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Marshall PR, Davies J, Zhao Q, Liau WS, Lee Y, Basic D, Periyakaruppiah A, Zajaczkowski EL, Leighton LJ, Madugalle SU, Musgrove M, Kielar M, Brueckner AM, Gong H, Ren H, Walsh A, Kaczmarczyk L, Jackson WS, Chen A, Spitale RC, Bredy TW. DNA G-Quadruplex Is a Transcriptional Control Device That Regulates Memory. J Neurosci 2024; 44:e0093232024. [PMID: 38418220 PMCID: PMC11007313 DOI: 10.1523/jneurosci.0093-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024] Open
Abstract
The conformational state of DNA fine-tunes the transcriptional rate and abundance of RNA. Here, we report that G-quadruplex DNA (G4-DNA) accumulates in neurons, in an experience-dependent manner, and that this is required for the transient silencing and activation of genes that are critically involved in learning and memory in male C57/BL6 mice. In addition, site-specific resolution of G4-DNA by dCas9-mediated deposition of the helicase DHX36 impairs fear extinction memory. Dynamic DNA structure states therefore represent a key molecular mechanism underlying memory consolidation.One-Sentence Summary: G4-DNA is a molecular switch that enables the temporal regulation of the gene expression underlying the formation of fear extinction memory.
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Affiliation(s)
- Paul R Marshall
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
- Genome Sciences and Cancer Division & Eccles Institute of Neuroscience, John Curtin School of Medical Research, Australian National University, Canberra 2601, Australia
| | - Joshua Davies
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Qiongyi Zhao
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Wei-Siang Liau
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Yujin Lee
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Dean Basic
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Ambika Periyakaruppiah
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Esmi L Zajaczkowski
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Laura J Leighton
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Sachithrani U Madugalle
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Mason Musgrove
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Marcin Kielar
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Arie Maeve Brueckner
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Hao Gong
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Haobin Ren
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Alexander Walsh
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Lech Kaczmarczyk
- Department of Biomedical and Clinical Sciences (BKV), Division of Neurobiology (NEURO), Linköping University, Linköping 581 83, Sweden
| | - Walker S Jackson
- Department of Biomedical and Clinical Sciences (BKV), Division of Neurobiology (NEURO), Linköping University, Linköping 581 83, Sweden
| | - Alon Chen
- Neurobiology of Stress Laboratory, Department Brain Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California 92697
| | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
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2
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Musgrove MRB, Mikhaylova M, Bredy TW. Fundamental Neurochemistry Review: At the intersection between the brain and the immune system: Non-coding RNAs spanning learning, memory and adaptive immunity. J Neurochem 2024. [PMID: 38339812 DOI: 10.1111/jnc.16071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024]
Abstract
Non-coding RNAs (ncRNAs) are highly plastic RNA molecules that can sequester cellular proteins and other RNAs, serve as transporters of cellular cargo and provide spatiotemporal feedback to the genome. Mounting evidence indicates that ncRNAs are central to biology, and are critical for neuronal development, metabolism and intra- and intercellular communication in the brain. Their plasticity arises from state-dependent dynamic structure states that can be influenced by cell type and subcellular environment, which can subsequently enable the same ncRNA with discrete functions in different contexts. Here, we highlight different classes of brain-enriched ncRNAs, including microRNA, long non-coding RNA and other enigmatic ncRNAs, that are functionally important for both learning and memory and adaptive immunity, and describe how they may promote cross-talk between these two evolutionarily ancient biological systems.
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Affiliation(s)
- Mason R B Musgrove
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Marina Mikhaylova
- AG Optobiologie, Institute für Biologie, Humboldt Universität zu Berlin, Berlin, Germany
| | - Timothy W Bredy
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
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3
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Hoffmann LB, Li B, Zhao Q, Wei W, Leighton LJ, Bredy TW, Pang TY, Hannan AJ. Chronically high stress hormone levels dysregulate sperm long noncoding RNAs and their embryonic microinjection alters development and affective behaviours. Mol Psychiatry 2023:10.1038/s41380-023-02350-2. [PMID: 38114632 DOI: 10.1038/s41380-023-02350-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 11/20/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023]
Abstract
Previous studies on paternal epigenetic inheritance have shown that sperm RNAs play a role in this type of inheritance. The microinjection of sperm small noncoding RNAs into fertilised mouse oocytes induces reprogramming of the early embryo, which is thought to be responsible for the differences observed in adult phenotype. While sperm long noncoding RNAs (lncRNAs) have also been investigated in a previous study, their microinjection into fertilised oocytes did not yield conclusive results regarding their role in modulating brain development and adult behavioural phenotypes. Therefore, in the current study we sought to investigate this further. We used our previously established paternal corticosterone (stress hormone) model to assess sperm lncRNA expression using CaptureSeq, a sequencing technique that is more sensitive than the ones used in other studies in the field. Paternal corticosterone exposure led to dysregulation of sperm long noncoding RNA expression, which encompassed lncRNAs, circular RNAs and transposable element transcripts. Although they have limited functional annotation, bioinformatic approaches indicated the potential of these lncRNAs in regulating brain development and function. We then separated and isolated the sperm lncRNAs and performed microinjections into fertilised oocytes, to generate embryos with modulated lncRNA populations. We observed that the resulting adult offspring had lower body weight and altered anxiety and affective behavioural responses, demonstrating roles for lncRNAs in modulating development and brain function. This study provides novel insights into the roles of lncRNAs in epigenetic inheritance, including impacts on brain development and behaviours of relevance to affective disorders.
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Affiliation(s)
- L B Hoffmann
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
- Florey Department of Neuroscience and Mental Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - B Li
- Florey Department of Neuroscience and Mental Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Q Zhao
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - W Wei
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - L J Leighton
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - T W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - T Y Pang
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
- Florey Department of Neuroscience and Mental Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - A J Hannan
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia.
- Florey Department of Neuroscience and Mental Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia.
- Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia.
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Liau WS, Zhao Q, Bademosi A, Gormal RS, Gong H, Marshall PR, Periyakaruppiah A, Madugalle SU, Zajaczkowski EL, Leighton LJ, Ren H, Musgrove M, Davies J, Rauch S, He C, Dickinson BC, Li X, Wei W, Meunier FA, Fernández-Moya SM, Kiebler MA, Srinivasan B, Banerjee S, Clark M, Spitale RC, Bredy TW. Fear extinction is regulated by the activity of long noncoding RNAs at the synapse. Nat Commun 2023; 14:7616. [PMID: 37993455 PMCID: PMC10665438 DOI: 10.1038/s41467-023-43535-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 11/12/2023] [Indexed: 11/24/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) represent a multidimensional class of regulatory molecules that are involved in many aspects of brain function. Emerging evidence indicates that lncRNAs are localized to the synapse; however, a direct role for their activity in this subcellular compartment in memory formation has yet to be demonstrated. Using lncRNA capture-seq, we identified a specific set of lncRNAs that accumulate in the synaptic compartment within the infralimbic prefrontal cortex of adult male C57/Bl6 mice. Among these was a splice variant related to the stress-associated lncRNA, Gas5. RNA immunoprecipitation followed by mass spectrometry and single-molecule imaging revealed that this Gas5 isoform, in association with the RNA binding proteins G3BP2 and CAPRIN1, regulates the activity-dependent trafficking and clustering of RNA granules. In addition, we found that cell-type-specific, activity-dependent, and synapse-specific knockdown of the Gas5 variant led to impaired fear extinction memory. These findings identify a new mechanism of fear extinction that involves the dynamic interaction between local lncRNA activity and RNA condensates in the synaptic compartment.
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Affiliation(s)
- Wei-Siang Liau
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.
| | - Qiongyi Zhao
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Adekunle Bademosi
- Single Molecule Neuroscience Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Rachel S Gormal
- Single Molecule Neuroscience Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Hao Gong
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Paul R Marshall
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Ambika Periyakaruppiah
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Sachithrani U Madugalle
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Esmi L Zajaczkowski
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Laura J Leighton
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Haobin Ren
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Mason Musgrove
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Joshua Davies
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Simone Rauch
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Xiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Medical Research Institute, Wuhan University, Wuhan, China
| | - Wei Wei
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Frédéric A Meunier
- Single Molecule Neuroscience Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Sandra M Fernández-Moya
- Biomedical Centre, Ludwig Maximilian University of Munich, Munich, Germany
- Gene Regulation of Cell Identity, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL) and Program for Advancing Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L'Hospitalet del Llobregat, 08908, Barcelona, Spain
| | - Michael A Kiebler
- Biomedical Centre, Ludwig Maximilian University of Munich, Munich, Germany
| | | | | | - Michael Clark
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC, Australia
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, The University of California, Irvine, CA, USA
| | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.
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5
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Madugalle SU, Liau WS, Zhao Q, Li X, Gong H, Marshall PR, Periyakaruppiah A, Zajaczkowski EL, Leighton LJ, Ren H, Musgrove MRB, Davies JWA, Kim G, Rauch S, He C, Dickinson BC, Fulopova B, Fletcher LN, Williams SR, Spitale RC, Bredy TW. Synapse-Enriched m 6A-Modified Malat1 Interacts with the Novel m 6A Reader, DPYSL2, and Is Required for Fear-Extinction Memory. J Neurosci 2023; 43:7084-7100. [PMID: 37669863 PMCID: PMC10601377 DOI: 10.1523/jneurosci.0943-23.2023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/07/2023] Open
Abstract
The RNA modification N6-methyladenosine (m6A) regulates the interaction between RNA and various RNA binding proteins within the nucleus and other subcellular compartments and has recently been shown to be involved in experience-dependent plasticity, learning, and memory. Using m6A RNA-sequencing, we have discovered a distinct population of learning-related m6A- modified RNAs at the synapse, which includes the long noncoding RNA metastasis-associated lung adenocarcinoma transcript 1 (Malat1). RNA immunoprecipitation and mass spectrometry revealed 12 new synapse-specific learning-induced m6A readers in the mPFC of male C57/BL6 mice, with m6A-modified Malat1 binding to a subset of these, including CYFIP2 and DPYSL2. In addition, a cell type- and synapse-specific, and state-dependent, reduction of m6A on Malat1 impairs fear-extinction memory; an effect that likely occurs through a disruption in the interaction between Malat1 and DPYSL2 and an associated decrease in dendritic spine formation. These findings highlight the critical role of m6A in regulating the functional state of RNA during the consolidation of fear-extinction memory, and expand the repertoire of experience-dependent m6A readers in the synaptic compartment.SIGNIFICANCE STATEMENT We have discovered that learning-induced m6A-modified RNA (including the long noncoding RNA, Malat1) accumulates in the synaptic compartment. We have identified several new m6A readers that are associated with fear extinction learning and demonstrate a causal relationship between m6A-modified Malat1 and the formation of fear-extinction memory. These findings highlight the role of m6A in regulating the functional state of an RNA during memory formation and expand the repertoire of experience-dependent m6A readers in the synaptic compartment.
