1
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Basu R, Preat T, Plaçais PY. Glial metabolism versatility regulates mushroom body-driven behavioral output in Drosophila. Learn Mem 2024; 31:a053823. [PMID: 38862167 PMCID: PMC11199944 DOI: 10.1101/lm.053823.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 04/23/2024] [Indexed: 06/13/2024]
Abstract
Providing metabolic support to neurons is now recognized as a major function of glial cells that is conserved from invertebrates to vertebrates. However, research in this field has focused for more than two decades on the relevance of lactate and glial glycolysis for neuronal energy metabolism, while overlooking many other facets of glial metabolism and their impact on neuronal physiology, circuit activity, and behavior. Here, we review recent work that has unveiled new features of glial metabolism, especially in Drosophila, in the modulation of behavioral traits involving the mushroom bodies (MBs). These recent findings reveal that spatially and biochemically distinct modes of glucose-derived neuronal fueling are implemented within the MB in a memory type-specific manner. In addition, cortex glia are endowed with several antioxidant functions, whereas astrocytes can serve as pro-oxidant agents that are beneficial to redox signaling underlying long-term memory. Finally, glial fatty acid oxidation seems to play a dual fail-safe role: first, as a mode of energy production upon glucose shortage, and, second, as a factor underlying the clearance of excessive oxidative load during sleep. Altogether, these integrated studies performed in Drosophila indicate that glial metabolism has a deterministic role on behavior.
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Affiliation(s)
- Ruchira Basu
- Energy & Memory, Brain Plasticity (UMR 8249), CNRS, ESPCI Paris, PSL Research University, 75005 Paris, France
| | - Thomas Preat
- Energy & Memory, Brain Plasticity (UMR 8249), CNRS, ESPCI Paris, PSL Research University, 75005 Paris, France
| | - Pierre-Yves Plaçais
- Energy & Memory, Brain Plasticity (UMR 8249), CNRS, ESPCI Paris, PSL Research University, 75005 Paris, France
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2
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Ahmed OM, Crocker A, Murthy M. Transcriptional profiling of Drosophila male-specific P1 (pC1) neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.07.566045. [PMID: 37986870 PMCID: PMC10659367 DOI: 10.1101/2023.11.07.566045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
In Drosophila melanogaster, the P1 (pC1) cluster of male-specific neurons both integrates sensory cues and drives or modulates behavioral programs such as courtship, in addition to contributing to a social arousal state. The behavioral function of these neurons is linked to the genes they express, which underpin their capacity for synaptic signaling, neuromodulation, and physiology. Yet, P1 (pC1) neurons have not been fully characterized at the transcriptome level. Moreover, it is unknown how the molecular landscape of P1 (pC1) neurons acutely changes after flies engage in social behaviors, where baseline P1 (pC1) neural activity is expected to increase. To address these two gaps, we use single cell-type RNA sequencing to profile and compare the transcriptomes of P1 (pC1) neurons harvested from socially paired versus solitary male flies. Compared to control transcriptome datasets, we find that P1 (pC1) neurons are enriched in 2,665 genes, including those encoding receptors, neuropeptides, and cell-adhesion molecules (dprs/DIPs). Furthermore, courtship is characterized by changes in ~300 genes, including those previously implicated in regulating behavior (e.g. DopEcR, Octβ3R, Fife, kairos, rad). Finally, we identify a suite of genes that link conspecific courtship with the innate immune system. Together, these data serve as a molecular map for future studies of an important set of higher-order and sexually-dimorphic neurons.
