovic
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Roger Fulton
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Department of Medical Physics, Westmead Hospital, Sydney, Australia
| | - Michael Kassiou
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia.
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5
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Mizuno K, Jeffries AR, Abel T, Giese KP. Long-lasting transcription in hippocampal area CA1 after contextual fear conditioning. Neurobiol Learn Mem 2020; 172:107250. [PMID: 32422278 DOI: 10.1016/j.nlm.2020.107250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/27/2020] [Accepted: 05/12/2020] [Indexed: 01/25/2023]
Abstract
A fundamental question is how memory is stored for several weeks and even longer. A long-lasting increase in gene transcription has been suggested to mediate such long-term memory storage. Here, we used contextual fear conditioning in mice to search for lasting transcription that may contribute to long-term memory storage. Our study focussed on hippocampal area CA1, which has been suggested to have a role for at least one week in contextual fear memory. Using an unbiased microarray analysis followed by confirmatory quantitative real-time PCR, we identified an upregulation of two transcription factors, Fosl2 and Nfil3, which lasted for seven days after conditioning. To our knowledge these are the longest transcriptional changes ever detected in the hippocampus after contextual fear conditioning. Thus, our findings suggest novel transcriptional candidates for long-term memory storage.
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Affiliation(s)
- Keiko Mizuno
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, UK.
| | - Aaron R Jeffries
- Biosciences, College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Ted Abel
- Department of Molecular Physiology and Biophysics, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - K Peter Giese
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, UK.
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6
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Kaldun JC, Sprecher SG. Initiated by CREB: Resolving Gene Regulatory Programs in Learning and Memory. Bioessays 2019; 41:e1900045. [DOI: 10.1002/bies.201900045] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/29/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Jenifer C. Kaldun
- Department of BiologyUniversity of Fribourg1700 Fribourg Switzerland
| | - Simon G. Sprecher
- Department of BiologyUniversity of Fribourg1700 Fribourg Switzerland
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7
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Bayraktar G, Kreutz MR. The Role of Activity-Dependent DNA Demethylation in the Adult Brain and in Neurological Disorders. Front Mol Neurosci 2018; 11:169. [PMID: 29875631 PMCID: PMC5975432 DOI: 10.3389/fnmol.2018.00169] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/04/2018] [Indexed: 01/11/2023] Open
Abstract
Over the last decade, an increasing number of reports underscored the importance of epigenetic regulations in brain plasticity. Epigenetic elements such as readers, writers and erasers recognize, establish, and remove the epigenetic tags in nucleosomes, respectively. One such regulation concerns DNA-methylation and demethylation, which are highly dynamic and activity-dependent processes even in the adult neurons. It is nowadays widely believed that external stimuli control the methylation marks on the DNA and that such processes serve transcriptional regulation in neurons. In this mini-review, we cover the current knowledge on the regulatory mechanisms controlling in particular DNA demethylation as well as the possible functional consequences in health and disease.
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Affiliation(s)
- Gonca Bayraktar
- RG Neuroplasticity, Leibniz Institute for Neurobiology Magdeburg, Germany
| | - Michael R Kreutz
- RG Neuroplasticity, Leibniz Institute for Neurobiology Magdeburg, Germany.,Leibniz Group 'Dendritic Organelles and Synaptic Function', Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf Hamburg, Germany
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8
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The microbiome regulates amygdala-dependent fear recall. Mol Psychiatry 2018; 23:1134-1144. [PMID: 28507320 PMCID: PMC5984090 DOI: 10.1038/mp.2017.100] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 02/20/2017] [Accepted: 03/16/2017] [Indexed: 12/25/2022]
Abstract
The amygdala is a key brain region that is critically involved in the processing and expression of anxiety and fear-related signals. In parallel, a growing number of preclinical and human studies have implicated the microbiome-gut-brain in regulating anxiety and stress-related responses. However, the role of the microbiome in fear-related behaviours is unclear. To this end we investigated the importance of the host microbiome on amygdala-dependent behavioural readouts using the cued fear conditioning paradigm. We also assessed changes in neuronal transcription and post-transcriptional regulation in the amygdala of naive and stimulated germ-free (GF) mice, using a genome-wide transcriptome profiling approach. Our results reveal that GF mice display reduced freezing during the cued memory retention test. Moreover, we demonstrate that under baseline conditions, GF mice display altered transcriptional profile with a marked increase in immediate-early genes (for example, Fos, Egr2, Fosb, Arc) as well as genes implicated in neural activity, synaptic transmission and nervous system development. We also found a predicted interaction between mRNA and specific microRNAs that are differentially regulated in GF mice. Interestingly, colonized GF mice (ex-GF) were behaviourally comparable to conventionally raised (CON) mice. Together, our data demonstrates a unique transcriptional response in GF animals, likely because of already elevated levels of immediate-early gene expression and the potentially underlying neuronal hyperactivity that in turn primes the amygdala for a different transcriptional response. Thus, we demonstrate for what is to our knowledge the first time that the presence of the host microbiome is crucial for the appropriate behavioural response during amygdala-dependent memory retention.
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9
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Minimal traumatic brain injury causes persistent changes in DNA methylation at BDNF gene promoters in rat amygdala: A possible role in anxiety-like behaviors. Neurobiol Dis 2017; 106:101-109. [DOI: 10.1016/j.nbd.2017.06.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 03/30/2017] [Accepted: 06/22/2017] [Indexed: 12/20/2022] Open
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10
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Taguchi YH. Principal component analysis based unsupervised feature extraction applied to publicly available gene expression profiles provides new insights into the mechanisms of action of histone deacetylase inhibitors. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.nepig.2016.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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11
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Poplawski SG, Peixoto L, Porcari GS, Wimmer ME, McNally AG, Mizuno K, Giese KP, Chatterjee S, Koberstein JN, Risso D, Speed TP, Abel T. Contextual fear conditioning induces differential alternative splicing. Neurobiol Learn Mem 2016; 134 Pt B:221-35. [PMID: 27451143 DOI: 10.1016/j.nlm.2016.07.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 07/16/2016] [Accepted: 07/19/2016] [Indexed: 12/20/2022]
Abstract
The process of memory consolidation requires transcription and translation to form long-term memories. Significant effort has been dedicated to understanding changes in hippocampal gene expression after contextual fear conditioning. However, alternative splicing by differential transcript regulation during this time period has received less attention. Here, we use RNA-seq to determine exon-level changes in expression after contextual fear conditioning and retrieval. Our work reveals that a short variant of Homer1, Ania-3, is regulated by contextual fear conditioning. The ribosome biogenesis regulator Las1l, small nucleolar RNA Snord14e, and the RNA-binding protein Rbm3 also change specific transcript usage after fear conditioning. The changes in Ania-3 and Las1l are specific to either the new context or the context-shock association, while the changes in Rbm3 occur after context or shock only. Our analysis revealed novel transcript regulation of previously undetected changes after learning, revealing the importance of high throughput sequencing approaches in the study of gene expression changes after learning.
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Affiliation(s)
- Shane G Poplawski
- Pharmacology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Lucia Peixoto
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA; Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA
| | - Giulia S Porcari
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Mathieu E Wimmer
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Anna G McNally
- Pharmacology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Keiko Mizuno
- Centre for the Cellular Basis of Behaviour, King's College London, London, UK
| | - K Peter Giese
- Centre for the Cellular Basis of Behaviour, King's College London, London, UK
| | | | - John N Koberstein
- Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA
| | - Davide Risso
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA, USA
| | - Terence P Speed
- Department of Statistics, University of California, Berkeley, CA, USA; Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Mathematics and Statistics, The University of Melbourne, Victoria, Australia
| | - Ted Abel
- Pharmacology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
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12
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Kigar SL, Chang L, Hayne MR, Karls NT, Auger AP. Sex differences in Gadd45b expression and methylation in the developing rodent amygdala. Brain Res 2016; 1642:461-466. [PMID: 27086974 PMCID: PMC6701186 DOI: 10.1016/j.brainres.2016.04.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 04/12/2016] [Accepted: 04/14/2016] [Indexed: 01/25/2023]
Abstract
Precise spatiotemporal epigenetic regulation of the genome facilitates species-typical development; sexual differentiation of the brain by gonadal hormones and sex chromosomes causes extensive epigenetic reprogramming of many cells in the body, including the brain, and may indirectly predispose males and females to different psychiatric conditions. We and others have demonstrated sex differences in DNA methylation, as well as in the enzymes that form, or 'write', this epigenetic modification. However, while a growing body of evidence suggests that DNA methylation undergoes rapid turnover and is dynamically regulated in vivo, to our knowledge no studies have been done investigating whether sex differences exist in the epigenetic 'erasers' during postnatal development. Here we report sex differences in the expression of growth arrest and DNA damage inducible factor β (Gadd45b), but not family members α (a) or γ (g), in the neonatal and juvenile rodent amygdala.