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Affiliation(s)
| | - Wei-Siang Liau
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Qiongyi Zhao
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Xiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China 430071
- Medical Research Institute, Wuhan University, Wuhan, China 430014
| | - Hao Gong
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Paul R Marshall
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Ambika Periyakaruppiah
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Esmi L Zajaczkowski
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Laura J Leighton
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Haobin Ren
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Mason R B Musgrove
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Joshua W A Davies
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Gwangmin Kim
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Simone Rauch
- Department of Chemistry, University of Chicago, Chicago, Illinois 60607
| | - Chuan He
- Department of Chemistry, University of Chicago, Chicago, Illinois 60607
| | - Bryan C Dickinson
- Department of Chemistry, University of Chicago, Chicago, Illinois 60607
| | - Barbora Fulopova
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Lee N Fletcher
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Stephen R Williams
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, California 92697
| | - Timothy W Bredy
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
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Chen CC, Han J, Chinn CA, Rounds JS, Li X, Nikan M, Myszka M, Tong L, Passalacqua LFM, Bredy TW, Wood MA, Lupták A. Inhibition of CPEB3 ribozyme elevates CPEB3 protein expression and polyadenylation of its target mRNAs, and enhances object location memory. bioRxiv 2023:2023.06.07.543953. [PMID: 37333407 PMCID: PMC10274809 DOI: 10.1101/2023.06.07.543953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
A self-cleaving ribozyme that maps to an intron of the cytoplasmic polyadenylation element binding protein 3 (CPEB3) gene is thought to play a role in human episodic memory, but the underlying mechanisms mediating this effect are not known. We tested the activity of the murine sequence and found that the ribozyme's self-scission half-life matches the time it takes an RNA polymerase to reach the immediate downstream exon, suggesting that the ribozyme-dependent intron cleavage is tuned to co-transcriptional splicing of the CPEB3 mRNA. Our studies also reveal that the murine ribozyme modulates maturation of its harboring mRNA in both cultured cortical neurons and the hippocampus: inhibition of the ribozyme using an antisense oligonucleotide leads to increased CPEB3 protein expression, which enhances polyadenylation and translation of localized plasticity-related target mRNAs, and subsequently strengthens hippocampal-dependent long-term memory. These findings reveal a previously unknown role for self-cleaving ribozyme activity in regulating experience-induced co-transcriptional and local translational processes required for learning and memory.
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Affiliation(s)
- Claire C. Chen
- Department of Pharmaceutical Sciences, University of California–Irvine, Irvine, California 92697, United States
| | - Joseph Han
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California–Irvine, Irvine, California 92697, United States
| | - Carlene A. Chinn
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California–Irvine, Irvine, California 92697, United States
| | - Jacob S. Rounds
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California–Irvine, Irvine, California 92697, United States
| | - Xiang Li
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California–Irvine, Irvine, California 92697, United States
| | - Mehran Nikan
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Marie Myszka
- Department of Chemistry, University of California–Irvine, Irvine, California 92697, United States
| | - Liqi Tong
- Institute for Memory Impairments and Neurological Disorders, University of California–Irvine, Irvine, California 92697, United States
| | - Luiz F. M. Passalacqua
- Department of Pharmaceutical Sciences, University of California–Irvine, Irvine, California 92697, United States
| | - Timothy W. Bredy
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California–Irvine, Irvine, California 92697, United States
| | - Marcelo A. Wood
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California–Irvine, Irvine, California 92697, United States
| | - Andrej Lupták
- Department of Pharmaceutical Sciences, University of California–Irvine, Irvine, California 92697, United States
- Department of Chemistry, University of California–Irvine, Irvine, California 92697, United States
- Department of Molecular Biology and Biochemistry, University of California–Irvine, Irvine, California 92697, United States
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7
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Wei W, Zhao Q, Wang Z, Liau WS, Basic D, Ren H, Marshall PR, Zajaczkowski EL, Leighton LJ, Madugalle SU, Musgrove M, Periyakaruppiah A, Shi J, Zhang J, Mattick JS, Mercer TR, Spitale RC, Li X, Bredy TW. ADRAM is an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3. Cell Rep 2022; 38:110546. [PMID: 35320727 PMCID: PMC9015815 DOI: 10.1016/j.celrep.2022.110546] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 02/03/2022] [Accepted: 02/28/2022] [Indexed: 11/25/2022] Open
Abstract
Here, we used RNA capture-seq to identify a large population of lncRNAs that are expressed in the infralimbic prefrontal cortex of adult male mice in response to fear-related learning. Combining these data with cell-type-specific ATAC-seq on neurons that had been selectively activated by fear extinction learning, we find inducible 434 lncRNAs that are derived from enhancer regions in the vicinity of protein-coding genes. In particular, we discover an experience-induced lncRNA we call ADRAM (activity-dependent lncRNA associated with memory) that acts as both a scaffold and a combinatorial guide to recruit the brain-enriched chaperone protein 14-3-3 to the promoter of the memory-associated immediate-early gene Nr4a2 and is required fear extinction memory. This study expands the lexicon of experience-dependent lncRNA activity in the brain and highlights enhancer-derived RNAs (eRNAs) as key players in the epigenomic regulation of gene expression associated with the formation of fear extinction memory. Wei et al. use targeted RNA capture sequencing to examine experience-dependent long noncoding RNA activity in the infralimbic prefrontal cortex of adult mice. They discover a gene, which they call ADRAM, that is directly involved in the epigenomic regulation of gene expression underlying memory formation.
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Affiliation(s)
- Wei Wei
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China; Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China; Medical Research Institute, Wuhan University, Wuhan, China.
| | - Qiongyi Zhao
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Ziqi Wang
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Wei-Siang Liau
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Dean Basic
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Haobin Ren
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Paul R Marshall
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Esmi L Zajaczkowski
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Laura J Leighton
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Sachithrani U Madugalle
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Mason Musgrove
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Ambika Periyakaruppiah
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Jichun Shi
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China; Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jianjian Zhang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - John S Mattick
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
| | - Timothy R Mercer
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, USA
| | - Xiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China; Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China; Medical Research Institute, Wuhan University, Wuhan, China
| | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia.
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8
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Dick AL, Zhao Q, Crossin R, Baker‐Andresen D, Li X, Edson J, Roeh S, Marshall V, Bredy TW, Lawrence AJ, Duncan JR. Adolescent chronic intermittent toluene inhalation dynamically regulates the transcriptome and neuronal methylome within the rat medial prefrontal cortex. Addict Biol 2021; 26:e12937. [PMID: 32638524 DOI: 10.1111/adb.12937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/25/2020] [Accepted: 06/24/2020] [Indexed: 12/14/2022]
Abstract
Inhalants containing the volatile solvent toluene are misused to induce euphoria or intoxication. Inhalant abuse is most common during adolescence and can result in cognitive impairments during an important maturational period. Despite evidence suggesting that epigenetic modifications may underpin the cognitive effects of inhalants, no studies to date have thoroughly investigated toluene-induced regulation of the transcriptome or discrete epigenetic modifications within the brain. To address this, we investigated effects of adolescent chronic intermittent toluene (CIT) inhalation on gene expression and DNA methylation profiles within the rat medial prefrontal cortex (mPFC), which undergoes maturation throughout adolescence and has been implicated in toluene-induced cognitive deficits. Employing both RNA-seq and genome-wide Methyl CpG Binding Domain (MBD) Ultra-seq analysis, we demonstrate that adolescent CIT inhalation (10 000 ppm for 1 h/day, 3 days/week for 4 weeks) induces both transient and persistent changes to the transcriptome and DNA methylome within the rat mPFC for at least 2 weeks following toluene exposure. We demonstrate for the first time that adolescent CIT exposure results in dynamic regulation of the mPFC transcriptome likely relating to acute inflammatory responses and persistent deficits in synaptic plasticity. These adaptations may contribute to the cognitive deficits associated with chronic toluene exposure and provide novel molecular targets for preventing long-term neurophysiological abnormalities following chronic toluene inhalation.
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Affiliation(s)
- Alec L.W. Dick
- Florey Institute of Neuroscience and Mental Health University of Melbourne Melbourne VIC Australia
- Department of Stress Neurobiology and Neurogenetics Max Planck Institute of Psychiatry Munich Germany
| | - Qiongyi Zhao
- Queensland Brain Institute University of Queensland Brisbane QLD Australia
| | - Rose Crossin
- Florey Institute of Neuroscience and Mental Health University of Melbourne Melbourne VIC Australia
| | | | - Xiang Li
- Queensland Brain Institute University of Queensland Brisbane QLD Australia
| | - Janette Edson
- Queensland Brain Institute University of Queensland Brisbane QLD Australia
| | - Simone Roeh
- Department of Translational Research in Psychiatry Max Planck Institute of Psychiatry Munich Germany
| | - Victoria Marshall
- Queensland Brain Institute University of Queensland Brisbane QLD Australia
| | - Timothy W. Bredy
- Queensland Brain Institute University of Queensland Brisbane QLD Australia
| | - Andrew J. Lawrence
- Florey Institute of Neuroscience and Mental Health University of Melbourne Melbourne VIC Australia
| | - Jhodie R. Duncan
- Florey Institute of Neuroscience and Mental Health University of Melbourne Melbourne VIC Australia
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9
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Liau WS, Samaddar S, Banerjee S, Bredy TW. On the functional relevance of spatiotemporally-specific patterns of experience-dependent long noncoding RNA expression in the brain. RNA Biol 2021; 18:1025-1036. [PMID: 33397182 DOI: 10.1080/15476286.2020.1868165] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The majority of transcriptionally active RNA derived from the mammalian genome does not code for protein. Long noncoding RNA (lncRNA) is the most abundant form of noncoding RNA found in the brain and is involved in many aspects of cellular metabolism. Beyond their fundamental role in the nucleus as decoys for RNA-binding proteins associated with alternative splicing or as guides for the epigenetic regulation of protein-coding gene expression, recent findings indicate that activity-induced lncRNAs also regulate neural plasticity. In this review, we discuss how lncRNAs may exert molecular control over brain function beyond their known roles in the nucleus. We propose that subcellular localization is a critical feature of experience-dependent lncRNA activity in the brain, and that lncRNA-mediated control over RNA metabolism at the synapse serves to regulate local mRNA stability and translation, thereby influencing neuronal function, learning and memory.