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Affiliation(s)
- Osama M Ahmed
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08540, USA
- Department of Psychology, University of Washington, Seattle, WA 98105, USA
| | - Amanda Crocker
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08540, USA
- Program in Neuroscience, Middlebury College, Middlebury, VT 05753, USA
| | - Mala Murthy
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08540, USA
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3
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Sgammeglia N, Widmer YF, Kaldun JC, Fritsch C, Bruggmann R, Sprecher SG. Memory phase-specific genes in the Mushroom Bodies identified using CrebB-target DamID. PLoS Genet 2023; 19:e1010802. [PMID: 37307281 DOI: 10.1371/journal.pgen.1010802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 05/29/2023] [Indexed: 06/14/2023] Open
Abstract
The formation of long-term memories requires changes in the transcriptional program and de novo protein synthesis. One of the critical regulators for long-term memory (LTM) formation and maintenance is the transcription factor CREB. Genetic studies have dissected the requirement of CREB activity within memory circuits, however less is known about the genetic mechanisms acting downstream of CREB and how they may contribute defining LTM phases. To better understand the downstream mechanisms, we here used a targeted DamID approach (TaDa). We generated a CREB-Dam fusion protein using the fruit fly Drosophila melanogaster as model. Expressing CREB-Dam in the mushroom bodies (MBs), a brain center implicated in olfactory memory formation, we identified genes that are differentially expressed between paired and unpaired appetitive training paradigm. Of those genes we selected candidates for an RNAi screen in which we identified genes causing increased or decreased LTM.
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Affiliation(s)
- Noemi Sgammeglia
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Yves F Widmer
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Jenifer C Kaldun
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Cornelia Fritsch
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Simon G Sprecher
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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4
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Zhuravlev AV, Zalomaeva ES, Egozova ES, Sokurova VV, Nikitina EA, Savvateeva-Popova EV. LIM-kinase 1 effects on memory abilities and male courtship song in Drosophila depend on the neuronal type. Vavilovskii Zhurnal Genet Selektsii 2023; 27:250-263. [PMID: 37293442 PMCID: PMC10244584 DOI: 10.18699/vjgb-23-31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/19/2022] [Accepted: 08/24/2022] [Indexed: 06/10/2023] Open
Abstract
The signal pathway of actin remodeling, including LIM-kinase 1 (LIMK1) and its substrate cofilin, regulates multiple processes in neurons of vertebrates and invertebrates. Drosophila melanogaster is widely used as a model object for studying mechanisms of memory formation, storage, retrieval and forgetting. Previously, active forgetting in Drosophila was investigated in the standard Pavlovian olfactory conditioning paradigm. The role of specific dopaminergic neurons (DAN) and components of the actin remodeling pathway in different forms of forgetting was shown. In our research, we investigated the role of LIMK1 in Drosophila memory and forgetting in the conditioned courtship suppression paradigm (CCSP). In the Drosophila brain, LIMK1 and p-cofilin levels appeared to be low in specific neuropil structures, including the mushroom body (MB) lobes and the central complex. At the same time, LIMK1 was observed in cell bodies, such as DAN clusters regulating memory formation in CCSP. We applied GAL4 × UAS binary system to induce limk1 RNA interference in different types of neurons. The hybrid strain with limk1 interference in MB lobes and glia showed an increase in 3-h short-term memory (STM), without significant effects on long-term memory. limk1 interference in cholinergic neurons (CHN) impaired STM, while its interference in DAN and serotoninergic neurons (SRN) also dramatically impaired the flies' learning ability. By contrast, limk1 interference in fruitless neurons (FRN) resulted in increased 15-60 min STM, indicating a possible LIMK1 role in active forgetting. Males with limk1 interference in CHN and FRN also showed the opposite trends of courtship song parameters changes. Thus, LIMK1 effects on the Drosophila male memory and courtship song appeared to depend on the neuronal type or brain structure.