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Affiliation(s)
- Stacey L Kigar
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, 1202 W Johnson St., Madison, WI 53706, United States.
| | - Liza Chang
- Department of Psychology, University of Wisconsin-Madison, 1202 W Johnson St., Madison, WI 53706, United States.
| | - Margaret R Hayne
- Department of Psychology, University of Wisconsin-Madison, 1202 W Johnson St., Madison, WI 53706, United States
| | - Nicolette T Karls
- Department of Psychology, University of Wisconsin-Madison, 1202 W Johnson St., Madison, WI 53706, United States
| | - Anthony P Auger
- Department of Psychology, University of Wisconsin-Madison, 1202 W Johnson St., Madison, WI 53706, United States; Neuroscience Training Program, University of Wisconsin-Madison, 1202 W Johnson St., Madison, WI 53706, United States.
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13
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Gavin DP, Kusumo H, Sharma RP, Guizzetti M, Guidotti A, Pandey SC. Gadd45b and N-methyl-D-aspartate induced DNA demethylation in postmitotic neurons. Epigenomics 2016; 7:567-79. [PMID: 26111030 DOI: 10.2217/epi.15.12] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
AIM In nondividing neurons examine the role of Gadd45b in active 5-methylcytosine (5MC) and 5-hydroxymethylcytosine (5HMC) removal at a gene promoter highly implicated in mental illnesses and cognition, Bdnf. MATERIALS & METHODS Mouse primary cortical neuronal cultures with and without Gadd45b siRNA transfection were treated with N-methyl-d-aspartate (NMDA). Expression changes of genes reportedly involved in DNA demethylation, Bdnf mRNA and protein and 5MC and 5HMC at Bdnf promoters were measured. RESULTS Gadd45b siRNA transfection in neurons abolishes the NMDA-induced increase in Bdnf IXa mRNA and reductions in 5MC and 5HMC at the Bdnf IXa promoter. CONCLUSION These results contribute to our understanding of DNA demethylation mechanisms in neurons, and its role in regulating NMDA responsive genes implicated in mental illnesses.
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Affiliation(s)
- David P Gavin
- Jesse Brown Veterans Affairs Medical Center, 820 South Damen Avenue (M/C 151), Chicago, IL 60612, USA.,Department of Psychiatry, University of Illinois at Chicago, 1601 W Taylor St, Chicago, IL 60612, USA
| | - Handojo Kusumo
- Jesse Brown Veterans Affairs Medical Center, 820 South Damen Avenue (M/C 151), Chicago, IL 60612, USA.,Department of Psychiatry, University of Illinois at Chicago, 1601 W Taylor St, Chicago, IL 60612, USA
| | - Rajiv P Sharma
- Jesse Brown Veterans Affairs Medical Center, 820 South Damen Avenue (M/C 151), Chicago, IL 60612, USA.,Department of Psychiatry, University of Illinois at Chicago, 1601 W Taylor St, Chicago, IL 60612, USA
| | - Marina Guizzetti
- Jesse Brown Veterans Affairs Medical Center, 820 South Damen Avenue (M/C 151), Chicago, IL 60612, USA.,Department of Psychiatry, University of Illinois at Chicago, 1601 W Taylor St, Chicago, IL 60612, USA.,Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR and VA Portland Health Care System, Portland, OR
| | - Alessandro Guidotti
- Department of Psychiatry, University of Illinois at Chicago, 1601 W Taylor St, Chicago, IL 60612, USA
| | - Subhash C Pandey
- Jesse Brown Veterans Affairs Medical Center, 820 South Damen Avenue (M/C 151), Chicago, IL 60612, USA.,Department of Psychiatry, University of Illinois at Chicago, 1601 W Taylor St, Chicago, IL 60612, USA
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14
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Borovok N, Nesher E, Levin Y, Reichenstein M, Pinhasov A, Michaelevski I. Dynamics of Hippocampal Protein Expression During Long-term Spatial Memory Formation. Mol Cell Proteomics 2015; 15:523-41. [PMID: 26598641 DOI: 10.1074/mcp.m115.051318] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Indexed: 01/08/2023] Open
Abstract
Spatial memory depends on the hippocampus, which is particularly vulnerable to aging. This vulnerability has implications for the impairment of navigation capacities in older people, who may show a marked drop in performance of spatial tasks with advancing age. Contemporary understanding of long-term memory formation relies on molecular mechanisms underlying long-term synaptic plasticity. With memory acquisition, activity-dependent changes occurring in synapses initiate multiple signal transduction pathways enhancing protein turnover. This enhancement facilitates de novo synthesis of plasticity related proteins, crucial factors for establishing persistent long-term synaptic plasticity and forming memory engrams. Extensive studies have been performed to elucidate molecular mechanisms of memory traces formation; however, the identity of plasticity related proteins is still evasive. In this study, we investigated protein turnover in mouse hippocampus during long-term spatial memory formation using the reference memory version of radial arm maze (RAM) paradigm. We identified 1592 proteins, which exhibited a complex picture of expression changes during spatial memory formation. Variable linear decomposition reduced significantly data dimensionality and enriched three principal factors responsible for variance of memory-related protein levels at (1) the initial phase of memory acquisition (165 proteins), (2) during the steep learning improvement (148 proteins), and (3) the final phase of the learning curve (123 proteins). Gene ontology and signaling pathways analysis revealed a clear correlation between memory improvement and learning phase-curbed expression profiles of proteins belonging to specific functional categories. We found differential enrichment of (1) neurotrophic factors signaling pathways, proteins regulating synaptic transmission, and actin microfilament during the first day of the learning curve; (2) transcription and translation machinery, protein trafficking, enhancement of metabolic activity, and Wnt signaling pathway during the steep phase of memory formation; and (3) cytoskeleton organization proteins. Taken together, this study clearly demonstrates dynamic assembly and disassembly of protein-protein interaction networks depending on the stage of memory formation engrams.
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Affiliation(s)
- Natalia Borovok
- From the ‡Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel-Aviv 6997801, Israel
| | - Elimelech Nesher
- §Department of Molecular Biology, Ariel University, Ariel 4070000, Israel
| | - Yishai Levin
- ¶de Botton Institute for Protein Profiling, The Nancy & Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michal Reichenstein
- From the ‡Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel-Aviv 6997801, Israel
| | - Albert Pinhasov
- §Department of Molecular Biology, Ariel University, Ariel 4070000, Israel
| | - Izhak Michaelevski
- From the ‡Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel-Aviv 6997801, Israel; ‖Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
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15
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Peixoto L, Risso D, Poplawski SG, Wimmer ME, Speed TP, Wood MA, Abel T. How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets. Nucleic Acids Res 2015. [PMID: 26202970 PMCID: PMC4652761 DOI: 10.1093/nar/gkv736] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The sequencing of the full transcriptome (RNA-seq) has become the preferred choice for the measurement of genome-wide gene expression. Despite its widespread use, challenges remain in RNA-seq data analysis. One often-overlooked aspect is normalization. Despite the fact that a variety of factors or ‘batch effects’ can contribute unwanted variation to the data, commonly used RNA-seq normalization methods only correct for sequencing depth. The study of gene expression is particularly problematic when it is influenced simultaneously by a variety of biological factors in addition to the one of interest. Using examples from experimental neuroscience, we show that batch effects can dominate the signal of interest; and that the choice of normalization method affects the power and reproducibility of the results. While commonly used global normalization methods are not able to adequately normalize the data, more recently developed RNA-seq normalization can. We focus on one particular method, RUVSeq and show that it is able to increase power and biological insight of the results. Finally, we provide a tutorial outlining the implementation of RUVSeq normalization that is applicable to a broad range of studies as well as meta-analysis of publicly available data.