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Affiliation(s)
- Wei-Siang Liau
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | | | | | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
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10
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Madugalle SU, Meyer K, Wang DO, Bredy TW. RNA N 6-Methyladenosine and the Regulation of RNA Localization and Function in the Brain. Trends Neurosci 2020; 43:1011-1023. [PMID: 33041062 PMCID: PMC7688512 DOI: 10.1016/j.tins.2020.09.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/01/2020] [Accepted: 09/15/2020] [Indexed: 12/17/2022]
Abstract
A major challenge in neurobiology in the 21st century is to understand how the brain adapts with experience. Activity-dependent gene expression is integral to the synaptic plasticity underlying learning and memory; however, this process cannot be explained by a simple linear trajectory of transcription to translation within a specific neuronal population. Many other regulatory mechanisms can influence RNA metabolism and the capacity of neurons to adapt. In particular, the RNA modification N6-methyladenosine (m6A) has recently been shown to regulate RNA processing through alternative splicing, RNA stability, and translation. Here, we discuss the emerging idea that m6A could also coordinate the transport, localization, and local translation of key mRNAs in learning and memory and expand on the notion of dynamic functional RNA states in the brain.
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Affiliation(s)
- Sachithrani U Madugalle
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.
| | - Kate Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA; Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
| | - Dan Ohtan Wang
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, China
| | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.
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11
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Abstract
Higher-order organisms possess information processing capabilities that
are only made possible by their biological complexity. Emerging
evidence indicates a critical role for regulatory RNAs in coordinating
many aspects of cellular function that are directly involved in
experience-dependent neural plasticity. Here, we focus on a
structurally distinct class of RNAs known as circular RNAs. These
closed loop, single-stranded RNA molecules are highly stable, enriched
in the brain, and functionally active in both healthy and disease
conditions. Current evidence implicating this ancient class of RNA as
a contributor toward higher-order functions such as cognition and
memory is discussed.
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Affiliation(s)
- Esmi L. Zajaczkowski
- Cognitive Neuroepigenetics
Laboratory, Queensland Brain Institute, The University of Queensland,
Brisbane, Queensland, Australia
- Esmi L. Zajaczkowski, The University
of Queensland, QBI Building 79, University of Queensland, Saint Lucia,
Queensland 4072, Australia.
| | - Timothy W. Bredy
- Cognitive Neuroepigenetics
Laboratory, Queensland Brain Institute, The University of Queensland,
Brisbane, Queensland, Australia
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12
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Leighton LJ, Wei W, Marshall PR, Ratnu VS, Li X, Zajaczkowski EL, Spadaro PA, Khandelwal N, Kumar A, Bredy TW. Disrupting the hippocampal Piwi pathway enhances contextual fear memory in mice. Neurobiol Learn Mem 2019; 161:202-209. [PMID: 30965112 DOI: 10.1016/j.nlm.2019.04.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 03/27/2019] [Accepted: 04/01/2019] [Indexed: 12/26/2022]
Abstract
The Piwi pathway is a conserved gene regulatory mechanism comprised of Piwi-like proteins and Piwi-interacting RNAs, which modulates gene expression via RNA interference and through interaction with epigenetic mechanisms. The mammalian Piwi pathway has been defined by its role in transposon control during spermatogenesis; however, despite an increasing number of studies demonstrating its expression in the nervous system, relatively little is known about its function in neurons or potential contribution to behavioural regulation. We have discovered that all three Piwi-like genes are expressed in the adult mouse brain, and that viral-mediated knockdown of the Piwi-like genes Piwil1 and Piwil2 in the dorsal hippocampus leads to enhanced contextual fear memory without affecting generalised anxiety. These results implicate the Piwi pathway in behavioural regulation in the adult mammalian brain, likely through modulation of plasticity-related gene expression.
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Affiliation(s)
- Laura J Leighton
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Wei Wei
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Paul R Marshall
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Vikram Singh Ratnu
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Xiang Li
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Esmi L Zajaczkowski
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Paola A Spadaro
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Nitin Khandelwal
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad 500007, India
| | - Arvind Kumar
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad 500007, India
| | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
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13
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Abstract
An understanding of how memory is acquired and how it can be modified in fear-related anxiety disorders, with the enhancement of failing memories on one side and a reduction or elimination of traumatic memories on the other, is a key unmet challenge in the fields of neuroscience and neuropsychiatry. The latter process depends on an important form of learning called fear extinction, where a previously acquired fear-related memory is decoupled from its ability to control behaviour through repeated non-reinforced exposure to the original fear-inducing cue. Although simple in description, fear extinction relies on a complex pattern of brain region and cell-type specific processes, some of which are unique to this form of learning and, for better or worse, contribute to the inherent instability of fear extinction memory. Here, we explore an emerging layer of biology that may compliment and enrich the synapse-centric perspective of fear extinction. As opposed to the more classically defined role of protein synthesis in the formation of fear extinction memory, a neuroepigenetic view of the experience-dependent gene expression involves an appreciation of dynamic changes in the state of the entire cell: from a transient change in plasticity at the level of the synapse, to potentially more persistent long-term effects within the nucleus. A deeper understanding of neuroepigenetic mechanisms and how they influence the formation and maintenance of fear extinction memory has the potential to enable the development of more effective treatment approaches for fear-related neuropsychiatric conditions.
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Affiliation(s)
- Paul R Marshall
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
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14
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Viola TW, Wearick-Silva LE, Creutzberg KC, Kestering-Ferreira É, Orso R, Centeno-Silva A, Albrechet-Souza L, Marshall PR, Li X, Bredy TW, Riva MA, Grassi-Oliveira R. Postnatal impoverished housing impairs adolescent risk-assessment and increases risk-taking: A sex-specific effect associated with histone epigenetic regulation of Crfr1 in the medial prefrontal cortex. Psychoneuroendocrinology 2019; 99:8-19. [PMID: 30172072 DOI: 10.1016/j.psyneuen.2018.08.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/21/2018] [Accepted: 08/24/2018] [Indexed: 01/01/2023]
Abstract
While increasing evidence posits poor decision-making as a central feature of mental disorders, very few studies investigated the effects of early-life stress (ELS) on specific components of reward-related choice behaviors. Risk-taking (RT) involves the exposure to some danger, or negative consequences, in order to achieve a goal-directed behavior. Such behaviors are likely to be preceded by risk-assessment (RA), which is a dynamic cognitive process involving the acquisition of information in potentially dangerous situations. Here, we investigated the effects of being raised in impoverished housing conditions during early life (P2-P9) on RT, RA and dopaminergic and corticotrophinergic gene expression of adolescent male and female mice. Phenotypes were assessed by two protocols: the elevated plus-maze (EPM) and the predator-odor risk-taking (PORT). We found decreased RA in mice exposed to impoverished housing in the absence of a reward (EPM), with a more pronounced effect among females. Moreover, when exposed to a predatory olfactory cue, increased RT was observed in these females in a reward-related task (PORT), as well as decreased HPA axis responsivity. This sex-specific behavioral effect was associated with increased Crfr1 mRNA expression in the medial prefrontal cortex (mPFC) and higher levels of the histone mark H3R2me2s, a histone modification known to be involved in transcriptional activation, within the promoter of the Crfr1 gene. These findings revealed that ELS exposure can impair the acquisition of environmental information in dangerous situations and increase RT in reward-related scenarios among females, with an important role regarding epigenetic regulation of the Crfr1 gene.
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Affiliation(s)
- Thiago Wendt Viola
- Pontifical Catholic University of Rio Grande do Sul (PUCRS), Brain Institute (InsCer), Developmental Cognitive Neuroscience Lab, Porto Alegre, RS, Brazil
| | - Luis Eduardo Wearick-Silva
- Pontifical Catholic University of Rio Grande do Sul (PUCRS), Brain Institute (InsCer), Developmental Cognitive Neuroscience Lab, Porto Alegre, RS, Brazil
| | - Kerstin C Creutzberg
- Pontifical Catholic University of Rio Grande do Sul (PUCRS), Brain Institute (InsCer), Developmental Cognitive Neuroscience Lab, Porto Alegre, RS, Brazil
| | - Érika Kestering-Ferreira
- Pontifical Catholic University of Rio Grande do Sul (PUCRS), Brain Institute (InsCer), Developmental Cognitive Neuroscience Lab, Porto Alegre, RS, Brazil
| | - Rodrigo Orso
- Pontifical Catholic University of Rio Grande do Sul (PUCRS), Brain Institute (InsCer), Developmental Cognitive Neuroscience Lab, Porto Alegre, RS, Brazil
| | - Anderson Centeno-Silva
- Pontifical Catholic University of Rio Grande do Sul (PUCRS), Brain Institute (InsCer), Developmental Cognitive Neuroscience Lab, Porto Alegre, RS, Brazil
| | - Lucas Albrechet-Souza
- Louisiana State University, Health Sciences Center, Department of Physiology, New Orleans, United States
| | - Paul R Marshall
- University of Queensland, Queensland Brain Institute, Brisbane, Australia
| | - Xiang Li
- University of Queensland, Queensland Brain Institute, Brisbane, Australia
| | - Timothy W Bredy
- University of Queensland, Queensland Brain Institute, Brisbane, Australia
| | - Marco A Riva
- Università degli Studi di Milano, Department of Pharmacological and Biomolecular Sciences, Milan, Italy
| | - Rodrigo Grassi-Oliveira
- Pontifical Catholic University of Rio Grande do Sul (PUCRS), Brain Institute (InsCer), Developmental Cognitive Neuroscience Lab, Porto Alegre, RS, Brazil.