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Affiliation(s)
- A V Zhuravlev
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia
| | - E S Zalomaeva
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, RussiaHerzen State Pedagogical University of Russia, St. Petersburg, Russia
| | - E S Egozova
- Herzen State Pedagogical University of Russia, St. Petersburg, Russia
| | - V V Sokurova
- Herzen State Pedagogical University of Russia, St. Petersburg, Russia
| | - E A Nikitina
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia Herzen State Pedagogical University of Russia, St. Petersburg, Russia
| | - E V Savvateeva-Popova
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia
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5
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Aging and memory are altered by genetically manipulating lactate dehydrogenase in the neurons or glia of flies. Aging (Albany NY) 2023; 15:947-981. [PMID: 36849157 PMCID: PMC10008500 DOI: 10.18632/aging.204565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/20/2023] [Indexed: 03/01/2023]
Abstract
The astrocyte-neuron lactate shuttle hypothesis posits that glial-generated lactate is transported to neurons to fuel metabolic processes required for long-term memory. Although studies in vertebrates have revealed that lactate shuttling is important for cognitive function, it is uncertain if this form of metabolic coupling is conserved in invertebrates or is influenced by age. Lactate dehydrogenase (Ldh) is a rate limiting enzyme that interconverts lactate and pyruvate. Here we genetically manipulated expression of Drosophila melanogaster lactate dehydrogenase (dLdh) in neurons or glia to assess the impact of altered lactate metabolism on invertebrate aging and long-term courtship memory at different ages. We also assessed survival, negative geotaxis, brain neutral lipids (the core component of lipid droplets) and brain metabolites. Both upregulation and downregulation of dLdh in neurons resulted in decreased survival and memory impairment with age. Glial downregulation of dLdh expression caused age-related memory impairment without altering survival, while upregulated glial dLdh expression lowered survival without disrupting memory. Both neuronal and glial dLdh upregulation increased neutral lipid accumulation. We provide evidence that altered lactate metabolism with age affects the tricarboxylic acid (TCA) cycle, 2-hydroxyglutarate (2HG), and neutral lipid accumulation. Collectively, our findings indicate that the direct alteration of lactate metabolism in either glia or neurons affects memory and survival but only in an age-dependent manner.
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6
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Palmer MJ, Fitzsimons HL. Herzog is not required for mushroom body development or courtship learning & memory but is required for eye development in Drosophila melanogaster. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000720. [PMID: 36798589 PMCID: PMC9926291 DOI: 10.17912/micropub.biology.000720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 02/18/2023]
Abstract
Herzog (Hzg, CG5830) shares similarity to members of the haloacid dehalogenase subfamily of small CTD phosphatases. In Drosophila it is a maternal gene essential for establishment of embryonic segment polarity, and oligomerization is required for activation of phosphatase activity. While Hzg is expressed in the brain, its role has not been investigated. To that end, we further characterized Hzg expression in the brain and found that it is highly expressed in neurons of the mushroom body where it localises to axons, and is also expressed in cortical glia. We investigated its role in mushroom body development as well as courtship learning and memory, but found that knockdown of Hzg had no impact on these processes. In contrast, knockdown in post-mitotic neurons in the eye resulted in disruption to ommatidial patterning and pigmentation, indicating it plays an important role in eye development.
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Affiliation(s)
- Madeleine J Palmer
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Helen L Fitzsimons
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
,
Correspondence to: Helen L Fitzsimons (
)
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7
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Styfhals R, Zolotarov G, Hulselmans G, Spanier KI, Poovathingal S, Elagoz AM, De Winter S, Deryckere A, Rajewsky N, Ponte G, Fiorito G, Aerts S, Seuntjens E. Cell type diversity in a developing octopus brain. Nat Commun 2022; 13:7392. [PMID: 36450803 PMCID: PMC9712504 DOI: 10.1038/s41467-022-35198-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 11/22/2022] [Indexed: 12/02/2022] Open
Abstract
Octopuses are mollusks that have evolved intricate neural systems comparable with vertebrates in terms of cell number, complexity and size. The brain cell types that control their sophisticated behavioral repertoire are still unknown. Here, we profile the cell diversity of the paralarval Octopus vulgaris brain to build a cell type atlas that comprises mostly neural cells, but also multiple glial subtypes, endothelial cells and fibroblasts. We spatially map cell types to the vertical, subesophageal and optic lobes. Investigation of cell type conservation reveals a shared gene signature between glial cells of mouse, fly and octopus. Genes related to learning and memory are enriched in vertical lobe cells, which show molecular similarities with Kenyon cells in Drosophila. We construct a cell type taxonomy revealing transcriptionally related cell types, which tend to appear in the same brain region. Together, our data sheds light on cell type diversity and evolution in the octopus brain.