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Affiliation(s)
- Lucia Peixoto
- Department of Biology, University of Pennsylvania, Smilow Center for Translational Research, Room 10-170, Building 421, 3400 Civic Center Boulevard, Philadelphia, PA 19104-6168, USA
| | - Davide Risso
- Division of Biostatistics, School of Public Health, University of California, Berkeley, 344 Li Ka Shing Center, #3370, Berkeley, CA 94720-3370, USA
| | - Shane G Poplawski
- Department of Biology, University of Pennsylvania, Smilow Center for Translational Research, Room 10-170, Building 421, 3400 Civic Center Boulevard, Philadelphia, PA 19104-6168, USA
| | - Mathieu E Wimmer
- Department of Biology, University of Pennsylvania, Smilow Center for Translational Research, Room 10-170, Building 421, 3400 Civic Center Boulevard, Philadelphia, PA 19104-6168, USA
| | - Terence P Speed
- Department of Statistics, University of California, Berkeley, Department of Mathematics and Statistics, The University of Melbourne, Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Australia
| | - Marcelo A Wood
- University of California, Irvine, Department of Neurobiology and Behavior, USA
| | - Ted Abel
- Department of Biology, University of Pennsylvania, Smilow Center for Translational Research, Room 10-170, Building 421, 3400 Civic Center Boulevard, Philadelphia, PA 19104-6168, USA
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16
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Peixoto LL, Wimmer ME, Poplawski SG, Tudor JC, Kenworthy CA, Liu S, Mizuno K, Garcia BA, Zhang NR, Giese K, Abel T. Memory acquisition and retrieval impact different epigenetic processes that regulate gene expression. BMC Genomics 2015; 16 Suppl 5:S5. [PMID: 26040834 PMCID: PMC4460846 DOI: 10.1186/1471-2164-16-s5-s5] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background A fundamental question in neuroscience is how memories are stored and retrieved in the brain. Long-term memory formation requires transcription, translation and epigenetic processes that control gene expression. Thus, characterizing genome-wide the transcriptional changes that occur after memory acquisition and retrieval is of broad interest and importance. Genome-wide technologies are commonly used to interrogate transcriptional changes in discovery-based approaches. Their ability to increase scientific insight beyond traditional candidate gene approaches, however, is usually hindered by batch effects and other sources of unwanted variation, which are particularly hard to control in the study of brain and behavior. Results We examined genome-wide gene expression after contextual conditioning in the mouse hippocampus, a brain region essential for learning and memory, at all the time-points in which inhibiting transcription has been shown to impair memory formation. We show that most of the variance in gene expression is not due to conditioning and that by removing unwanted variance through additional normalization we are able provide novel biological insights. In particular, we show that genes downregulated by memory acquisition and retrieval impact different functions: chromatin assembly and RNA processing, respectively. Levels of histone 2A variant H2AB are reduced only following acquisition, a finding we confirmed using quantitative proteomics. On the other hand, splicing factor Rbfox1 and NMDA receptor-dependent microRNA miR-219 are only downregulated after retrieval, accompanied by an increase in protein levels of miR-219 target CAMKIIγ. Conclusions We provide a thorough characterization of coding and non-coding gene expression during long-term memory formation. We demonstrate that unwanted variance dominates the signal in transcriptional studies of learning and memory and introduce the removal of unwanted variance through normalization as a necessary step for the analysis of genome-wide transcriptional studies in the context of brain and behavior. We show for the first time that histone variants are downregulated after memory acquisition, and splicing factors and microRNAs after memory retrieval. Our results provide mechanistic insights into the molecular basis of cognition by highlighting the differential involvement of epigenetic mechanisms, such as histone variants and post-transcriptional RNA regulation, after acquisition and retrieval of memory.
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17
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Kigar SL, Chang L, Auger AP. Gadd45b is an epigenetic regulator of juvenile social behavior and alters local pro-inflammatory cytokine production in the rodent amygdala. Brain Behav Immun 2015; 46:60-9. [PMID: 25728234 PMCID: PMC4440808 DOI: 10.1016/j.bbi.2015.02.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 02/17/2015] [Accepted: 02/20/2015] [Indexed: 11/29/2022] Open
Abstract
Precise regulation of the epigenome during perinatal development is critical to the formation of species-typical behavior later in life. Recent data suggests that Gadd45b facilitates active DNA demethylation by recruiting proteins involved in base excision repair (BER), which will catalyze substitution of 5-methyl-cytosine (5mC) for an unmodified cytosine. While a role for Gadd45b has been implicated in both hippocampal and amygdalar learning tasks, to the best of our knowledge, no study has been done investigating the involvement of Gadd45b in neurodevelopmental programming of social behavior. To address this, we used a targeted siRNA delivery approach to transiently knock down Gadd45b expression in the neonatal rat amygdala. We chose to examine social behavior in the juvenile period, as social deficits associated with neurodevelopmental disorders tend to emerge in humans at an equivalent age. We find that neonatal Gadd45b knock-down results in altered juvenile social behavior and reduced expression of several genes implicated in psychiatric disorders, including methyl-CpG-binding protein 2 (MeCP2), Reelin, and brain derived neurotrophic factor (BDNF). We furthermore report a novel role for Gadd45b in the programmed expression of α2-adrenoceptor (Adra2a). Consistent with Gadd45b's role in the periphery, we also observed changes in the expression of pro-inflammatory cytokines interleukin-6 (Il-6) and interleukin-1beta (Il-1beta) in the amygdala, which could potentially mediate or exacerbate effects of Gadd45b knockdown on the organization of social behavior. These data suggest a prominent role for Gadd45b in the epigenetic programming of complex juvenile social interactions, and may provide insight into the etiology of juvenile behavioral disorders such as ADHD, autism, and/or schizophrenia.
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Affiliation(s)
- Stacey L. Kigar
- Molecular and Cellular Pharmacology Program, University of Wisconsin–Madison, Madison, WI 53706, United States
| | - Liza Chang
- Department of Psychology, University of Wisconsin–Madison, Madison, WI 53706, United States
| | - Anthony P. Auger
- Department of Psychology, University of Wisconsin–Madison, Madison, WI 53706, United States,Neuroscience Training Program, University of Wisconsin–Madison, Madison, WI 53706, United States,Corresponding author at: 1202 W, Johnson St, Madison, WI 53706, United States. (A.P. Auger)
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18
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Francis C, Natarajan S, Lee MT, Khaladkar M, Buckley PT, Sul JY, Eberwine J, Kim J. Divergence of RNA localization between rat and mouse neurons reveals the potential for rapid brain evolution. BMC Genomics 2014; 15:883. [PMID: 25301173 PMCID: PMC4203888 DOI: 10.1186/1471-2164-15-883] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 09/23/2014] [Indexed: 12/12/2022] Open
Abstract
Background Neurons display a highly polarized architecture. Their ability to modify their features under intracellular and extracellular stimuli, known as synaptic plasticity, is a key component of the neurochemical basis of learning and memory. A key feature of synaptic plasticity involves the delivery of mRNAs to distinct sub-cellular domains where they are locally translated. Regulatory coordination of these spatio-temporal events is critical for synaptogenesis and synaptic plasticity as defects in these processes can lead to neurological diseases. In this work, using microdissected dendrites from primary cultures of hippocampal neurons of two mouse strains (C57BL/6 and Balb/c) and one rat strain (Sprague–Dawley), we investigate via microarrays, subcellular localization of mRNAs in dendrites of neurons to assay the evolutionary differences in subcellular dendritic transcripts localization. Results Our microarray analysis highlighted significantly greater evolutionary diversification of RNA localization in the dendritic transcriptomes (81% gene identity difference among the top 5% highly expressed genes) compared to the transcriptomes of 11 different central nervous system (CNS) and non-CNS tissues (average of 44% gene identity difference among the top 5% highly expressed genes). Differentially localized genes include many genes involved in CNS function. Conclusions Species differences in sub-cellular localization may reflect non-functional neutral drift. However, the functional categories of mRNA showing differential localization suggest that at least part of the divergence may reflect activity-dependent functional differences of neurons, mediated by species-specific RNA subcellular localization mechanisms. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-883) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - James Eberwine
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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19
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Poplawski SG, Schoch H, Wimmer M, Hawk JD, Walsh JL, Giese KP, Abel T. Object-location training elicits an overlapping but temporally distinct transcriptional profile from contextual fear conditioning. Neurobiol Learn Mem 2014; 116:90-95. [PMID: 25242102 DOI: 10.1016/j.nlm.2014.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 08/25/2014] [Accepted: 09/04/2014] [Indexed: 12/19/2022]
Abstract
Hippocampus-dependent learning is known to induce changes in gene expression, but information on gene expression differences between different learning paradigms that require the hippocampus is limited. The bulk of studies investigating RNA expression after learning use the contextual fear conditioning task, which couples a novel environment with a footshock. Although contextual fear conditioning has been useful in discovering gene targets, gene expression after spatial memory tasks has received less attention. In this study, we used the object-location memory task and studied gene expression at two time points after learning in a high-throughput manner using a microfluidic qPCR approach. We found that expression of the classic immediate-early genes changes after object-location training in a fashion similar to that observed after contextual fear conditioning. However, the temporal dynamics of gene expression are different between the two tasks, with object-location memory producing gene expression changes that last at least 2 hours. Our findings indicate that different training paradigms may give rise to distinct temporal dynamics of gene expression after learning.
