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Sengupta A, Tudor JC, Cusmano D, Baur JA, Abel T, Weljie AM. Sleep deprivation and aging are metabolically linked across tissues. Sleep 2023; 46:zsad246. [PMID: 37738102 DOI: 10.1093/sleep/zsad246] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 05/05/2023] [Revised: 08/21/2023] [Indexed: 09/24/2023] Open
Abstract
STUDY OBJECTIVES Insufficient sleep is a concerning hallmark of modern society because sleep deprivation (SD) is a risk factor for neurodegenerative and cardiometabolic disorders. SD imparts an aging-like effect on learning and memory, although little is known about possible common molecular underpinnings of SD and aging. Here, we examine this question by profiling metabolic features across different tissues after acute SD in young adult and aged mice. METHODS Young adult and aged mice were subjected to acute SD for 5 hours. Blood plasma, hippocampus, and liver samples were subjected to UPLC-MS/MS-based metabolic profiling. RESULTS SD preferentially impacts peripheral plasma and liver profiles (e.g. ketone body metabolism) whereas the hippocampus is more impacted by aging. We further demonstrate that aged animals exhibit SD-like metabolic features at baseline. Hepatic alterations include parallel changes in nicotinamide metabolism between aging and SD in young animals. Overall, metabolism in young adult animals is more impacted by SD, which in turn induces aging-like features. A set of nine metabolites was classified (79% correct) based on age and sleep status across all four groups. CONCLUSIONS Our metabolic observations demonstrate striking parallels to previous observations in studies of learning and memory and define a molecular metabolic signature of sleep loss and aging.
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Affiliation(s)
- Arjun Sengupta
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer C Tudor
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
- Current affiliation: Department of Biology, Saint Joseph's University, Philadelphia, PA, USA
| | - Danielle Cusmano
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph A Baur
- Department of Physiology and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ted Abel
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
- Current Affiliation: Iowa Neuroscience Institute, Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 2312 PBDB, Iowa City, IA, USA
| | - Aalim M Weljie
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Sengupta A, Tudor JC, Cusmano D, Baur JA, Abel T, Weljie A. 0346 Metabolic Aging and Sleep Loss: Metabolite Signatures Link Sleep Deprivation and Aging Across Tissues. Sleep 2020. [DOI: 10.1093/sleep/zsaa056.343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Introduction
Insufficient sleep is a hallmark of modern society, and sleep deprivation (SD) is a risk factor for neurodegenerative and cardiometabolic disorders. The interactions of aging with systemic and local metabolic alterations induced by sleep deprivation are essentially unexplored. In this study, we demonstrate a shared metabolic imprint of SD and aging in plasma, liver, and hippocampus.
Methods
Young (2 - 4 months) and aged (22 - 24 months) mice were sleep deprived (N = 10/group) for 5 hours followed by collection of blood plasma, liver and hippocampus. The samples were extracted and subjected to UPLC-MS/MS based targeted metabolomics analysis.
Results
Young animals displayed greater sensitivity to SD induced metabolic changes with >40% more metabolites perturbed in each sample type measured compared to aged animals. Enrichment analysis based on known disease-associated metabolites suggests that plasma change in young animals are of pathological relevance, but not in aged animals. A common hepatic signature of sleep-loss across the two age groups consisted of ketosis and urea cycle perturbation. Approximately 20-30% of measured metabolites exhibit similar changes when the sleep deprivation induced signature is compared with the aging metabolic imprint in a tissue-dependent manner. Central energetics, urea cycle and aromatic amino acid metabolism highlight the common pathways altered by sleep and aging in the periphery. In the hippocampus, choline and acetylcholine pools were depleted, potentially providing insight into the changes in metabolism that accompany analogous defects in memory consolidation.
Conclusion
These results support the notion that SD makes the ‘young seem old’. The results further connect neurobehavioral observations tying together aging and sleep loss, by implicating molecular mechanisms at the level of metabolism.