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Affiliation(s)
- Ruth Styfhals
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Grygoriy Zolotarov
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115, Berlin, Germany
| | - Gert Hulselmans
- Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
- VIB Center for Brain & Disease Research, KU Leuven, Leuven, 3000, Belgium
| | - Katina I Spanier
- Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
- VIB Center for Brain & Disease Research, KU Leuven, Leuven, 3000, Belgium
| | | | - Ali M Elagoz
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Seppe De Winter
- Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
- VIB Center for Brain & Disease Research, KU Leuven, Leuven, 3000, Belgium
| | - Astrid Deryckere
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
- Department of Biological Sciences, Columbia University, New York, US
| | - Nikolaus Rajewsky
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115, Berlin, Germany
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Giovanna Ponte
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Graziano Fiorito
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Stein Aerts
- Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
- VIB Center for Brain & Disease Research, KU Leuven, Leuven, 3000, Belgium
| | - Eve Seuntjens
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium.
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8
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Consolidation and maintenance of long-term memory involve dual functions of the developmental regulator Apterous in clock neurons and mushroom bodies in the Drosophila brain. PLoS Biol 2021; 19:e3001459. [PMID: 34860826 PMCID: PMC8641882 DOI: 10.1371/journal.pbio.3001459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 10/25/2021] [Indexed: 11/23/2022] Open
Abstract
Memory is initially labile but can be consolidated into stable long-term memory (LTM) that is stored in the brain for extended periods. Despite recent progress, the molecular and cellular mechanisms underlying the intriguing neurobiological processes of LTM remain incompletely understood. Using the Drosophila courtship conditioning assay as a memory paradigm, here, we show that the LIM homeodomain (LIM-HD) transcription factor Apterous (Ap), which is known to regulate various developmental events, is required for both the consolidation and maintenance of LTM. Interestingly, Ap is involved in these 2 memory processes through distinct mechanisms in different neuronal subsets in the adult brain. Ap and its cofactor Chip (Chi) are indispensable for LTM maintenance in the Drosophila memory center, the mushroom bodies (MBs). On the other hand, Ap plays a crucial role in memory consolidation in a Chi-independent manner in pigment dispersing factor (Pdf)-containing large ventral–lateral clock neurons (l-LNvs) that modulate behavioral arousal and sleep. Since disrupted neurotransmission and electrical silencing in clock neurons impair memory consolidation, Ap is suggested to contribute to the stabilization of memory by ensuring the excitability of l-LNvs. Indeed, ex vivo imaging revealed that a reduced function of Ap, but not Chi, results in exaggerated Cl− responses to the inhibitory neurotransmitter gamma-aminobutyric acid (GABA) in l-LNvs, indicating that wild-type (WT) Ap maintains high l-LNv excitability by suppressing the GABA response. Consistently, enhancing the excitability of l-LNvs by knocking down GABAA receptors compensates for the impaired memory consolidation in ap null mutants. Overall, our results revealed unique dual functions of the developmental regulator Ap for LTM consolidation in clock neurons and LTM maintenance in MBs. A neurogenetic study using Drosophila reveals that the centrally expressed LIM-homeodomain transcription factor Apterous plays a crucial neuron-type-dependent role in two different memory processes - consolidation and maintenance of long-term memory.