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Affiliation(s)
- Shane G Poplawski
- Pharmacology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hannah Schoch
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mathieu Wimmer
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joshua D Hawk
- Department of Cell Biology, Yale University, New Haven, CT 06520, USA
| | - Jennifer L Walsh
- Departments of Psychology and Mathematics, Swarthmore College, Swarthmore, PA, 19081, United States
| | - Karl P Giese
- Centre for the Cellular Basis of Behaviour, King's College London, London, UK SE5 9NU
| | - Ted Abel
- Pharmacology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA.,Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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20
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Gavin DP, Floreani C. Epigenetics of schizophrenia: an open and shut case. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2014; 115:155-201. [PMID: 25131545 DOI: 10.1016/b978-0-12-801311-3.00005-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
During the last decade and a half, there has been an explosion of data regarding epigenetic changes in schizophrenia. Most initial studies have suggested that schizophrenia is characterized by an overly restrictive chromatin state based on increases in transcription silencing histone modifications and DNA methylation at schizophrenia candidate gene promoters and increases in the expression of enzymes that catalyze their formation. However, recent studies indicate that the pathology is more complex. This complexity may greatly impact pharmacological approaches directed at targeting epigenetic abnormalities in schizophrenia. The current review explores epigenetic studies of schizophrenia and what this can tell us about the underlying pathophysiology. We hypothesize based on recent studies that it is also plausible that drugs that further restrict chromatin may be efficacious.
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Affiliation(s)
- David P Gavin
- Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA; Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, USA.
| | - Christina Floreani
- Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA; Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, USA
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21
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Stankiewicz AM, Swiergiel AH, Lisowski P. Epigenetics of stress adaptations in the brain. Brain Res Bull 2013; 98:76-92. [DOI: 10.1016/j.brainresbull.2013.07.003] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 07/04/2013] [Accepted: 07/06/2013] [Indexed: 02/07/2023]
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22
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Gavin DP, Chase KA, Sharma RP. Active DNA demethylation in post-mitotic neurons: a reason for optimism. Neuropharmacology 2013; 75:233-45. [PMID: 23958448 DOI: 10.1016/j.neuropharm.2013.07.036] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 07/22/2013] [Accepted: 07/30/2013] [Indexed: 12/13/2022]
Abstract
Over the last several years proteins involved in base excision repair (BER) have been implicated in active DNA demethylation. We review the literature supporting BER as a means of active DNA demethylation, and explain how the various components function and cooperate to remove the potentially most enduring means of epigenetic gene regulation. Recent evidence indicates that the same pathways implicated during periods of widespread DNA demethylation, such as the erasure of methyl marks in the paternal pronucleus soon after fertilization, are operational in post-mitotic neurons. Neuronal functional identities, defined here as the result of a combination of neuronal subtype, location, and synaptic connections are largely maintained through DNA methylation. Chronic mental illnesses, such as schizophrenia, may be the result of both altered neurotransmitter levels and neurons that have assumed dysfunctional neuronal identities. A limitation of most current psychopharmacological agents is their focus on the former, while not addressing the more profound latter pathophysiological process. Previously, it was believed that active DNA demethylation in post-mitotic neurons was rare if not impossible. If this were the case, then reversing the factors that maintain neuronal identity, would be highly unlikely. The emergence of an active DNA demethylation pathway in the brain is a reason for great optimism in psychiatry as it provides a means by which previously pathological neurons may be reprogrammed to serve a more favorable role. Agents targeting epigenetic processes have shown much promise in this regard, and may lead to substantial gains over traditional pharmacological approaches.
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Affiliation(s)
- David P Gavin
- The Psychiatric Institute, Department of Psychiatry, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60612, USA; Jesse Brown Veterans Affairs Medical Center, 820 South Damen Avenue (M/C 151), Chicago, IL 60612, USA.
| | - Kayla A Chase
- The Psychiatric Institute, Department of Psychiatry, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60612, USA
| | - Rajiv P Sharma
- The Psychiatric Institute, Department of Psychiatry, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60612, USA; Jesse Brown Veterans Affairs Medical Center, 820 South Damen Avenue (M/C 151), Chicago, IL 60612, USA
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23
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Partin AC, Hosek MP, Luong JA, Lella SK, Sharma SAR, Ploski JE. Amygdala nuclei critical for emotional learning exhibit unique gene expression patterns. Neurobiol Learn Mem 2013; 104:110-21. [PMID: 23831498 DOI: 10.1016/j.nlm.2013.06.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 06/24/2013] [Accepted: 06/25/2013] [Indexed: 01/09/2023]
Abstract
The amygdala is a heterogeneous, medial temporal lobe structure that has been implicated in the formation, expression and extinction of emotional memories. This structure is composed of numerous nuclei that vary in cytoarchitectonics and neural connections. In particular the lateral nucleus of the amygdala (LA), central nucleus of the amygdala (CeA), and the basal (B) nucleus contribute an essential role to emotional learning. However, to date it is still unclear to what extent these nuclei differ at the molecular level. Therefore we have performed whole genome gene expression analysis on these nuclei to gain a better understanding of the molecular differences and similarities among these nuclei. Specifically the LA, CeA and B nuclei were laser microdissected from the rat brain, and total RNA was isolated from these nuclei and subjected to RNA amplification. Amplified RNA was analyzed by whole genome microarray analysis which revealed that 129 genes are differentially expressed among these nuclei. Notably gene expression patterns differed between the CeA nucleus and the LA and B nuclei. However gene expression differences were not considerably different between the LA and B nuclei. Secondary confirmation of numerous genes was performed by in situ hybridization to validate the microarray findings, which also revealed that for many genes, expression differences among these nuclei were consistent with the embryological origins of these nuclei. Knowing the stable gene expression differences among these nuclei will provide novel avenues of investigation into how these nuclei contribute to emotional arousal and emotional learning, and potentially offer new genetic targets to manipulate emotional learning and memory.
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Affiliation(s)
- Alexander C Partin
- School of Behavioral and Brain Sciences,Department of Molecular & Cell Biology, University of Texas at Dallas, USA
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24
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Bousiges O, Neidl R, Majchrzak M, Muller MA, Barbelivien A, Pereira de Vasconcelos A, Schneider A, Loeffler JP, Cassel JC, Boutillier AL. Detection of histone acetylation levels in the dorsal hippocampus reveals early tagging on specific residues of H2B and H4 histones in response to learning. PLoS One 2013; 8:e57816. [PMID: 23469244 PMCID: PMC3587615 DOI: 10.1371/journal.pone.0057816] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 01/26/2013] [Indexed: 12/21/2022] Open
Abstract
The recent literature provides evidence that epigenetic mechanisms such as DNA methylation and histone modification are crucial to gene transcription linked to synaptic plasticity in the mammalian brain--notably in the hippocampus--and memory formation. We measured global histone acetylation levels in the rat hippocampus at an early stage of spatial or fear memory formation. We found that H3, H4 and H2B underwent differential acetylation at specific sites depending on whether rats had been exposed to the context of a task without having to learn or had to learn about a place or fear therein: H3K9K14 acetylation was mostly responsive to any experimental conditions compared to naive animals, whereas H2B N-terminus and H4K12 acetylations were mostly associated with memory for either spatial or fear learning. Altogether, these data suggest that behavior/experience-dependent changes differently regulate specific acetylation modifications of histones in the hippocampus, depending on whether a memory trace is established or not: tagging of H3K9K14 could be associated with perception/processing of testing-related manipulations and context, thereby enhancing chromatin accessibility, while tagging of H2B N-terminus tail and H4K12 could be more closely associated with the formation of memories requiring an engagement of the hippocampus.