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15
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Ploense KL, Li X, Baker-Andresen D, Carr AE, Woodward N, Bagley J, Szumlinski KK, Bredy TW, Kippin TE. Prolonged-access to cocaine induces distinct Homer2 DNA methylation, hydroxymethylation, and transcriptional profiles in the dorsomedial prefrontal cortex of Male Sprague-Dawley rats. Neuropharmacology 2018; 143:299-305. [PMID: 30268522 DOI: 10.1016/j.neuropharm.2018.09.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/17/2018] [Accepted: 09/20/2018] [Indexed: 12/16/2022]
Abstract
Repeated cocaine administration induces many long-term structural and molecular changes in the dorsal medial prefrontal cortex (dmPFC) and are known to underlie aspects of cocaine-seeking behavior. DNA methylation is a key long-lasting epigenetic determinant of gene expression and is implicated in neuroplasticity, however, the extent to which this epigenetic modification is involved in the neuroplasticity associated with drug addiction has received limited attention. Here, we examine the relation between DNA methylation and gene expression within the dorsal medial prefrontal cortex (dmPFC) following limited cocaine self-administration (1 h/day), prolonged cocaine self-administration (6 h/day), and saline self-administration (1 h/day). Rats were fitted with intravenous catheters and allowed to lever press for saline or cocaine (0.25 mg/kg/0.1 mL infusion) in the different access conditions for 20 days. Prolonged-access rats exhibited escalation in cocaine intake over the course of training, while limited-access rats did not escalate cocaine intake. Additionally, limited-access and prolonged-access rats exhibited unique Homer2 epigenetic profiles and mRNA expression. In prolonged-access rats, Homer2 mRNA levels in the dmPFC were increased, which was accompanied by decreased DNA methylation and p300 binding within the Homer2 promoter. Limited-access animals exhibited decreased DNA methylation, decreased DNA hydroxymethylation, and increased p300 binding within the Homer2 promoter. These data indicate that distinct epigenetic profiles are induced by limited-versus prolonged-access self-administration conditions that contribute to transcriptional profiles and lend support to the notion that covalent modification of DNA is implicated in addiction-like changes in cocaine-seeking behavior.
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Affiliation(s)
- Kyle L Ploense
- Department of Psychological & Brain Sciences, University of California, Santa Barbara, CA, USA; Institute for Collaborative Biotechnology, University of California, Santa Barbara, CA, USA; Department of Chemistry & Biochemistry, University of California, Santa Barbara, CA, USA.
| | - Xiang Li
- Queensland Brain Institute, University of Queensland, St Lucia, QLD, Australia
| | | | - Amanda E Carr
- Department of Psychological & Brain Sciences, University of California, Santa Barbara, CA, USA
| | - Nick Woodward
- Department of Psychological & Brain Sciences, University of California, Santa Barbara, CA, USA
| | - Jared Bagley
- Department of Psychological & Brain Sciences, University of California, Santa Barbara, CA, USA; Department of Psychology, Binghamton University, Binghamton, NY, USA
| | - Karen K Szumlinski
- Department of Psychological & Brain Sciences, University of California, Santa Barbara, CA, USA; Neuroscience Research Institute, University of California, Santa Barbara, CA, USA; Department of Molecular Cellular Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Timothy W Bredy
- Queensland Brain Institute, University of Queensland, St Lucia, QLD, Australia
| | - Tod E Kippin
- Department of Psychological & Brain Sciences, University of California, Santa Barbara, CA, USA; Neuroscience Research Institute, University of California, Santa Barbara, CA, USA; Department of Molecular Cellular Developmental Biology, University of California, Santa Barbara, CA, USA; Institute for Collaborative Biotechnology, University of California, Santa Barbara, CA, USA
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16
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Zajaczkowski EL, Zhao QY, Zhang ZH, Li X, Wei W, Marshall PR, Leighton LJ, Nainar S, Feng C, Spitale RC, Bredy TW. Bioorthogonal Metabolic Labeling of Nascent RNA in Neurons Improves the Sensitivity of Transcriptome-Wide Profiling. ACS Chem Neurosci 2018; 9:1858-1865. [PMID: 29874042 PMCID: PMC6272126 DOI: 10.1021/acschemneuro.8b00197] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Transcriptome-wide expression profiling of neurons has provided important insights into the underlying molecular mechanisms and gene expression patterns that transpire during learning and memory formation. However, there is a paucity of tools for profiling stimulus-induced RNA within specific neuronal cell populations. A bioorthogonal method to chemically label nascent (i.e., newly transcribed) RNA in a cell-type-specific and temporally controlled manner, which is also amenable to bioconjugation via click chemistry, was recently developed and optimized within conventional immortalized cell lines. However, its value within a more fragile and complicated cellular system such as neurons, as well as for transcriptome-wide expression profiling, has yet to be demonstrated. Here, we report the visualization and sequencing of activity-dependent nascent RNA derived from neurons using this labeling method. This work has important implications for improving transcriptome-wide expression profiling and visualization of nascent RNA in neurons, which has the potential to provide valuable insights into the mechanisms underlying neural plasticity, learning, and memory.
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Affiliation(s)
- Esmi L. Zajaczkowski
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Qiong-Yi Zhao
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Zong Hong Zhang
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Xiang Li
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Wei Wei
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Paul R. Marshall
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Laura J. Leighton
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | | | - Chao Feng
- Department of Pharmaceutical Sciences
| | - Robert C. Spitale
- Department of Pharmaceutical Sciences
- Department of Chemistry, University of California, Irvine, Irvine, California, 92697, United States
| | - Timothy W. Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
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17
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Leighton LJ, Bredy TW. Functional Interplay between Small Non-Coding RNAs and RNA Modification in the Brain. Noncoding RNA 2018; 4:E15. [PMID: 29880782 PMCID: PMC6027130 DOI: 10.3390/ncrna4020015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/23/2018] [Accepted: 05/30/2018] [Indexed: 12/11/2022] Open
Abstract
Small non-coding RNAs are essential for transcription, translation and gene regulation in all cell types, but are particularly important in neurons, with known roles in neurodevelopment, neuroplasticity and neurological disease. Many small non-coding RNAs are directly involved in the post-transcriptional modification of other RNA species, while others are themselves substrates for modification, or are functionally modulated by modification of their target RNAs. In this review, we explore the known and potential functions of several distinct classes of small non-coding RNAs in the mammalian brain, focusing on the newly recognised interplay between the epitranscriptome and the activity of small RNAs. We discuss the potential for this relationship to influence the spatial and temporal dynamics of gene activation in the brain, and predict that further research in the field of epitranscriptomics will identify interactions between small RNAs and RNA modifications which are essential for higher order brain functions such as learning and memory.
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Affiliation(s)
- Laura J Leighton
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
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18
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Leighton LJ, Ke K, Zajaczkowski EL, Edmunds J, Spitale RC, Bredy TW. Experience-dependent neural plasticity, learning, and memory in the era of epitranscriptomics. Genes Brain Behav 2018; 17:e12426. [PMID: 28926184 PMCID: PMC5858957 DOI: 10.1111/gbb.12426] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/15/2017] [Accepted: 09/15/2017] [Indexed: 12/23/2022]
Abstract
In this short review, we highlight recent findings in the emerging field of epitranscriptomic mechanisms and discuss their potential role in neural plasticity, learning and memory. These include the influence of RNA modifications on activity-induced RNA structure states, RNA editing and RNA localization, and how qualitative state changes in RNA increase the functional diversity and information-carrying capacity of RNA molecules. We predict that RNA modifications may be just as important for synaptic plasticity and memory as quantitative changes in transcript and protein abundance, but with the added advantage of not being required to signal back to the nucleus, and therefore better suited to be coordinated with the temporal dynamics of learning.
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Affiliation(s)
- Laura J. Leighton
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia 4072
| | - Ke Ke
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA 92697
| | - Esmi L. Zajaczkowski
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia 4072
| | - Jordan Edmunds
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia 4072
| | - Robert C. Spitale
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA 92697
| | - Timothy W. Bredy
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia 4072
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19
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Ratnu VS, Emami MR, Bredy TW. Genetic and epigenetic factors underlying sex differences in the regulation of gene expression in the brain. J Neurosci Res 2017; 95:301-310. [PMID: 27870402 DOI: 10.1002/jnr.23886] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/13/2016] [Accepted: 07/25/2016] [Indexed: 12/14/2022]
Abstract
There are inherent biological differences between males and females that contribute to sex differences in brain function and to many sex-specific illnesses and disorders. Traditionally, it has been thought that such differences are due largely to hormonal regulation; however, there are also genetic and epigenetic effects caused by the inheritance and unequal dosage of genes located on the X and Y chromosomes. Here we discuss the evidence in favor of a genetic and epigenetic basis for sexually dimorphic behavior, as a consequence of underlying differences in the regulation of genes that drive brain function. A better understanding of sex-specific molecular processes in the brain will provide further insight for the development of novel therapeutic approaches for the treatment of neuropsychiatric disorders characterized by sex differences. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Vikram S Ratnu
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Michael R Emami
- Department of Neurobiology and Behavior, University of California, Irvine, California
| | - Timothy W Bredy
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.,Department of Neurobiology and Behavior, University of California, Irvine, California
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20
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Castino MR, Baker-Andresen D, Ratnu VS, Shevchenko G, Morris KV, Bredy TW, Youngson NA, Clemens KJ. Persistent histone modifications at the BDNF and Cdk-5 promoters following extinction of nicotine-seeking in rats. Genes Brain Behav 2017; 17:98-106. [PMID: 28857504 DOI: 10.1111/gbb.12421] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 08/24/2017] [Accepted: 08/25/2017] [Indexed: 02/03/2023]
Abstract
Drugs of addiction lead to a wide range of epigenetic changes at the promoter regions of genes directly implicated in learning and memory processes. We have previously shown that the histone deactylase inhibitor, sodium butyrate (NaB), accelerates the extinction of nicotine-seeking and provides resistance to relapse. Here, we explore the potential molecular mechanisms underlying this effect. Rats received intravenous nicotine or saline self-administration, followed by 6 days of extinction training, with each extinction session followed immediately by treatment with NaB or vehicle. On the last day of extinction, rats were killed and the medial ventral prefrontal cortex retained for chromatin immunoprecipitation and quantitative polymerase chain reaction (qPCR). A history of nicotine exposure significantly decreased H3K14 acetylation at the brain-derived neurotrophic factor (BDNF) exon IV promoter, and this effect was abolished with NaB treatment. In contrast, nicotine self-administration alone, resulted in a significant decrease in histone methylation at the H3K27me3 and H3K9me2 marks in the promoter regions of BDNF exon IV and cyclin-dependent kinase 5 (Cdk-5). Quantitative PCR-identified changes in several genes associated with NaB treatment that were independent of nicotine exposure; however, an interaction of nicotine history and NaB treatment was detected only in the expression of BDNF IV and BDNF IX. Together these results suggest that nicotine self-administration leads to a number of epigenetic changes at both the BDNF and Cdk-5 promoters, and that these changes may contribute to the enhanced extinction of nicotine-seeking by NaB.