Support
This work was supported by NIH grant R21AG052905 (AMW, AS), P50AG017628 (TA; A.I. Pack, PI) and R01AG062398 (TA, JT). TA was supported by the Brush Family Chair in Biology at Penn and is currently supported by the Roy J. Carver Chair of Neuroscience at Iowa.
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Affiliation(s)
- A Sengupta
- University of Pennsylvania, Philadelphia, PA
| | - J C Tudor
- Saint Joseph’s University, Philadelphia, PA
| | - D Cusmano
- University of Pennsylvania, Philadelphia, PA
| | - J A Baur
- University of Pennsylvania, Philadelphia, PA
| | - T Abel
- University of Iowa, Iowa City, IA
| | - A Weljie
- University of Pennsylvania, Philadelphia, PA
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Dougherty MK, Saul C, Carman L, Nelson MD, Tudor JC. 0028 Sleep Duration Influences the Kinetics of Stress Granule Formation. Sleep 2020. [DOI: 10.1093/sleep/zsaa056.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Introduction
Stress granules are non-membrane bound aggregates of messenger ribonucleoproteins that are biomarkers of cellular stress. It has been shown in cells in vitro that suppression of the mammalian target of rapamycin (mTOR) pathway and its non-mammalian orthologue target of rapamycin (TOR) is associated with an increase in stress granule formation. It has also been shown that the mTOR pathway is suppressed in response to sleep deprivation in mice. Despite the possible connection via the TOR/mTOR pathway, there has not been any previous evidence linking sleep deprivation with stress granule formation.
Methods
Our present investigation uses the nematode Caenorhabditis elegans to model how stress granule formation and clearance are modified by sleep duration. We developed novel strains of C. elegans that model each type of sleep deprivation or enhancement and have RFP-labeled PAB-1 protein, a key component of stress granules. In addition to modifying sleep duration via genetic means, we also sleep deprived wildtype fluorescently labeled animals using mechanical disturbances.
Results
Animals with enhanced stress-induced sleep have stress granules that are smaller in size and cleared faster than wildtype, while sleep deprived animals have granules that are slower to clear (F11,473 = 7.752, ***p < 0.0001, one-way ANOVA). Animals that were manually deprived of stress-induced sleep were similarly slower to clear stress granules (F5,209 = 5.476 ***p < 0.0001, one-way ANOVA). Interestingly, animals genetically deprived of developmentally-timed sleep does not appear to have more stress granules in the middle of their sleep period than the sleeping wildtype stage (F2,42 = 2.659, p = 0.0729, one-way ANOVA).
Conclusion
This work demonstrates that the amount of sleep affects stress granule kinetics, which impacts the flow of genetic information inside cells.
Support
This work was supported by an R15GM122058 (NIH), John P. McNulty scholars program (SJU) and summer scholars program (SJU).
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Affiliation(s)
| | - C Saul
- Saint Joseph’s University, Philadelphia, PA
| | - L Carman
- Saint Joseph’s University, Philadelphia, PA
| | - M D Nelson
- Saint Joseph’s University, Philadelphia, PA
| | - J C Tudor
- Saint Joseph’s University, Philadelphia, PA
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Angelakos CC, Tudor JC, Ferri SL, Jongens TA, Abel T. Home-cage hypoactivity in mouse genetic models of autism spectrum disorder. Neurobiol Learn Mem 2019; 165:107000. [PMID: 30797034 DOI: 10.1016/j.nlm.2019.02.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 11/28/2017] [Revised: 11/28/2018] [Accepted: 02/19/2019] [Indexed: 11/16/2022]
Abstract
Genome-wide association and whole exome sequencing studies from Autism Spectrum Disorder (ASD) patient populations have implicated numerous risk factor genes whose mutation or deletion results in significantly increased incidence of ASD. Behavioral studies of monogenic mutant mouse models of ASD-associated genes have been useful for identifying aberrant neural circuitry. However, behavioral results often differ from lab to lab, and studies incorporating both males and females are often not performed despite the significant sex-bias of ASD. In this study, we sought to investigate the simple, passive behavior of home-cage activity monitoring across multiple 24-h days in four different monogenic mouse models of ASD: Shank3b-/-, Cntnap2-/-, Pcdh10+/-, and Fmr1 knockout mice. Relative to sex-matched wildtype (WT) littermates, we discovered significant home-cage hypoactivity, particularly in the dark (active) phase of the light/dark cycle, in male mice of all four ASD-associated transgenic models. For Cntnap2-/- and Pcdh10+/- mice, these activity alterations were sex-specific, as female mice did not exhibit home-cage activity differences relative to sex-matched WT controls. These home-cage hypoactivity alterations differ from activity findings previously reported using short-term activity measurements in a novel open field. Despite circadian problems reported in human ASD patients, none of the mouse models studied had alterations in free-running circadian period. Together, these findings highlight a shared phenotype across several monogenic mouse models of ASD, outline the importance of methodology on behavioral interpretation, and in some genetic lines parallel the male-enhanced phenotypic presentation observed in human ASDs.