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Affiliation(s)
- Olivier Bousiges
- Laboratoire de Neurosciences Cognitives et Adaptatives, UMR7364, Université de Strasbourg-CNRS, GDR CNRS 2905, Faculté de Psychologie, Strasbourg, France
| | - Romain Neidl
- Laboratoire de Neurosciences Cognitives et Adaptatives, UMR7364, Université de Strasbourg-CNRS, GDR CNRS 2905, Faculté de Psychologie, Strasbourg, France
| | - Monique Majchrzak
- Laboratoire de Neurosciences Cognitives et Adaptatives, UMR7364, Université de Strasbourg-CNRS, GDR CNRS 2905, Faculté de Psychologie, Strasbourg, France
| | - Marc-Antoine Muller
- Laboratoire de Neurosciences Cognitives et Adaptatives, UMR7364, Université de Strasbourg-CNRS, GDR CNRS 2905, Faculté de Psychologie, Strasbourg, France
| | - Alexandra Barbelivien
- Laboratoire de Neurosciences Cognitives et Adaptatives, UMR7364, Université de Strasbourg-CNRS, GDR CNRS 2905, Faculté de Psychologie, Strasbourg, France
| | - Anne Pereira de Vasconcelos
- Laboratoire de Neurosciences Cognitives et Adaptatives, UMR7364, Université de Strasbourg-CNRS, GDR CNRS 2905, Faculté de Psychologie, Strasbourg, France
| | - Anne Schneider
- Laboratoire de Neurosciences Cognitives et Adaptatives, UMR7364, Université de Strasbourg-CNRS, GDR CNRS 2905, Faculté de Psychologie, Strasbourg, France
| | - Jean-Philippe Loeffler
- Inserm, U692, Laboratoire de Signalisations Moléculaires et Neurodégénérescence, Université de Strasbourg, Faculté de Médecine, UMRS692, Strasbourg, France
| | - Jean-Christophe Cassel
- Laboratoire de Neurosciences Cognitives et Adaptatives, UMR7364, Université de Strasbourg-CNRS, GDR CNRS 2905, Faculté de Psychologie, Strasbourg, France
| | - Anne-Laurence Boutillier
- Laboratoire de Neurosciences Cognitives et Adaptatives, UMR7364, Université de Strasbourg-CNRS, GDR CNRS 2905, Faculté de Psychologie, Strasbourg, France
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25
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McNulty SE, Barrett RM, Vogel-Ciernia A, Malvaez M, Hernandez N, Davatolhagh MF, Matheos DP, Schiffman A, Wood MA. Differential roles for Nr4a1 and Nr4a2 in object location vs. object recognition long-term memory. Learn Mem 2012; 19:588-92. [PMID: 23161447 DOI: 10.1101/lm.026385.112] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Nr4a1 and Nr4a2 are transcription factors and immediate early genes belonging to the nuclear receptor Nr4a family. In this study, we examine their role in long-term memory formation for object location and object recognition. Using siRNA to block expression of either Nr4a1 or Nr4a2, we found that Nr4a2 is necessary for both long-term memory for object location and object recognition. In contrast, Nr4a1 appears to be necessary only for object location. Indeed, their roles in these different types of long-term memory may be dependent on their expression in the brain, as NR4A2 was found to be expressed in hippocampal neurons (associated with object location memory) as well as in the insular and perirhinal cortex (associated with object recognition memory), whereas NR4A1 showed minimal neuronal expression in these cortical areas. These results begin to elucidate how NR4A1 and NR4A2 differentially contribute to object location versus object recognition memory.
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Affiliation(s)
- Susan E McNulty
- Department of Neurobiology & Behavior, Center for the Neurobiology of Learning & Memory, University of California, Irvine, Irvine, California 92697-3800, USA
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26
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Hawk JD, Bookout AL, Poplawski SG, Bridi M, Rao AJ, Sulewski ME, Kroener BT, Manglesdorf DJ, Abel T. NR4A nuclear receptors support memory enhancement by histone deacetylase inhibitors. J Clin Invest 2012; 122:3593-602. [PMID: 22996661 DOI: 10.1172/jci64145] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 07/26/2012] [Indexed: 02/06/2023] Open
Abstract
The formation of a long-lasting memory requires a transcription-dependent consolidation period that converts a short-term memory into a long-term memory. Nuclear receptors compose a class of transcription factors that regulate diverse biological processes, and several nuclear receptors have been implicated in memory formation. Here, we examined the potential contribution of nuclear receptors to memory consolidation by measuring the expression of all 49 murine nuclear receptors after learning. We identified 13 nuclear receptors with increased expression after learning, including all 3 members of the Nr4a subfamily. These CREB-regulated Nr4a genes encode ligand-independent "orphan" nuclear receptors. We found that blocking NR4A activity in memory-supporting brain regions impaired long-term memory but did not impact short-term memory in mice. Further, expression of Nr4a genes increased following the memory-enhancing effects of histone deacetylase (HDAC) inhibitors. Blocking NR4A signaling interfered with the ability of HDAC inhibitors to enhance memory. These results demonstrate that the Nr4a gene family contributes to memory formation and is a promising target for improving cognitive function.
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Affiliation(s)
- Joshua D Hawk
- Neuroscience Graduate Group and Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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27
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Gadd45b knockout mice exhibit selective deficits in hippocampus-dependent long-term memory. Learn Mem 2012; 19:319-24. [PMID: 22802593 DOI: 10.1101/lm.024984.111] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Growth arrest and DNA damage-inducible β (Gadd45b) has been shown to be involved in DNA demethylation and may be important for cognitive processes. Gadd45b is abnormally expressed in subjects with autism and psychosis, two disorders associated with cognitive deficits. Furthermore, several high-throughput screens have identified Gadd45b as a candidate plasticity-related gene. However, a direct demonstration of a link between Gadd45b and memory has not been established. The current studies first determined whether expression of the Gadd45 family of genes was affected by contextual fear conditioning. Gadd45b, and to a lesser extent Gadd45g, were up-regulated in the hippocampus following contextual fear conditioning, whereas Gadd45a was not. Next, Gadd45b knockout mice were tested for contextual and cued fear conditioning. Gadd45b knockout mice exhibited a significant deficit in long-term contextual fear conditioning; however, they displayed normal levels of short-term contextual fear conditioning. No differences between Gadd45b knockout and wild-type mice were observed in cued fear conditioning. Because cued fear conditioning is hippocampus independent, while contextual fear conditioning is hippocampus dependent, the current studies suggest that Gadd45b may be important for long-term hippocampus-dependent memory storage. Therefore, Gadd45b may be a novel therapeutic target for the cognitive deficits associated with many neurodevelopmental, neurological, and psychiatric disorders.
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Increased expression of axogenesis-related genes and mossy fibre length in dentate granule cells from adult HuD overexpressor mice. ASN Neuro 2012; 3:259-70. [PMID: 22004431 PMCID: PMC3234101 DOI: 10.1042/an20110015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The neuronal RNA-binding protein HuD plays a critical role in the post-transcriptional regulation of short-lived mRNAs during the initial establishment and remodelling of neural connections. We have generated transgenic mice overexpressing this protein (HuD-Tg) in adult DGCs (dentate granule cells) and shown that their mossy fibres contain high levels of GAP-43 (growth-associated protein 43) and exhibit distinct morphological and electrophysiological properties. To investigate the basis for these changes and identify other molecular targets of HuD, DGCs from HuD-Tg and control mice were collected by LCM (laser capture microscopy) and RNAs analysed using DNA microarrays. Results show that 216 known mRNAs transcripts and 63 ESTs (expressed sequence tags) are significantly up-regulated in DGCs from these transgenic mice. Analyses of the 3'-UTRs (3'-untranslated regions) of these transcripts revealed an increased number of HuD-binding sites and the presence of several known instability-conferring sequences. Among these, the mRNA for TTR (transthyretin) shows the highest level of up-regulation, as confirmed by qRT-PCR (quantitative reverse transcription-PCR) and ISH (in situ hybridization). GO (gene ontology) analyses of up-regulated transcripts revealed a large over-representation of genes associated with neural development and axogenesis. In correlation with these gene expression changes, we found an increased length of the infrapyramidal mossy fibre bundle in HuD-Tg mice. These results support the notion that HuD stabilizes a number of developmentally regulated mRNAs in DGCs, resulting in increased axonal elongation.