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9
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Shields EJ, Sorida M, Sheng L, Sieriebriennikov B, Ding L, Bonasio R. Genome annotation with long RNA reads reveals new patterns of gene expression and improves single-cell analyses in an ant brain. BMC Biol 2021; 19:254. [PMID: 34838024 PMCID: PMC8626913 DOI: 10.1186/s12915-021-01188-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 11/10/2021] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Functional genomic analyses rely on high-quality genome assemblies and annotations. Highly contiguous genome assemblies have become available for a variety of species, but accurate and complete annotation of gene models, inclusive of alternative splice isoforms and transcription start and termination sites, remains difficult with traditional approaches. RESULTS Here, we utilized full-length isoform sequencing (Iso-Seq), a long-read RNA sequencing technology, to obtain a comprehensive annotation of the transcriptome of the ant Harpegnathos saltator. The improved genome annotations include additional splice isoforms and extended 3' untranslated regions for more than 4000 genes. Reanalysis of RNA-seq experiments using these annotations revealed several genes with caste-specific differential expression and tissue- or caste-specific splicing patterns that were missed in previous analyses. The extended 3' untranslated regions afforded great improvements in the analysis of existing single-cell RNA-seq data, resulting in the recovery of the transcriptomes of 18% more cells. The deeper single-cell transcriptomes obtained with these new annotations allowed us to identify additional markers for several cell types in the ant brain, as well as genes differentially expressed across castes in specific cell types. CONCLUSIONS Our results demonstrate that Iso-Seq is an efficient and effective approach to improve genome annotations and maximize the amount of information that can be obtained from existing and future genomic datasets in Harpegnathos and other organisms.
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Affiliation(s)
- Emily J Shields
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Urology and Institute of Neuropathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Masato Sorida
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Lihong Sheng
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Bogdan Sieriebriennikov
- Department of Biology, New York University, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Long Ding
- Department of Biology, New York University, New York, NY, USA
| | - Roberto Bonasio
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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10
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Kummeling J, Stremmelaar DE, Raun N, Reijnders MRF, Willemsen MH, Ruiterkamp-Versteeg M, Schepens M, Man CCO, Gilissen C, Cho MT, McWalter K, Sinnema M, Wheless JW, Simon MEH, Genetti CA, Casey AM, Terhal PA, van der Smagt JJ, van Gassen KLI, Joset P, Bahr A, Steindl K, Rauch A, Keller E, Raas-Rothschild A, Koolen DA, Agrawal PB, Hoffman TL, Powell-Hamilton NN, Thiffault I, Engleman K, Zhou D, Bodamer O, Hoefele J, Riedhammer KM, Schwaibold EMC, Tasic V, Schubert D, Top D, Pfundt R, Higgs MR, Kramer JM, Kleefstra T. Characterization of SETD1A haploinsufficiency in humans and Drosophila defines a novel neurodevelopmental syndrome. Mol Psychiatry 2021; 26:2013-2024. [PMID: 32346159 DOI: 10.1038/s41380-020-0725-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 04/01/2020] [Accepted: 04/01/2020] [Indexed: 12/18/2022]
Abstract
Defects in histone methyltransferases (HMTs) are major contributing factors in neurodevelopmental disorders (NDDs). Heterozygous variants of SETD1A involved in histone H3 lysine 4 (H3K4) methylation were previously identified in individuals with schizophrenia. Here, we define the clinical features of the Mendelian syndrome associated with haploinsufficiency of SETD1A by investigating 15 predominantly pediatric individuals who all have de novo SETD1A variants. These individuals present with a core set of symptoms comprising global developmental delay and/or intellectual disability, subtle facial dysmorphisms, behavioral and psychiatric problems. We examined cellular phenotypes in three patient-derived lymphoblastoid cell lines with three variants: p.Gly535Alafs*12, c.4582-2_4582delAG, and p.Tyr1499Asp. These patient cell lines displayed DNA damage repair defects that were comparable to previously observed RNAi-mediated depletion of SETD1A. This suggested that these variants, including the p.Tyr1499Asp in the catalytic SET domain, behave as loss-of-function (LoF) alleles. Previous studies demonstrated a role for SETD1A in cell cycle control and differentiation. However, individuals with SETD1A variants do not show major structural brain defects or severe microcephaly, suggesting that defective proliferation and differentiation of neural progenitors is unlikely the single underlying cause of the disorder. We show here that the Drosophila melanogaster SETD1A orthologue is required in postmitotic neurons of the fly brain for normal memory, suggesting a role in post development neuronal function. Together, this study defines a neurodevelopmental disorder caused by dominant de novo LoF variants in SETD1A and further supports a role for H3K4 methyltransferases in the regulation of neuronal processes underlying normal cognitive functioning.