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Affiliation(s)
- M R Castino
- School of Psychology, University of New South Wales, Sydney, Australia
| | - D Baker-Andresen
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - V S Ratnu
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - G Shevchenko
- Center for Gene Therapy, City of Hope, Duarte, CA, USA
| | - K V Morris
- Center for Gene Therapy, City of Hope, Duarte, CA, USA
| | - T W Bredy
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - N A Youngson
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - K J Clemens
- School of Psychology, University of New South Wales, Sydney, Australia
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21
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Nainar S, Marshall PR, Tyler CR, Spitale RC, Bredy TW. Evolving insights into RNA modifications and their functional diversity in the brain. Nat Neurosci 2017; 19:1292-8. [PMID: 27669990 DOI: 10.1038/nn.4378] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 08/04/2016] [Indexed: 12/12/2022]
Abstract
In this Perspective, we expand the notion of temporal regulation of RNA in the brain and propose that the qualitative nature of RNA and its metabolism, together with RNA abundance, are essential for the molecular mechanisms underlying experience-dependent plasticity. We discuss emerging concepts in the newly burgeoning field of epitranscriptomics, which are predicted to be heavily involved in cognitive function. These include activity-induced RNA modifications, RNA editing, dynamic changes in the secondary structure of RNA, and RNA localization. Each is described with an emphasis on its role in regulating the function of both protein-coding genes, as well as various noncoding regulatory RNAs, and how each might influence learning and memory.
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Affiliation(s)
- Sarah Nainar
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California, USA
| | - Paul R Marshall
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, California, USA.,Center for the Neurobiology of Learning and Memory, University of California Irvine, Irvine, California, USA
| | - Christina R Tyler
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, California, USA.,Center for the Neurobiology of Learning and Memory, University of California Irvine, Irvine, California, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California, USA
| | - Timothy W Bredy
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, California, USA.,Center for the Neurobiology of Learning and Memory, University of California Irvine, Irvine, California, USA.,Queensland Brain Institute, University of Queensland, Brisbane, Australia
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22
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Pang TYC, Short AK, Bredy TW, Hannan AJ. Transgenerational paternal transmission of acquired traits: Stress-induced modification of the sperm regulatory transcriptome and offspring phenotypes. Curr Opin Behav Sci 2017; 14:140-147. [PMID: 29270445 PMCID: PMC5734660 DOI: 10.1016/j.cobeha.2017.02.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In recent years, it has become evident that pre-conceptual exposure of males to various environmental factors induces epigenetic changes in sperm, which can mediate the transmission of acquired traits in their offspring. The most thoroughly examined paternal exposures involve stress and elevated corticosterone, which have been shown to modulate offspring phenotypes in a manner that is relevant to predisposition to brain disorders, and psychiatric illness in particular. Recent seminal studies have demonstrated that key epigenetic information transmitted via the paternal germline involves small non-coding (snc) RNA transcripts such as microRNAs. Following fertilisation, these sncRNAs appear to regulate development so as to modify the phenotype of the offspring. Understanding the mechanisms involved in such transgenerational effects may facilitate future screening of human sperm for 'epigenetic health' and the tailoring of therapeutic interventions according to genetic and epigenetic contributions to illness.
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Affiliation(s)
- Terence Y C Pang
- Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, University of Melbourne, Parkville, VIC 3010, Australia
| | - Annabel K Short
- Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, University of Melbourne, Parkville, VIC 3010, Australia
- Department of Anatomy and Neurobiology, University of California, Irvine, CA 92617, USA
| | - Timothy W Bredy
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
- Center for the Neurobiology of Learning and Memory and Department of Neurobiology and Behavior, University of California, Irvine, CA 92617, USA
| | - Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, University of Melbourne, Parkville, VIC 3010, Australia
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, VIC 3010, Australia
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23
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Nguyen K, Fazio M, Kubota M, Nainar S, Feng C, Li X, Atwood SX, Bredy TW, Spitale RC. Cell-Selective Bioorthogonal Metabolic Labeling of RNA. J Am Chem Soc 2017; 139:2148-2151. [PMID: 28139910 DOI: 10.1021/jacs.6b11401] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Stringent chemical methods to profile RNA expression within discrete cellular populations remains a key challenge in biology. To address this issue, we developed a chemical-genetic strategy for metabolic labeling of RNA. Cell-specific labeling of RNA can be profiled and imaged using bioorthogonal chemistry. We anticipate that this platform will provide the community with a much-needed chemical toolset for cell-type specific profiling of cell-specific transcriptomes derived from complex biological systems.
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Affiliation(s)
- Kim Nguyen
- Department of Pharmaceutical Sciences, ‡Department of Neurobiology, §Department of Developmental & Cellular Biology and ∥Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States
| | - Michael Fazio
- Department of Pharmaceutical Sciences, ‡Department of Neurobiology, §Department of Developmental & Cellular Biology and ∥Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States
| | - Miles Kubota
- Department of Pharmaceutical Sciences, ‡Department of Neurobiology, §Department of Developmental & Cellular Biology and ∥Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States
| | - Sarah Nainar
- Department of Pharmaceutical Sciences, ‡Department of Neurobiology, §Department of Developmental & Cellular Biology and ∥Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States
| | - Chao Feng
- Department of Pharmaceutical Sciences, ‡Department of Neurobiology, §Department of Developmental & Cellular Biology and ∥Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States
| | - Xiang Li
- Department of Pharmaceutical Sciences, ‡Department of Neurobiology, §Department of Developmental & Cellular Biology and ∥Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States
| | - Scott X Atwood
- Department of Pharmaceutical Sciences, ‡Department of Neurobiology, §Department of Developmental & Cellular Biology and ∥Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States
| | - Timothy W Bredy
- Department of Pharmaceutical Sciences, ‡Department of Neurobiology, §Department of Developmental & Cellular Biology and ∥Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, ‡Department of Neurobiology, §Department of Developmental & Cellular Biology and ∥Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States
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24
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Wearick-Silva LE, Marshall P, Viola TW, Centeno-Silva A, de Azeredo LA, Orso R, Li X, Donadio MV, Bredy TW, Grassi-Oliveira R. Running during adolescence rescues a maternal separation-induced memory impairment in female mice: Potential role of differential exon-specific BDNF expression. Dev Psychobiol 2016; 59:268-274. [PMID: 27807856 DOI: 10.1002/dev.21487] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 10/19/2016] [Indexed: 12/19/2022]
Abstract
Exposure to early life stress has been associated with memory impairments related to changes in brain-derived neurotrophic factor (BDNF) signaling. However, the potential impact of physical exercise to reverse these effects of maternal separation has been under investigated. Mice were subjected to maternal separation during the first 2 weeks of life and then exposed to a 3-week running protocol during adolescence. The spontaneous object recognition task was performed during adolescence followed by analysis of hippocampal expression of exons I, IV, and IX of the BDNF gene. As expected, maternal separation impaired recognition memory and this effect was reversed by exercise. In addition, running increased BDNF exon I expression, but decreased expression of BDNF exon IV in all groups, while exon IX expression increased only in MS animals exposed to exercise. Our data suggest that memory deficits can be attenuated by exercise and specific transcripts of the BDNF gene are dynamically regulated following both MS and exercise.
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Affiliation(s)
- Luis Eduardo Wearick-Silva
- Graduate Program in Pediatrics and Child Health, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil.,Developmental Cognitive Neuroscience Laboratory (DCNL) Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Paul Marshall
- Department of Neurobiology and Behavior, University of California - Irvine, Irvine, California
| | - Thiago Wendt Viola
- Graduate Program in Pediatrics and Child Health, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil.,Developmental Cognitive Neuroscience Laboratory (DCNL) Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Anderson Centeno-Silva
- Graduate Program in Pediatrics and Child Health, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil.,Developmental Cognitive Neuroscience Laboratory (DCNL) Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Lucas Araújo de Azeredo
- Graduate Program in Pediatrics and Child Health, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil.,Developmental Cognitive Neuroscience Laboratory (DCNL) Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Rodrigo Orso
- Graduate Program in Pediatrics and Child Health, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil.,Developmental Cognitive Neuroscience Laboratory (DCNL) Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Xiang Li
- Department of Neurobiology and Behavior, University of California - Irvine, Irvine, California
| | - Márcio V Donadio
- Graduate Program in Pediatrics and Child Health, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Timothy W Bredy
- Department of Neurobiology and Behavior, University of California - Irvine, Irvine, California
| | - Rodrigo Grassi-Oliveira
- Graduate Program in Pediatrics and Child Health, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil.,Developmental Cognitive Neuroscience Laboratory (DCNL) Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
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25
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Viola TW, Wearick-Silva LE, De Azeredo LA, Centeno-Silva A, Murphy C, Marshall P, Li X, Singewald N, Garcia F, Bredy TW, Grassi-Oliveira R. Increased cocaine-induced conditioned place preference during periadolescence in maternally separated male BALB/c mice: the role of cortical BDNF, microRNA-212, and MeCP2. Psychopharmacology (Berl) 2016; 233:3279-88. [PMID: 27392631 DOI: 10.1007/s00213-016-4373-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/18/2016] [Indexed: 12/15/2022]
Abstract
RATIONALE Early life stress is a major risk factor for cocaine addiction; however, the underlying molecular mechanisms remain relatively unexplored. MicroRNA-212 (miR-212) and methyl CpG binding protein 2 (MeCP2) have recently emerged as key regulators of brain-derived neurotrophic factor (BDNF) signaling during the acquisition and maintenance of cocaine-seeking behaviors. OBJECTIVES We therefore investigated the effect of maternal separation (MS) on cocaine-induced conditioned place preference (CPP) during periadolescence and how this influences miR-212, Mecp2, and Bdnf expressions in the prefrontal cortex. METHODS Male BALB/c mice subjected to MS (3 h/day) from postnatal day 2 to 15 or normal animal facility rearing (AFR) were tested for CPP at postnatal day 45, or not exposed to experimental manipulations (drug-naïve animals). Cultured primary cortical neurons were used to determine miR-212 expression changes following depolarization by KCL treatment. RESULTS MS increased cocaine-induced CPP and decreased Bdnf exon IV expression, which correlated with higher CPP scores in such animals. An experience-dependent decrease in miR-212 expression was observed following CPP test. This effect was mimicked in primary cortical neurons in vitro, under activity-dependent conditions. In contrast, increased Mecp2 expression was found after CPP test, suggesting an opposing relationship between miR-212 and Mecp2 expression following cocaine place preference acquisition. However, these effects were not present in mice exposed to MS. CONCLUSIONS Together, our results suggest that early life stress can enhance the motivational salience for cocaine-paired cues during periadolescence, and that altered expression of miR-212, Mecp2, and Bdnf in the prefrontal cortex is involved in this process.