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Johansen JP, Cain CK, Ostroff LE, LeDoux JE. Molecular mechanisms of fear learning and memory. Cell 2011; 147:509-24. [PMID: 22036561 DOI: 10.1016/j.cell.2011.10.009] [Citation(s) in RCA: 714] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Indexed: 01/08/2023]
Abstract
Pavlovian fear conditioning is a particularly useful behavioral paradigm for exploring the molecular mechanisms of learning and memory because a well-defined response to a specific environmental stimulus is produced through associative learning processes. Synaptic plasticity in the lateral nucleus of the amygdala (LA) underlies this form of associative learning. Here, we summarize the molecular mechanisms that contribute to this synaptic plasticity in the context of auditory fear conditioning, the form of fear conditioning best understood at the molecular level. We discuss the neurotransmitter systems and signaling cascades that contribute to three phases of auditory fear conditioning: acquisition, consolidation, and reconsolidation. These studies suggest that multiple intracellular signaling pathways, including those triggered by activation of Hebbian processes and neuromodulatory receptors, interact to produce neural plasticity in the LA and behavioral fear conditioning. Collectively, this body of research illustrates the power of fear conditioning as a model system for characterizing the mechanisms of learning and memory in mammals and potentially for understanding fear-related disorders, such as PTSD and phobias.
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Affiliation(s)
- Joshua P Johansen
- Center for Neural Science, New York University, New York, NY 10003, USA
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Abstract
In addition to its role in cellular development and proliferation, there are emerging in vitro data implicating the Wnt/β-catenin pathway in synaptic plasticity. Yet in vivo studies have not examined whether Wnt activity is required for learning and memory. In the amygdala during fear memory formation, we found that many Wnt-signaling genes were dynamically regulated, with an immediate decrease, followed by an eventual normalization during memory consolidation. This rapid decrease in Wnt mRNA was confirmed with individual quantitative PCR and in situ hybridization. We then manipulated Wnt signaling with a specific peptide antagonist (Dkk-1) or agonist (Wnt1) injected stereotaxically into the adult amygdala during fear learning. We found that neither manipulation had an effect on locomotion, anxiety, fear acquisition, or fear expression. However, both Wnt modulators prevented long-term fear memory consolidation without affecting short-term memory. Dkk-1 and Wnt infusions had destabilizing, but opposite, effects on the requisite β-catenin/cadherin dynamic interactions that occur during consolidation. These data suggest that dynamic modulation of Wnt/β-catenin signaling during consolidation is critical for the structural basis of long-term memory formation.
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Monopoli MP, Raghnaill MN, Loscher JS, O'Sullivan NC, Pangalos MN, Ring RH, von Schack D, Dunn MJ, Regan CM, Pennington S, Murphy KJ. Temporal proteomic profile of memory consolidation in the rat hippocampal dentate gyrus. Proteomics 2011; 11:4189-201. [DOI: 10.1002/pmic.201100072] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 07/21/2011] [Accepted: 08/04/2011] [Indexed: 11/06/2022]
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Lisowski P, Juszczak GR, Goscik J, Wieczorek M, Zwierzchowski L, Swiergiel AH. Effect of chronic mild stress on hippocampal transcriptome in mice selected for high and low stress-induced analgesia and displaying different emotional behaviors. Eur Neuropsychopharmacol 2011; 21:45-62. [PMID: 20961740 DOI: 10.1016/j.euroneuro.2010.08.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2010] [Revised: 08/13/2010] [Accepted: 08/18/2010] [Indexed: 12/18/2022]
Abstract
There is increasing evidence that mood disorders may derive from the impact of environmental pressure on genetically susceptible individuals. Stress-induced hippocampal plasticity has been implicated in depression. We studied hippocampal transcriptomes in strains of mice that display high (HA) and low (LA) swim stress-induced analgesia and that differ in emotional behaviors and responses to different classes of antidepressants. Chronic mild stress (CMS) affected expression of a number of genes common for both strains. CMS also produced strain specific changes in expression suggesting that hippocampal responses to stress depend on genotype. Considerably larger number of genes, biological processes, molecular functions, biochemical pathways, and gene networks were affected by CMS in LA than in HA mice. The results suggest that potential drug targets against detrimental effects of stress include glutamate transporters, and cholinergic, cholecystokinin (CCK), glucocorticoids, and thyroid hormones receptors. Furthermore, some biological processes evoked by stress and different between the strains, such as apoptosis, neurogenesis and chromatin modifications, may be responsible for the long-term, irreversible effects of stress and suggest a role for epigenetic regulation of mood related stress responses.
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Affiliation(s)
- Pawel Lisowski
- Department of Molecular Biology, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzebiec, Poland
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Morris MJ, Karra AS, Monteggia LM. Histone deacetylases govern cellular mechanisms underlying behavioral and synaptic plasticity in the developing and adult brain. Behav Pharmacol 2010; 21:409-19. [PMID: 20555253 PMCID: PMC2923662 DOI: 10.1097/fbp.0b013e32833c20c0] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Histone deacetylases (HDACs) are a family of enzymes that alter gene expression patterns by modifying chromatin architecture. There are 11 mammalian HDACs that are classified by homology into four subfamilies, all with distinct expression patterns in the brain. Through the use of pharmacological HDAC inhibitors, and more recently HDAC knockout mice, the role of these enzymes in the central nervous system are starting to be elucidated. We will discuss the latest findings on the specific or redundant roles of individual HDACs in the brain as well as the impact of HDAC function on complex behavior, with a focus on learning, memory formation, and affective behavior. Potential HDAC-mediated cellular mechanisms underlying those behaviors are discussed.
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Affiliation(s)
- Michael J Morris
- Department of Psychiatry, UT Southwestern Medical Center, Dallas, Texas 75390-9070, USA
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35
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Ponomarev I, Rau V, Eger EI, Harris RA, Fanselow MS. Amygdala transcriptome and cellular mechanisms underlying stress-enhanced fear learning in a rat model of posttraumatic stress disorder. Neuropsychopharmacology 2010; 35:1402-11. [PMID: 20147889 PMCID: PMC3040562 DOI: 10.1038/npp.2010.10] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Severe stress or trauma can cause permanent changes in brain circuitry, leading to dysregulation of fear responses and the development of posttraumatic stress disorder (PTSD). To date, little is known about the molecular mechanisms underlying stress-induced long-term plasticity in fear circuits. We addressed this question by using global gene expression profiling in an animal model of PTSD, stress-enhanced fear learning (SEFL). A total of 15 footshocks were used to induce SEFL and the volatile anesthetic isoflurane was used to suppress the behavioral effects of stress. Gene expression in lateral/basolateral amygdala was measured using microarrays at 3 weeks after the exposure to different combinations of shock and isoflurane. Shock produced robust effects on amygdalar transcriptome and isoflurane blocked or reversed many of the stress-induced changes. We used a modular approach to molecular profiles of shock and isoflurane and built a network of regulated genes, functional categories, and cell types that represent a mechanistic foundation of perturbation-induced plasticity in the amygdala. This analysis partitioned perturbation-induced changes in gene expression into neuron- and astrocyte-specific changes, highlighting a previously underappreciated role of astroglia in amygdalar plasticity. Many neuron-enriched genes were highly correlated with astrocyte-enriched genes, suggesting coordinated transcriptional responses to environmental challenges in these cell types. Several individual genes were validated using RT-PCR and behavioral pharmacology. This study is the first to propose specific cellular and molecular mechanisms underlying SEFL, an animal model of PTSD, and to nominate novel molecular and cellular targets with potential for therapeutic intervention in PTSD, including glycine and neuropeptide systems, chromatin remodeling, and gliotransmission.