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Affiliation(s)
- Christopher C Angelakos
- Neuroscience Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Jennifer C Tudor
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, United States; Department of Biology, Saint Joseph's University, Philadelphia, PA 19131, United States
| | - Sarah L Ferri
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, United States; Molecular Physiology and Biophysics, Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, United States
| | - Thomas A Jongens
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Ted Abel
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, United States; Molecular Physiology and Biophysics, Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, United States.
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Park AJ, Havekes R, Fu X, Hansen R, Tudor JC, Peixoto L, Li Z, Wu YC, Poplawski SG, Baraban JM, Abel T. Learning induces the translin/trax RNase complex to express activin receptors for persistent memory. eLife 2017; 6. [PMID: 28927503 PMCID: PMC5606845 DOI: 10.7554/elife.27872] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [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: 05/11/2017] [Accepted: 09/01/2017] [Indexed: 12/16/2022] Open
Abstract
Long-lasting forms of synaptic plasticity and memory require de novo protein synthesis. Yet, how learning triggers this process to form memory is unclear. Translin/trax is a candidate to drive this learning-induced memory mechanism by suppressing microRNA-mediated translational silencing at activated synapses. We find that mice lacking translin/trax display defects in synaptic tagging, which requires protein synthesis at activated synapses, and long-term memory. Hippocampal samples harvested from these mice following learning show increases in several disease-related microRNAs targeting the activin A receptor type 1C (ACVR1C), a component of the transforming growth factor-β receptor superfamily. Furthermore, the absence of translin/trax abolishes synaptic upregulation of ACVR1C protein after learning. Finally, synaptic tagging and long-term memory deficits in mice lacking translin/trax are mimicked by ACVR1C inhibition. Thus, we define a new memory mechanism by which learning reverses microRNA-mediated silencing of the novel plasticity protein ACVR1C via translin/trax.
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Affiliation(s)
- Alan Jung Park
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Robbert Havekes
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Xiuping Fu
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, United States
| | - Rolf Hansen
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Jennifer C Tudor
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Lucia Peixoto
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Zhi Li
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, United States
| | - Yen-Ching Wu
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, United States
| | - Shane G Poplawski
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Jay M Baraban
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, United States
| | - Ted Abel
- Department of Biology, University of Pennsylvania, Philadelphia, United States.,Molecular Physiology and Biophysics, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States
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Kreutzmann JC, Tudor JC, Angelakos CC, Abel T. The Impact of Sleep Deprivation on Molecular Mechanisms of Memory Consolidation in Rodents. Cognitive Neuroscience of Memory Consolidation 2017. [DOI: 10.1007/978-3-319-45066-7_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Havekes R, Park AJ, Tudor JC, Luczak VG, Hansen RT, Ferri SL, Bruinenberg VM, Poplawski SG, Day JP, Aton SJ, Radwańska K, Meerlo P, Houslay MD, Baillie GS, Abel T. Sleep deprivation causes memory deficits by negatively impacting neuronal connectivity in hippocampal area CA1. eLife 2016; 5. [PMID: 27549340 PMCID: PMC4996653 DOI: 10.7554/elife.13424] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [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: 12/01/2015] [Accepted: 07/29/2016] [Indexed: 12/18/2022] Open
Abstract
Brief periods of sleep loss have long-lasting consequences such as impaired memory consolidation. Structural changes in synaptic connectivity have been proposed as a substrate of memory storage. Here, we examine the impact of brief periods of sleep deprivation on dendritic structure. In mice, we find that five hours of sleep deprivation decreases dendritic spine numbers selectively in hippocampal area CA1 and increased activity of the filamentous actin severing protein cofilin. Recovery sleep normalizes these structural alterations. Suppression of cofilin function prevents spine loss, deficits in hippocampal synaptic plasticity, and impairments in long-term memory caused by sleep deprivation. The elevated cofilin activity is caused by cAMP-degrading phosphodiesterase-4A5 (PDE4A5), which