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Affiliation(s)
- Thiago Wendt Viola
- Postgraduate Program in Pediatrics and Child Health, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.,Developmental Cognitive Neuroscience Lab (DCNL), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Avenida Ipiranga, 6681, prédio 11, sala 928, Porto Alegre, 90619-900, RS, Brazil
| | - Luis Eduardo Wearick-Silva
- Postgraduate Program in Pediatrics and Child Health, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.,Developmental Cognitive Neuroscience Lab (DCNL), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Avenida Ipiranga, 6681, prédio 11, sala 928, Porto Alegre, 90619-900, RS, Brazil
| | - Lucas Araújo De Azeredo
- Developmental Cognitive Neuroscience Lab (DCNL), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Avenida Ipiranga, 6681, prédio 11, sala 928, Porto Alegre, 90619-900, RS, Brazil.,Postgraduate Program in Medicine and Health Sciences, PUCRS, Porto Alegre, RS, Brazil
| | - Anderson Centeno-Silva
- Developmental Cognitive Neuroscience Lab (DCNL), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Avenida Ipiranga, 6681, prédio 11, sala 928, Porto Alegre, 90619-900, RS, Brazil
| | - Conor Murphy
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Paul Marshall
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California-Irvine, Irvine, 92697, CA, USA
| | - Xiang Li
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California-Irvine, Irvine, 92697, CA, USA
| | - Nicolas Singewald
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Frederico Garcia
- Department of Psychiatry, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Timothy W Bredy
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California-Irvine, Irvine, 92697, CA, USA.,Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Rodrigo Grassi-Oliveira
- Postgraduate Program in Pediatrics and Child Health, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil. .,Developmental Cognitive Neuroscience Lab (DCNL), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Avenida Ipiranga, 6681, prédio 11, sala 928, Porto Alegre, 90619-900, RS, Brazil.
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26
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Alaghband Y, Bredy TW, Wood MA. The role of active DNA demethylation and Tet enzyme function in memory formation and cocaine action. Neurosci Lett 2016; 625:40-6. [PMID: 26806038 DOI: 10.1016/j.neulet.2016.01.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 11/29/2015] [Accepted: 01/14/2016] [Indexed: 01/12/2023]
Abstract
Active DNA modification is a major epigenetic mechanism that regulates gene expression in an experience-dependent manner, which is thought to establish stable changes in neuronal function and behavior. Recent discoveries regarding the Ten eleven translocation (Tet1-3) family of DNA hydroxylases have provided a new avenue for the study of active DNA demethylation, and may thus help to advance our understanding of how dynamic DNA modifications lead to long-lasting changes in brain regions underlying learning and memory, as well as drug-seeking and propensity for relapse following abstinence. Drug addiction is a complex, relapsing disorder in which compulsive drug-seeking behavior can persist despite aversive consequences. Therefore, understanding the molecular mechanisms that underlie the onset and persistence of drug addiction, as well as the pronounced propensity for relapse observed in addicts, is necessary for the development of selective treatments and therapies. In this mini-review, we provide an overview of the involvement of active DNA demethylation with an emphasis on the Tet family of enzymes and 5-hydroxymethylcytosine (5-hmC) in learning and memory, as well as in drug-seeking behavior. Memory and addiction share overlapping molecular, cellular, and circuit functions allowing research in one area to inform the other. Current discrepancies and directions for future studies focusing on the dynamic interplay between DNA methylation and demethylation, and how they orchestrate gene expression required for neuronal plasticity underlying memory formation, are discussed.
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Affiliation(s)
- Yasaman Alaghband
- Department of Neurobiology & Behavior, UC Irvine, USA; Center for the Neurobiology of Learning and Memory, UC Irvine, USA; UC Irvine Center for Addiction Neuroscience, UC Irvine, USA
| | - Timothy W Bredy
- Department of Neurobiology & Behavior, UC Irvine, USA; Center for the Neurobiology of Learning and Memory, UC Irvine, USA; Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Marcelo A Wood
- Department of Neurobiology & Behavior, UC Irvine, USA; Center for the Neurobiology of Learning and Memory, UC Irvine, USA; UC Irvine Center for Addiction Neuroscience, UC Irvine, USA.
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27
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Marshall P, Bredy TW. Cognitive neuroepigenetics: the next evolution in our understanding of the molecular mechanisms underlying learning and memory? NPJ Sci Learn 2016; 1:16014. [PMID: 27512601 PMCID: PMC4977095 DOI: 10.1038/npjscilearn.2016.14] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
A complete understanding of the fundamental mechanisms of learning and memory continues to elude neuroscientists. Although many important discoveries have been made, the question of how memories are encoded and maintained at the molecular level remains. To date, this issue has been framed within the context of one of the most dominant concepts in molecular biology, the central dogma, and the result has been a protein-centric view of memory. Here we discuss the evidence supporting a role for neuroepigenetic mechanisms, which constitute dynamic and reversible, state-dependent modifications at all levels of control over cellular function, and their role in learning and memory. This neuroepigenetic view suggests that DNA, RNA and protein each influence one another to produce a holistic cellular state that contributes to the formation and maintenance of memory, and predicts a parallel and distributed system for the consolidation, storage and retrieval of the engram.
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Affiliation(s)
- Paul Marshall
- Department of Neurobiology and Behavior and Center for the Neurobiology of Learning and Memory, University of California Irvine, Irvine, CA, USA
| | - Timothy W Bredy
- Department of Neurobiology and Behavior and Center for the Neurobiology of Learning and Memory, University of California Irvine, Irvine, CA, USA
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- ()
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28
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Ratnu VS, Wei W, Bredy TW. Activation-induced cytidine deaminase regulates activity-dependent BDNF expression in post-mitotic cortical neurons. Eur J Neurosci 2014; 40:3032-9. [PMID: 25041363 DOI: 10.1111/ejn.12678] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 06/11/2014] [Accepted: 06/16/2014] [Indexed: 01/22/2023]
Abstract
Activity-dependent gene expression depends, in part, on transcriptional regulation that is coordinated by rapid changes in the chromatin landscape as well as the covalent modification of DNA. Here we demonstrate that the expression of brain-derived neurotrophic factor (BDNF), a gene that is critically involved in neural plasticity and subject to epigenetic regulation, is regulated by the RNA/DNA editing enzyme, activation-induced cytidine deaminase (AID). Similar to previous reports, we observed an activity-dependent induction of BDNF exon IV mRNA expression, which correlated with a reduction in DNA methylation within the BDNF P4 promoter. Lentiviral-mediated knockdown of AID disrupted these effects and inhibited BDNF exon IV mRNA expression, an effect that was associated with decreased cAMP response element-binding protein occupancy within the BDNF P4 promoter. Thus, together with other epigenetic mechanisms, AID plays a key role in regulating activity-dependent BDNF expression in post-mitotic cortical neurons.
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Affiliation(s)
- Vikram S Ratnu
- Psychiatric Epigenomics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Qld, 4072, Australia
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29
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Fenton GE, Pollard AK, Halliday DM, Mason R, Bredy TW, Stevenson CW. Persistent prelimbic cortex activity contributes to enhanced learned fear expression in females. Learn Mem 2014; 21:55-60. [PMID: 24429423 PMCID: PMC3895223 DOI: 10.1101/lm.033514.113] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Anxiety disorders, such as post-traumatic stress, are more prevalent in women and are characterized by impaired inhibition of learned fear and medial prefrontal cortex (mPFC) dysfunction. Here we examined sex differences in fear extinction and mPFC activity in rats. Females showed more learned fear expression during extinction and its recall, but not fear conditioning. They also showed more spontaneous fear recovery and more contextual fear before extinction and its recall. Moreover, enhanced learned fear expression in females was associated with sustained prelimbic (PL) cortex activity. These results suggest that sex differences in learned fear expression may involve persistent PL activation.
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Affiliation(s)
- Georgina E Fenton
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
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30
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Flavell CR, Lambert EA, Winters BD, Bredy TW. Mechanisms governing the reactivation-dependent destabilization of memories and their role in extinction. Front Behav Neurosci 2013; 7:214. [PMID: 24421762 PMCID: PMC3872723 DOI: 10.3389/fnbeh.2013.00214] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 12/13/2013] [Indexed: 12/28/2022] Open
Abstract
The extinction of learned associations has traditionally been considered to involve new learning, which competes with the original memory for control over behavior. However, a recent resurgence of interest in reactivation-dependent amnesia has revealed that the retrieval of fear-related memory (with what is essentially a brief extinction session) can result in its destabilization. This review discusses some of the cellular and molecular mechanisms that are involved in the destabilization of a memory following its reactivation and/or extinction, and investigates the evidence that extinction may involve both new learning as well as a partial destabilization-induced erasure of the original memory trace.
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Affiliation(s)
- Charlotte R Flavell
- Queensland Brain Institute, The University of Queensland Brisbane, QLD, Australia
| | - Elliot A Lambert
- Queensland Brain Institute, The University of Queensland Brisbane, QLD, Australia
| | - Boyer D Winters
- Department of Psychology, University of Guelph Guelph, ON, Canada
| | - Timothy W Bredy
- Queensland Brain Institute, The University of Queensland Brisbane, QLD, Australia
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31
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Abstract
There are significant sex differences in vulnerability to develop fear-related anxiety disorders. Females exhibit twice the rate of post-traumatic stress disorder (PTSD) as males and sex differences have been observed in fear extinction learning in both humans and rodents, with a failure to inhibit fear emerging as a precipitating factor in the development of PTSD. Here we report that female mice are resistant to fear extinction, and exhibit increased DNA methylation of Bdnf exon IV and a concomitant decrease in mRNA expression within the medial prefrontal cortex. Activation of BDNF signaling by the trkB agonist 7,8-dihydroxyflavone blocks the return of fear in female mice after extinction training, and thus represents a novel approach to treating fear-related anxiety disorders that are characterized by a resistance to extinction and increased propensity for renewal.