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Affiliation(s)
- Igor Ponomarev
- Waggoner Center for Alcohol and Addiction Research and the College of Pharmacy, University of Texas, 1 University Station, Austin, TX, USA,Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, 1 University Station, A4800, Austin, TX 78712, USA, Tel: +512-471-5122, Fax: +512-232-2525, E-mail:
| | - Vinuta Rau
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA, USA
| | - Edmond I Eger
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA, USA
| | - R Adron Harris
- Waggoner Center for Alcohol and Addiction Research and the College of Pharmacy, University of Texas, 1 University Station, Austin, TX, USA
| | - Michael S Fanselow
- Department of Psychology, University of California, Los Angeles, CA, USA
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Ploski JE, Park KW, Ping J, Monsey MS, Schafe GE. Identification of plasticity-associated genes regulated by Pavlovian fear conditioning in the lateral amygdala. J Neurochem 2009; 112:636-50. [PMID: 19912470 DOI: 10.1111/j.1471-4159.2009.06491.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Most recent studies aimed at defining the cellular and molecular mechanisms of Pavlovian fear conditioning have focused on protein kinase signaling pathways and the transcription factor cAMP-response element binding protein (CREB) that promote fear memory consolidation in the lateral nucleus of the amygdala (LA). Despite this progress, there still remains a paucity of information regarding the genes downstream of CREB that are required for long-term fear memory formation in the LA. We have adopted a strategy of using microarray technology to initially identify genes induced within the dentate gyrus following in vivo long-term potentiation (LTP) followed by analysis of whether these same genes are also regulated by fear conditioning within the LA. In the present study, we first identified 34 plasticity-associated genes that are induced within 30 min following LTP induction utilizing a combination of DNA microarray, qRT-PCR, and in situ hybridization. To determine whether these genes are also induced in the LA following Pavlovian fear conditioning, we next exposed rats to an auditory fear conditioning protocol or to control conditions that do not support fear learning followed by qRT-PCR on mRNA from microdissected LA samples. Finally, we asked whether identified genes induced by fear learning in the LA are downstream of the extracellular-regulated kinase/mitogen-activated protein kinase signaling cascade. Collectively, our findings reveal a comprehensive list of genes that represent the first wave of transcription following both LTP induction and fear conditioning that largely belong to a class of genes referred to as 'neuronal activity dependent genes' that are likely calcium, extracellular-regulated kinase/mitogen-activated protein kinase, and CREB-dependent.
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Affiliation(s)
- Jonathan E Ploski
- Department of Psychology, Yale University, New Haven, Connecticut 06520, USA
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Sirri A, Bianchi V, Pelizzola M, Mayhaus M, Ricciardi-Castagnoli P, Toniolo D, D'Adamo P. Temporal gene expression profile of the hippocampus following trace fear conditioning. Brain Res 2009; 1308:14-23. [PMID: 19857472 DOI: 10.1016/j.brainres.2009.10.049] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Revised: 10/15/2009] [Accepted: 10/19/2009] [Indexed: 10/20/2022]
Abstract
In this paper we report the results of gene expression profiling of C57Bl/6N mice hippocampus after trace fear conditioning (TFC), and the identification of genes regulated at early and late steps after conditioning. Several of the genes regulated at early steps following TFC appeared common to many training protocols. At later stages (2 and 6 h), most of the genes identified were different from those identified following other learning paradigms resulting in memory consolidation. At 6 h after training, few genes were upregulated in respect to the naïve condition, suggesting that many gene products have eventually to be downregulated to achieve stable synapses modification and memory formation. In conclusion, the results presented highlight a number of genes whose expression is specifically modified in the mouse hippocampus following TFC and demonstrate the specificity associated to different forms of conditioning.
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Affiliation(s)
- Alessandra Sirri
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
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38
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Lamprecht R, Dracheva S, Assoun S, LeDoux JE. Fear conditioning induces distinct patterns of gene expression in lateral amygdala. GENES BRAIN AND BEHAVIOR 2009; 8:735-43. [PMID: 19689454 DOI: 10.1111/j.1601-183x.2009.00515.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The lateral nucleus of the amygdala (LA) has been implicated in the formation of long-term associative memory (LTM) of stimuli associated with danger through fear conditioning. The current study aims to detect genes that are expressed in LA following associative fear conditioning. Using oligonucleotide microarrays, we monitored gene expression in rats subjected to paired training where a tone co-terminates with a footshock, or unpaired training where the tone and footshock are presented in a non-overlapping manner. The paired protocol consistently leads to auditory fear conditioning memory formation, whereas the unpaired protocol does not. When the paired group was compared with the unpaired group 5 h after training, the expression of genes coding for the limbic system-associated membrane protein (Lsamp), kinesin heavy chain member 2 (Kif2), N-ethylmaleimide-sensitive fusion protein (NSF) and Hippocalcin-like 4 protein (Hpcal4) was higher in the paired group. These genes encode proteins that regulate neuronal axonal morphology (Lsamp, Kif2), presynaptic vesicle cycling and release (Hpcal4 and NSF), and AMPA receptor maintenance in synapses (NSF). Quantitative real-time PCR (qPCR) showed that Kif2 and Lsamp are expressed hours following fear conditioning but minutes after unpaired training. Hpcal4 is induced by paired stimulation only 5 h after the training. These results show that fear conditioning induces a unique temporal activation of molecular pathways involved in regulating synaptic transmission and axonal morphology in LA, which is different from non-associative stimulation.
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Affiliation(s)
- R Lamprecht
- Department of Neurobiology and Ethology, University of Haifa, Haifa, Israel.
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39
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Abel T, Nguyen PV. Regulation of hippocampus-dependent memory by cyclic AMP-dependent protein kinase. PROGRESS IN BRAIN RESEARCH 2008; 169:97-115. [PMID: 18394470 DOI: 10.1016/s0079-6123(07)00006-4] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The hippocampus is crucial for the consolidation of new declarative long-term memories. Genetic and behavioral experimentation have revealed that several protein kinases are critical for the formation of hippocampus-dependent long-term memories. Cyclic-AMP dependent protein kinase (PKA) is a serine-threonine kinase that has been strongly implicated in the expression of specific forms of hippocampus-dependent memory. We review evidence that PKA is required for hippocampus-dependent memory in mammals, and we highlight some of the proteins that have been implicated as targets of PKA. Future directions and open questions regarding the role of PKA in memory storage are also described.
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Affiliation(s)
- Ted Abel
- University of Pennsylvania, Department of Biology, Biological Basis of Behavior Program, Philadelphia, PA 19104, USA
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40
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Vecsey CG, Hawk JD, Lattal KM, Stein JM, Fabian SA, Attner MA, Cabrera SM, McDonough CB, Brindle PK, Abel T, Wood MA. Histone deacetylase inhibitors enhance memory and synaptic plasticity via CREB:CBP-dependent transcriptional activation. J Neurosci 2007; 27:6128-40. [PMID: 17553985 PMCID: PMC2925045 DOI: 10.1523/jneurosci.0296-07.2007] [Citation(s) in RCA: 609] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Histone deacetylase (HDAC) inhibitors increase histone acetylation and enhance both memory and synaptic plasticity. The current model for the action of HDAC inhibitors assumes that they alter gene expression globally and thus affect memory processes in a nonspecific manner. Here, we show that the enhancement of hippocampus-dependent memory and hippocampal synaptic plasticity by HDAC inhibitors is mediated by the transcription factor cAMP response element-binding protein (CREB) and the recruitment of the transcriptional coactivator and histone acetyltransferase CREB-binding protein (CBP) via the CREB-binding domain of CBP. Furthermore, we show that the HDAC inhibitor trichostatin A does not globally alter gene expression but instead increases the expression of specific genes during memory consolidation. Our results suggest that HDAC inhibitors enhance memory processes by the activation of key genes regulated by the CREB:CBP transcriptional complex.