hampers cAMP-PKA-LIMK signaling. Attenuating PDE4A5 function prevents changes in cAMP-PKA-LIMK-cofilin signaling and cognitive deficits associated with sleep deprivation. Our work demonstrates the necessity of an intact cAMP-PDE4-PKA-LIMK-cofilin activation-signaling pathway for sleep deprivation-induced memory disruption and reduction in hippocampal spine density. DOI:http://dx.doi.org/10.7554/eLife.13424.001 The demands of modern society means that millions of people do not get sufficient sleep on a daily basis. Sleep deprivation, even if only for brief periods, can impair learning and memory. In many cases, this impairment appears to be related to changes in the activity of a brain region called the hippocampus. However, the exact processes responsible for producing the effects of sleep deprivation remain unclear. During learning or forming a new memory, the connections between the relevant neurons in the brain change. Havekes et al. found that depriving mice of sleep for just five hours dramatically reduced the connectivity between neurons in the hippocampus. This reduction is caused by the increased activity of cofilin, a protein that breaks down the actin filaments that shape the connections between neurons. Havekes et al. then used a virus to introduce an inactive version of cofilin into hippocampal neurons to suppress the activity of the naturally present cofilin. This manipulation prevented both the loss of the connections between neurons and the memory deficits normally associated with sleep deprivation. Havekes et al. also found that recovery sleep leads to the re-wiring of neurons in the hippocampus. Future studies are now needed to determine how the neurons are able to re-wire themselves during recovery sleep. DOI:http://dx.doi.org/10.7554/eLife.13424.002
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Affiliation(s)
- Robbert Havekes
- Department of Biology, University of Pennsylvania, Philadelphia, United States.,Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Alan J Park
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Jennifer C Tudor
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Vincent G Luczak
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Rolf T Hansen
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Sarah L Ferri
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Vibeke M Bruinenberg
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Shane G Poplawski
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Jonathan P Day
- Institute of Cardiovascular and Medical Science, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Sara J Aton
- LSA Molecular, Cellular, and Developmental Biology, University of Michigan-Ann Arbor, Ann Arbor, United States
| | - Kasia Radwańska
- Laboratory of Molecular Basis of Behavior, Head Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Peter Meerlo
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Miles D Houslay
- Institute of Pharmaceutical Science, King's College London, London, United Kingdom
| | - George S Baillie
- Institute of Cardiovascular and Medical Science, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Ted Abel
- Department of Biology, University of Pennsylvania, Philadelphia, United States
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Tudor JC, Davis EJ, Peixoto L, Wimmer ME, van Tilborg E, Park AJ, Poplawski SG, Chung CW, Havekes R, Huang J, Gatti E, Pierre P, Abel T. Sleep deprivation impairs memory by attenuating mTORC1-dependent protein synthesis. Sci Signal 2016; 9:ra41. [PMID: 27117251 DOI: 10.1126/scisignal.aad4949] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Sleep deprivation is a public health epidemic that causes wide-ranging deleterious consequences, including impaired memory and cognition. Protein synthesis in hippocampal neurons promotes memory and cognition. The kinase complex mammalian target of rapamycin complex 1 (mTORC1) stimulates protein synthesis by phosphorylating and inhibiting the eukaryotic translation initiation factor 4E-binding protein 2 (4EBP2). We investigated the involvement of the mTORC1-4EBP2 axis in the molecular mechanisms mediating the cognitive deficits caused by sleep deprivation in mice. Using an in vivo protein translation assay, we found that loss of sleep impaired protein synthesis in the hippocampus. Five hours of sleep loss attenuated both mTORC1-mediated phosphorylation of 4EBP2 and the interaction between eukaryotic initiation factor 4E (eIF4E) and eIF4G in the hippocampi of sleep-deprived mice. Increasing the abundance of 4EBP2 in hippocampal excitatory neurons before sleep deprivation increased the abundance of phosphorylated 4EBP2, restored the amount of eIF4E-eIF4G interaction and hippocampal protein synthesis to that seen in mice that were not sleep-deprived, and prevented the hippocampus-dependent memory deficits associated with sleep loss. These findings collectively demonstrate that 4EBP2-regulated protein synthesis is a critical mediator of the memory deficits caused by sleep deprivation.