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Affiliation(s)
- Danay Baker-Andresen
- Psychiatric Epigenomics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
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32
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Abstract
Fear conditioning and fear extinction are Pavlovian conditioning paradigms extensively used to study the mechanisms that underlie learning and memory formation. The neural circuits that mediate this learning are evolutionarily conserved, and seen in virtually all species from flies to humans. In mammals, the amygdala and medial prefrontal cortex are two structures that play a key role in the acquisition, consolidation and retrieval of fear memory, as well extinction of fear. These two regions have extensive bidirectional connections, and in recent years, the neural circuits that mediate fear learning and fear extinction are beginning to be elucidated. In this review, we provide an overview of our current understanding of the neural architecture within the amygdala and medial prefrontal cortex. We describe how sensory information is processed in these two structures and the neural circuits between them thought to mediate different aspects of fear learning. Finally, we discuss how changes in circuits within these structures may mediate fear responses following fear conditioning and extinction.
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Affiliation(s)
- Roger Marek
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
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Baker-Andresen D, Ratnu VS, Bredy TW. Dynamic DNA methylation: a prime candidate for genomic metaplasticity and behavioral adaptation. Trends Neurosci 2012; 36:3-13. [PMID: 23041052 DOI: 10.1016/j.tins.2012.09.003] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 08/22/2012] [Accepted: 09/10/2012] [Indexed: 10/27/2022]
Abstract
DNA methylation was once considered to be a static epigenetic modification whose primary function was restricted to directing the development of cellular phenotype. However, it is now evident that the methylome is dynamically regulated across the lifespan: during development as a putative mechanism by which early experience leaves a lasting signature on the genome and during adulthood as a function of behavioral adaptation. Here, we propose that experience-dependent variations in DNA methylation, particularly within the context of learning and memory, represent a form of genomic metaplasticity that serves to prime the transcriptional response to later learning-related stimuli and neuronal reactivation.
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Affiliation(s)
- Danay Baker-Andresen
- Psychiatric Epigenomics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
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Spadaro PA, Bredy TW. Emerging role of non-coding RNA in neural plasticity, cognitive function, and neuropsychiatric disorders. Front Genet 2012; 3:132. [PMID: 22811697 PMCID: PMC3395882 DOI: 10.3389/fgene.2012.00132] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 06/28/2012] [Indexed: 11/18/2022] Open
Abstract
Non-coding RNAs (ncRNAs) have emerged as critical regulators of transcription, epigenetic processes, and gene silencing, which make them ideal candidates for insight into molecular evolution and a better understanding of the molecular pathways of neuropsychiatric disease. Here, we provide an overview of the current state of knowledge regarding various classes of ncRNAs and their role in neural plasticity and cognitive function, and highlight the potential contribution they may make to the development of a variety of neuropsychiatric disorders, including schizophrenia, addiction, and fear-related anxiety disorders.
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Affiliation(s)
- Paola A Spadaro
- Psychiatric Epigenomics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
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Lin Q, Wei W, Coelho CM, Li X, Baker-Andresen D, Dudley K, Ratnu VS, Boskovic Z, Kobor MS, Sun YE, Bredy TW. The brain-specific microRNA miR-128b regulates the formation of fear-extinction memory. Nat Neurosci 2011; 14:1115-7. [PMID: 21841775 DOI: 10.1038/nn.2891] [Citation(s) in RCA: 145] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 07/05/2011] [Indexed: 12/14/2022]
Abstract
MicroRNAs are small non-coding RNAs that mediate post-transcriptional gene silencing. Fear-extinction learning in C57/Bl6J mice led to increased expression of the brain-specific microRNA miR-128b, which disrupted stability of several plasticity-related target genes and regulated formation of fear-extinction memory. Increased miR-128b activity may therefore facilitate the transition from retrieval of the original fear memory toward the formation of a new fear-extinction memory.
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Affiliation(s)
- Quan Lin
- Intellectual Development and Disabilities Research Center, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
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Bredy TW, Lin Q, Wei W, Baker-Andresen D, Mattick JS. MicroRNA regulation of neural plasticity and memory. Neurobiol Learn Mem 2011; 96:89-94. [DOI: 10.1016/j.nlm.2011.04.004] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 03/29/2011] [Accepted: 04/08/2011] [Indexed: 01/05/2023]
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Dudley KJ, Li X, Kobor MS, Kippin TE, Bredy TW. Epigenetic mechanisms mediating vulnerability and resilience to psychiatric disorders. Neurosci Biobehav Rev 2011; 35:1544-51. [PMID: 21251925 DOI: 10.1016/j.neubiorev.2010.12.016] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Revised: 12/13/2010] [Accepted: 12/20/2010] [Indexed: 01/22/2023]
Abstract
The impact that stressful encounters have upon long-lasting behavioural phenotypes is varied. Whereas a significant proportion of the population will develop "stress-related" conditions such as post-traumatic stress disorder or depression in later life, the majority are considered "resilient" and are able to cope with stress and avoid such psychopathologies. The reason for this heterogeneity is undoubtedly multi-factorial, involving a complex interplay between genetic and environmental factors. Both genes and environment are of critical importance when it comes to developmental processes, and it appears that subtle differences in either of these may be responsible for altering developmental trajectories that confer vulnerability or resilience. At the molecular level, developmental processes are regulated by epigenetic mechanisms, with recent clinical and pre-clinical data obtained by ourselves and others suggesting that epigenetic differences in various regions of the brain are associated with a range of psychiatric disorders, including many that are stress-related. Here we provide an overview of how these epigenetic differences, and hence susceptibility to psychiatric disorders, might arise through exposure to stress-related factors during critical periods of development.
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Affiliation(s)
- Kevin J Dudley
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
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Abstract
Epigenetics commonly refers to the developmental process by which cellular traits are established and inherited without a change in DNA sequence. These mechanisms of cellular memory also orchestrate gene expression in the adult brain and recent evidence suggests that the "epigenome" represents a critical interface between environmental signals, activation, repression and maintenance of genomic responses, and persistent behavior. We here review the current state of knowledge regarding the contribution of the epigenome toward the development of psychiatric disorders.
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Affiliation(s)
- Timothy W Bredy
- Queensland Brain Institute, University of Queensland, Brisbane, QC 4072, Australia.
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Abstract
Mice communicate through visual, vocal, and olfactory cues that influence innate, nonassociative behavior. We here report that exposure to a recently fear-conditioned familiar mouse impairs acquisition of conditioned fear and facilitates fear extinction, effects mimicked by both an olfactory chemosignal emitted by a recently fear-conditioned familiar mouse and by the putative stress-related anxiogenic pheromone beta-phenylethylamine (beta-PEA). Together, these findings suggest social modulation of higher-order cognitive processing through pheromone communication and support the concurrent excitor hypothesis of extinction learning.
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Affiliation(s)
- Timothy W Bredy
- Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles, California 90095, USA.
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Bredy TW, Barad M. The histone deacetylase inhibitor valproic acid enhances acquisition, extinction, and reconsolidation of conditioned fear. Learn Mem 2008; 15:39-45. [PMID: 18174372 DOI: 10.1101/lm.801108] [Citation(s) in RCA: 207] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Histone modifications contribute to the epigenetic regulation of gene expression, a process now recognized to be important for the consolidation of long-term memory. Valproic acid (VPA), used for many years as an anticonvulsant and a mood stabilizer, has effects on learning and memory and enhances the extinction of conditioned fear through its function as a histone deacetylase inhibitor (HDAC). Here we report that VPA enhances long-term memory for both acquisition and extinction of cued-fear. Interestingly, VPA enhances extinction, but also enhances renewal of the original conditioned fear when tested in a within-subjects design. This effect appears to be related to a reconsolidation-like process since a single CS reminder in the presence of VPA can enhance long-term memory for the original fear in the context in which fear conditioning takes place. We also show that by modifying the intertrial interval during extinction training, VPA can strengthen reconsolidation of the original fear memory or enhance long-term memory for extinction such that it becomes independent of context. These findings have important implications for the use of HDAC inhibitors as adjuncts to behavior therapy in the treatment of phobia and related anxiety disorders.
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Affiliation(s)
- Timothy W Bredy
- Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles, California 90095, USA
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Bredy TW, Wu H, Crego C, Zellhoefer J, Sun YE, Barad M. Histone modifications around individual BDNF gene promoters in prefrontal cortex are associated with extinction of conditioned fear. Learn Mem 2007; 14:268-76. [PMID: 17522015 PMCID: PMC2216532 DOI: 10.1101/lm.500907] [Citation(s) in RCA: 415] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Extinction of conditioned fear is an important model both of inhibitory learning and of behavior therapy for human anxiety disorders. Like other forms of learning, extinction learning is long-lasting and depends on regulated gene expression. Epigenetic mechanisms make an important contribution to persistent changes in gene expression; therefore, in these studies, we have investigated whether epigenetic regulation of gene expression contributes to fear extinction. Since brain-derived neurotrophic factor (BDNF) is crucial for synaptic plasticity and for the maintenance of long-term memory, we examined histone modifications around two BDNF gene promoters after extinction of cued fear, as potential targets of learning-induced epigenetic regulation of gene expression. Valproic acid (VPA), used for some time as an anticonvulsant and a mood stabilizer, modulates the expression of BDNF, and is a histone deacetylase (HDAC) inhibitor. Here, we report that extinction of conditioned fear is accompanied by a significant increase in histone H4 acetylation around the BDNF P4 gene promoter and increases in BDNF exon I and IV mRNA expression in prefrontal cortex, that VPA enhances long-term memory for extinction because of its HDAC inhibitor effects, and that VPA potentiates the effect of weak extinction training on histone H4 acetylation around both the BDNF P1 and P4 gene promoters and on BDNF exon IV mRNA expression. These results suggest a relationship between histone H4 modification, epigenetic regulation of BDNF gene expression, and long-term memory for extinction of conditioned fear. In addition, they suggest that HDAC inhibitors may become a useful pharmacological adjunct to psychotherapy for human anxiety disorders.