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Affiliation(s)
| | | | - K. Matthew Lattal
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon 97239
| | - Joel M. Stein
- Cell and Molecular Biology Graduate Group, University of Pennsylvania 19104
| | | | | | - Sara M. Cabrera
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California, Irvine, Irvine, California 92697, and
| | | | - Paul K. Brindle
- Department of Biochemistry, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Ted Abel
- Neuroscience Graduate Group
- Department of Biology, and
- Cell and Molecular Biology Graduate Group, University of Pennsylvania 19104
| | - Marcelo A. Wood
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California, Irvine, Irvine, California 92697, and
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Rowe WB, Blalock EM, Chen KC, Kadish I, Wang D, Barrett JE, Thibault O, Porter NM, Rose GM, Landfield PW. Hippocampal expression analyses reveal selective association of immediate-early, neuroenergetic, and myelinogenic pathways with cognitive impairment in aged rats. J Neurosci 2007; 27:3098-110. [PMID: 17376971 PMCID: PMC6672456 DOI: 10.1523/jneurosci.4163-06.2007] [Citation(s) in RCA: 174] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Although expression of some genes is known to change during neuronal activity or plasticity, the overall relationship of gene expression changes to memory or memory disorders is not well understood. Here, we combined extensive statistical microarray analyses with behavioral testing to comprehensively identify genes and pathways associated with aging and cognitive dysfunction. Aged rats were separated into cognitively unimpaired (AU) or impaired (AI) groups based on their Morris water maze performance relative to young-adult (Y) animals. Hippocampal gene expression was assessed in Y, AU, and AI on the fifth (last) day of maze training (5T) or 21 d posttraining (21PT) and in nontrained animals (eight groups total, one array per animal; n = 78 arrays). ANOVA and linear contrasts identified genes that differed from Y generally with aging (differed in both AU and AI) or selectively, with cognitive status (differed only in AI or AU). Altered pathways/processes were identified by overrepresentation analyses of changed genes. With general aging, there was downregulation of axonal growth, cytoskeletal assembly/transport, signaling, and lipogenic/uptake pathways, concomitant with upregulation in immune/inflammatory, lysosomal, lipid/protein degradation, cholesterol transport, transforming growth factor, and cAMP signaling pathways, primarily independent of training condition. Selectively, in AI, there was downregulation at 5T of immediate-early gene, Wnt (wingless integration site), insulin, and G-protein signaling, lipogenesis, and glucose utilization pathways, whereas Notch2 (oligodendrocyte development) and myelination pathways were upregulated, particularly at 21PT. In AU, receptor/signal transduction genes were upregulated, perhaps as compensatory responses. Immunohistochemistry confirmed and extended selected microarray results. Together, the findings suggest a new model, in which deficient neuroenergetics leads to downregulated neuronal signaling and increased glial activation, resulting in aging-related cognitive dysfunction.
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Affiliation(s)
- Wayne B. Rowe
- Department of Functional Neuroscience, Memory Pharmaceuticals Corporation, Montvale, New Jersey 07645
| | - Eric M. Blalock
- Department of Molecular and Biomedical Pharmacology, University of Kentucky, Lexington, Kentucky 40536
| | - Kuey-Chu Chen
- Department of Molecular and Biomedical Pharmacology, University of Kentucky, Lexington, Kentucky 40536
| | - Inga Kadish
- Department of Cell Biology, University of Alabama, Birmingham, Alabama 35294, and
| | - Daguang Wang
- Department of Functional Neuroscience, Memory Pharmaceuticals Corporation, Montvale, New Jersey 07645
| | | | - Olivier Thibault
- Department of Molecular and Biomedical Pharmacology, University of Kentucky, Lexington, Kentucky 40536
| | - Nada M. Porter
- Department of Molecular and Biomedical Pharmacology, University of Kentucky, Lexington, Kentucky 40536
| | - Gregory M. Rose
- Department of Functional Neuroscience, Memory Pharmaceuticals Corporation, Montvale, New Jersey 07645
| | - Philip W. Landfield
- Department of Molecular and Biomedical Pharmacology, University of Kentucky, Lexington, Kentucky 40536
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Bornstein SR, Wong ML, Licinio J. 150 years of Sigmund Freud: What would Freud have said about the obesity epidemic? Mol Psychiatry 2006; 11:1070-2. [PMID: 17130885 DOI: 10.1038/sj.mp.4001912] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The 150th birthday of Sigmund Freud has triggered widespread interest and media coverage on his unique contribution and impact on society. Recent evidence from neuroscience and advanced imaging technology has provided support for some of his major concepts including the unconscious and the key role of early life events. In this perspective, we attempt to write on his behalf an updated version of a Freudian way of thinking focused on the current high rates of obesity and depression.
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Affiliation(s)
- S R Bornstein
- Department of Medicine, University of Dresden, Dresden, Germany.
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Blaeser F, Sanders MJ, Truong N, Ko S, Wu LJ, Wozniak DF, Fanselow MS, Zhuo M, Chatila TA. Long-term memory deficits in Pavlovian fear conditioning in Ca2+/calmodulin kinase kinase alpha-deficient mice. Mol Cell Biol 2006; 26:9105-15. [PMID: 17015467 PMCID: PMC1636841 DOI: 10.1128/mcb.01452-06] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Signaling by the Ca(2+)/calmodulin kinase (CaMK) cascade has been implicated in neuronal gene transcription, synaptic plasticity, and long-term memory consolidation. The CaM kinase kinase alpha (CaMKKalpha) isoform is an upstream component of the CaMK cascade whose function in different behavioral and learning and memory paradigms was analyzed by targeted gene disruption in mice. CaMKKalpha mutants exhibited normal long-term spatial memory formation and cued fear conditioning but showed deficits in context fear during both conditioning and long-term follow-up testing. They also exhibited impaired activation of the downstream kinase CaMKIV/Gr and its substrate, the transcription factor cyclic AMP-responsive element binding protein (CREB) upon fear conditioning. Unlike CaMKIV/Gr-deficient mice, the CaMKKalpha mutants exhibited normal long-term potentiation and normal levels of anxiety-like behavior. These results demonstrate a selective role for CaMKKalpha in contextual fear memory and suggest that different combinations of upstream and downstream components of the CaMK cascade may serve distinct physiological functions.
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Affiliation(s)
- Frank Blaeser
- Department of Pediatrics, The David Geffen School of Medicine, University of California at Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA 90095-1752, USA
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44
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Wood MA, Attner MA, Oliveira AM, Brindle PK, Abel T. A transcription factor-binding domain of the coactivator CBP is essential for long-term memory and the expression of specific target genes. Learn Mem 2006; 13:609-17. [PMID: 16980541 PMCID: PMC1783615 DOI: 10.1101/lm.213906] [Citation(s) in RCA: 168] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Transcriptional activation is a key process required for long-term memory formation. Recently, the transcriptional coactivator CREB-binding protein (CBP) was shown to be critical for hippocampus-dependent long-term memory and hippocampal synaptic plasticity. As a coactivator with intrinsic histone acetyltransferase activity, CBP interacts with numerous transcription factors and contains multiple functional domains. Currently, it is not known which transcription factor-binding domain of CBP is essential for memory storage. Using mice that carry inactivating mutations in the CREB-binding (KIX) domain of the coactivator CBP (CBPKIX/KIX mice), we show that the KIX domain is required for long-term memory storage. These results are the first to identify an in vivo function for the KIX domain of CBP in the brain, and they suggest that KIX-interacting transcription factors recruit CBP histone acetyltransferase activity during long-term memory storage. One such KIX-interacting factor is the transcription factor CREB. Using quantitative real-time RT-PCR, we find that the expression of specific CREB target genes is reduced in the hippocampi of CBPKIX/KIX mice during memory consolidation. The recruitment of the transcriptional coactivator CBP via the KIX domain thus imparts target gene-dependent selectivity to CREB-driven transcriptional regulation, thereby activating genes required for the long-term storage of hippocampus-dependent memory.
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Affiliation(s)
- Marcelo A. Wood
- Department of Neurobiology & Behavior, Center for the Neurobiology of Learning & Memory, University of California at Irvine, Irvine, California 92697, USA
- Corresponding authors.E-mail ; fax (949) 824-6633;E-mail ; fax (215) 898-8780
| | - Michelle A. Attner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ana M.M. Oliveira
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Paul K. Brindle
- Department of Biochemistry, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA
| | - Ted Abel
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Corresponding authors.E-mail ; fax (949) 824-6633;E-mail ; fax (215) 898-8780
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