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Affiliation(s)
- Jennifer C Tudor
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Emily J Davis
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lucia Peixoto
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mathieu E Wimmer
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erik van Tilborg
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alan J Park
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shane G Poplawski
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Caroline W Chung
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robbert Havekes
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jiayan Huang
- Global Statistical Science, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | - Evelina Gatti
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, INSERM U1104, CNRS UMR7280, 13288 Marseille, France. Institute for Research in Biomedicine (iBiMED) and Aveiro Health Sciences Program, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Philippe Pierre
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, INSERM U1104, CNRS UMR7280, 13288 Marseille, France. Institute for Research in Biomedicine (iBiMED) and Aveiro Health Sciences Program, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Ted Abel
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Peixoto LL, Wimmer ME, Poplawski SG, Tudor JC, Kenworthy CA, Liu S, Mizuno K, Garcia BA, Zhang NR, Giese K, Abel T. Memory acquisition and retrieval impact different epigenetic processes that regulate gene expression. BMC Genomics 2015; 16 Suppl 5:S5. [PMID: 26040834 PMCID: PMC4460846 DOI: 10.1186/1471-2164-16-s5-s5] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background A fundamental question in neuroscience is how memories are stored and retrieved in the brain. Long-term memory formation requires transcription, translation and epigenetic processes that control gene expression. Thus, characterizing genome-wide the transcriptional changes that occur after memory acquisition and retrieval is of broad interest and importance. Genome-wide technologies are commonly used to interrogate transcriptional changes in discovery-based approaches. Their ability to increase scientific insight beyond traditional candidate gene approaches, however, is usually hindered by batch effects and other sources of unwanted variation, which are particularly hard to control in the study of brain and behavior. Results We examined genome-wide gene expression after contextual conditioning in the mouse hippocampus, a brain region essential for learning and memory, at all the time-points in which inhibiting transcription has been shown to impair memory formation. We show that most of the variance in gene expression is not due to conditioning and that by removing unwanted variance through additional normalization we are able provide novel biological insights. In particular, we show that genes downregulated by memory acquisition and retrieval impact different functions: chromatin assembly and RNA processing, respectively. Levels of histone 2A variant H2AB are reduced only following acquisition, a finding we confirmed using quantitative proteomics. On the other hand, splicing factor Rbfox1 and NMDA receptor-dependent microRNA miR-219 are only downregulated after retrieval, accompanied by an increase in protein levels of miR-219 target CAMKIIγ. Conclusions We provide a thorough characterization of coding and non-coding gene expression during long-term memory formation. We demonstrate that unwanted variance dominates the signal in transcriptional studies of learning and memory and introduce the removal of unwanted variance through normalization as a necessary step for the analysis of genome-wide transcriptional studies in the context of brain and behavior. We show for the first time that histone variants are downregulated after memory acquisition, and splicing factors and microRNAs after memory retrieval. Our results provide mechanistic insights into the molecular basis of cognition by highlighting the differential involvement of epigenetic mechanisms, such as histone variants and post-transcriptional RNA regulation, after acquisition and retrieval of memory.
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