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Affiliation(s)
- Timothy W. Bredy
- Department of Psychiatry and Biobehavioral Sciences, Brain Research Institute, Semel Institute for Neuroscience and Human Behavior, Los Angeles, California 90095, USA
| | - Hao Wu
- Department of Psychiatry and Biobehavioral Sciences, Brain Research Institute, Semel Institute for Neuroscience and Human Behavior, Los Angeles, California 90095, USA
| | - Cortney Crego
- Department of Psychiatry and Biobehavioral Sciences, Brain Research Institute, Semel Institute for Neuroscience and Human Behavior, Los Angeles, California 90095, USA
| | - Jessica Zellhoefer
- Department of Psychiatry and Biobehavioral Sciences, Brain Research Institute, Semel Institute for Neuroscience and Human Behavior, Los Angeles, California 90095, USA
| | - Yi E. Sun
- Department of Psychiatry and Biobehavioral Sciences, Brain Research Institute, Semel Institute for Neuroscience and Human Behavior, Los Angeles, California 90095, USA
| | - Mark Barad
- Department of Psychiatry and Biobehavioral Sciences, Brain Research Institute, Semel Institute for Neuroscience and Human Behavior, Los Angeles, California 90095, USA
- West Los Angeles VA Medical Center, Los Angeles, California 90073, USA
- Corresponding author.E-mail ; fax (310) 825-9870
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Bredy TW, Brown RE, Meaney MJ. Effect of resource availability on biparental care, and offspring neural and behavioral development in the California mouse (Peromyscus californicus). Eur J Neurosci 2007; 25:567-75. [PMID: 17284199 DOI: 10.1111/j.1460-9568.2006.05266.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Maternal care influences cognitive function in humans, primates and rodents; however, little is known about the effect of biparental care. Environmental factors such as resource availability play an important role in modulating parental investment strategies with subsequent effects on the offspring. Thus, we examined the interaction between foraging demand and biparental care on hippocampal development and novel object recognition in the monogamous, biparental California mouse. We characterized biparental behavior for 15 days in families exposed to either control (ad libitum feeding) or a high-foraging demand across the weaning period. Adult male offspring were then tested in the open field, and for novel object and place recognition, as well as for hippocampal synaptic density and the expression of genes encoding for subunits of the N-methyl-D-aspartate (NMDA) receptor complex, and the postsynaptic density (PSD)-95 scaffolding protein. Under high-foraging demand, the mothers' body weight was decreased at weaning and fathers spent significantly less time in contact with pups. Offspring reared under high-foraging demand weighed less at weaning and, as adults, were more fearful in the open field and showed profound deficits in both novel object and place recognition. While synaptic density and NR1 mRNA expression were unaffected, offspring reared under high-foraging demand showed increased NR2A and decreased NR2B mRNA expression. Further, PSD-95 protein expression was decreased in mice reared under high-foraging demand. Together, the results suggest that resource availability affects biparental investment strategies, with subsequent effects on hippocampal development and novel object recognition in the offspring.
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Affiliation(s)
- Timothy W Bredy
- Department of Psychiatry and Biobehavioral Sciences, UCLA, Los Angeles, CA 90095, USA
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Zhang TY, Bagot R, Parent C, Nesbitt C, Bredy TW, Caldji C, Fish E, Anisman H, Szyf M, Meaney MJ. Maternal programming of defensive responses through sustained effects on gene expression. Biol Psychol 2006; 73:72-89. [PMID: 16513241 DOI: 10.1016/j.biopsycho.2006.01.009] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2005] [Indexed: 11/21/2022]
Abstract
There are profound maternal effects on individual differences in defensive responses and reproductive strategies in species ranging literally from plants to insects to birds. Maternal effects commonly reflect the quality of the environment and are most likely mediated by the quality of the maternal provision (egg, propagule, etc.), which in turn determines growth rates and adult phenotype. In this paper we review data from the rat that suggest comparable forms of maternal effects on defensive responses stress, which are mediated by the effects of variations in maternal behavior on gene expression. Under conditions of environmental adversity maternal effects enhance the capacity for defensive responses in the offspring. In mammals, these effects appear to 'program' emotional, cognitive and endocrine systems towards increased sensitivity to adversity. In environments with an increased level of adversity, such effects can be considered adaptive, enhancing the probability of offspring survival to sexual maturity; the cost is that of an increased risk for multiple forms of pathology in later life.
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Affiliation(s)
- Tie-Yuan Zhang
- McGill Program for the Study of Behavior, Genes and Environment, McGill University, Canada
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Bredy TW, Zhang TY, Grant RJ, Diorio J, Meaney MJ. Peripubertal environmental enrichment reverses the effects of maternal care on hippocampal development and glutamate receptor subunit expression. Eur J Neurosci 2004; 20:1355-62. [PMID: 15341607 DOI: 10.1111/j.1460-9568.2004.03599.x] [Citation(s) in RCA: 154] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Maternal care in the rat influences the development of cognitive function in the offspring through neural systems known to mediate activity-dependent synaptic plasticity. The offspring of mothers that exhibit increased levels of pup licking/grooming (high-LG mothers) show increased hippocampal N-methyl-D-aspartate (NMDA) subunit mRNA expression, enhanced synaptogenesis and improved hippocampal-dependent spatial learning in comparison with animals reared by low-LG mothers. The effects of reduced maternal care on cognitive function are reversed with peripubertal environmental enrichment; however, the neural mechanisms mediating this effect are not known. In these studies we exposed the offspring of high- and low-LG mothers to environmental enrichment from days 22 to 70 of life, and measured the expression of genes encoding for glutamate receptor subunits and synaptophysin expression as a measure of synaptic density. Environmental enrichment reversed the effects of maternal care on synaptic density and this effect was, in turn, associated with a reversal of the effect of maternal care on the NR2A and NR2B subunits of the NMDA receptor, as well as effects on (RS)-alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor subunits. Finally, direct infusion of an NR2B-specific NMDA receptor antagonist into the hippocampus eliminated the effects of maternal care on spatial learning/memory in the Morris water maze. These findings suggest that: (1) the effects of maternal care are mediated by changes in NR2B gene expression; and (2) that environmental enrichment reverses the effects of reduced maternal care through the same genomic target, the NR2B gene, and possibly effects on other subunits of the NMDA and AMPA receptors.
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Affiliation(s)
- Timothy W Bredy
- Developmental Neuroendocrinology Laboratory, Genes and Environment, Douglas Hospital Research Center, Montrèal, Canada H4H 1R3
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Bredy TW, Lee AW, Meaney MJ, Brown RE. Effect of neonatal handling and paternal care on offspring cognitive development in the monogamous California mouse (Peromyscus californicus). Horm Behav 2004; 46:30-8. [PMID: 15215039 DOI: 10.1016/j.yhbeh.2003.09.017] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2003] [Revised: 05/01/2003] [Accepted: 09/23/2003] [Indexed: 11/24/2022]
Abstract
In the laboratory rat and mouse, neonatal handling enhances hippocampal-dependent learning in adulthood, an effect mediated by changes in maternal behavior toward the handled young. In the present study, we examined the interaction between neonatal handling and biparental care during the early postnatal period and its effect on cognitive function in adult California mice (Peromyscus californicus). We characterized the parental behavior of handled and nonhandled father-present and father-absent families over the first 15 days of life. We then assessed cognitive performance of male and female offspring in the Barnes maze and object recognition test after they were 60 days of age. We found that the amount of licking and grooming received by pups was decreased in father-absent families. By postnatal days 12-15, licking and grooming in handled, father-absent families were equivalent to that of nonhandled, father-present families. Handling enhanced novel object recognition in father-present male mice with no effect in females. In the nonhandled group, the presence of the father had no effect on object recognition learning in male or female mice. Handling also enhanced spatial learning in the Barnes maze. In nonhandled families, the presence of the father appeared to have no effect on spatial learning in the male offspring. Interestingly, spatial learning in nonhandled, father-absent, female offspring was similar to that of handled animals. The average amount of licking and grooming received by pups was negatively correlated with the average number of errors made on the first day of reversal training in the Barnes maze. These data support previous findings that neonatal handling facilitates learning and memory in adulthood, suggest that under certain environmental conditions, there is a sex difference in the response of pups to paternal care, and further demonstrate the importance of active parental investment for offspring cognitive development.
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Affiliation(s)
- Timothy W Bredy
- Developmental Neuroendocrinology Laboratory, Douglas Hospital Research Centre, and Department of Psychiatry, Dalhousie University, Halifax, Nova Scotia, Canada
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Abstract
Maternal care during the first week of postnatal life influences hippocampal development and function (Liu et al., 2000; Nature Neurosci., 3, 799-806). Offspring reared by mothers who exhibit increased levels of pup licking/grooming (LG) show increased hippocampal synaptic density and enhanced spatial learning and memory. Using 5-bromo-2'-deoxyuridine (BrdU), a thymidine analogue incorporated into cells during DNA synthesis, we examined the effects of early maternal care on hippocampal cell proliferation and neuronal survival in the rat. Twenty-four hours following injection on day 7 of life (P7) there were no differences in BrdU labelling in the offspring of high- compared with low-LG mothers, suggesting no maternal effect on the rate of proliferation at this age. However, 14 and 83 days following injection (P21 and P90), the offspring of high-LG mothers had significantly more surviving BrdU-labelled cells and BrdU-NeuN+-colabelled neurons in the dentate gyrus subgranular zone and granule cell layer. At P21, the offspring of high-LG mothers showed increased protein expression of basic fibroblast growth factor and significantly decreased levels of pyknosis. These findings suggest an influence of maternal care on neuronal survival in the hippocampus. Conversely, at the same time point there was a significantly higher level of hippocampal glial fibrillary acidic protein expression in the offspring of low-LG mothers. These findings emphasize the importance of early maternal care for hippocampal development.
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Affiliation(s)
- Timothy W Bredy
- Developmental Neuroendocrinology Laboratory and McGill Program for the Study of Behaviour, Genes and Environment, Douglas Hospital Research Centre, 6875 Boul. LaSalle Blvd, Montréal, Canada, H4H 1R3
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48
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Abstract
Maternal care influences hippocampal development in the rat. The offspring of mothers that exhibit increased levels of pup licking/grooming and arched-back nursing (High LG-ABN mothers) show increased hippocampal N-methyl-D-aspartate (NMDA) receptor binding and enhanced hippocampal-dependent spatial learning. In these studies we examined whether environmental enrichment from days 22-70 of life might reverse the effects of low maternal care. Environmental enrichment eliminated the differences between the offspring of High and Low LG-ABN mothers in both Morris water maze learning and object recognition. However, enrichment did not reverse the effect of maternal care on long-term potentiation in the dentate gyrus or on hippocampal NMDA receptor binding. In contrast, peripubertal enrichment did reverse the effects of maternal care on hippocampal alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor binding. These findings provide evidence for the reversal of the effects of reduced maternal investment in early life on cognitive function in adulthood. Such effects might involve compensatory changes associated with peripubertal enrichment.
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Affiliation(s)
- T W Bredy
- Douglas Hospital Research Centre, Department of Psychiatry, McGill University, 6875 Boulevard LaSalle, Montreal, Canada H4H 1R3
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