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Affiliation(s)
- Joost Kummeling
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Diante E Stremmelaar
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Nicholas Raun
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada.,Department of Physiology and Pharmacology, The University of Western Ontario, London, ON, Canada
| | - Margot R F Reijnders
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6229 ER, Maastricht, The Netherlands
| | - Marjolein H Willemsen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Martina Ruiterkamp-Versteeg
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Marga Schepens
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Calvin C O Man
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | | | | | - Margje Sinnema
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6229 ER, Maastricht, The Netherlands
| | - James W Wheless
- Division of Pediatric Neurology, University of Tennessee Health Science Center, Memphis, TN, USA.,Neuroscience Institute & Le Bonheur Comprehensive Epilepsy Program, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - Marleen E H Simon
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Casie A Genetti
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital/Harvard Medical School, Boston, MA, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Alicia M Casey
- Division of Pulmonary and Respiratory Diseases, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Paulien A Terhal
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jasper J van der Smagt
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Schlieren, 8952, Zurich, Switzerland
| | - Angela Bahr
- Institute of Medical Genetics, University of Zurich, Schlieren, 8952, Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren, 8952, Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren, 8952, Zurich, Switzerland
| | - Elmar Keller
- Division of Neuropediatrics, Cantonal Hospital Graubuenden, Chur, Switzerland
| | - Annick Raas-Rothschild
- Institute of Rare Disease, Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - David A Koolen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital/Harvard Medical School, Boston, MA, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.,Division of Newborn Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Trevor L Hoffman
- Regional Department of Genetics, Southern California Kaiser Permanente Medical Group, 1188N. Euclid Street, Anaheim, CA, 92801, USA
| | - Nina N Powell-Hamilton
- Division of Medical Genetics, Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA.,Department of Pathology and Laboratory Medicine, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA.,Division of Clinical Genetics, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Kendra Engleman
- Department of Pediatrics, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Dihong Zhou
- Department of Pediatrics, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Olaf Bodamer
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital/Harvard Medical School, Boston, MA, USA
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Korbinian M Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | | | - Velibor Tasic
- Medical School Skopje, University Children's Hospital, Skopje, North Macedonia
| | - Dirk Schubert
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Deniz Top
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Martin R Higgs
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Jamie M Kramer
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada.,Department of Physiology and Pharmacology, The University of Western Ontario, London, ON, Canada
| | - Tjitske Kleefstra
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
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11
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Jauregui-Lozano J, Bakhle K, Weake VM. In vivo tissue-specific chromatin profiling in Drosophila melanogaster using GFP-tagged nuclei. Genetics 2021; 218:6281219. [PMID: 34022041 DOI: 10.1093/genetics/iyab079] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/17/2021] [Indexed: 12/23/2022] Open
Abstract
The chromatin landscape defines cellular identity in multicellular organisms with unique patterns of DNA accessibility and histone marks decorating the genome of each cell type. Thus, profiling the chromatin state of different cell types in an intact organism under disease or physiological conditions can provide insight into how chromatin regulates cell homeostasis in vivo. To overcome the many challenges associated with characterizing chromatin state in specific cell types, we developed an improved approach to isolate Drosophila melanogaster nuclei tagged with a GFPKASH protein. The perinuclear space-localized KASH domain anchors GFP to the outer nuclear membrane, and expression of UAS-GFPKASH can be controlled by tissue-specific Gal4 drivers. Using this protocol, we profiled chromatin accessibility using an improved version of Assay for Transposable Accessible Chromatin followed by sequencing (ATAC-seq), called Omni-ATAC. In addition, we examined the distribution of histone marks using Chromatin immunoprecipitation followed by sequencing (ChIP-seq) and Cleavage Under Targets and Tagmentation (CUT&Tag) in adult photoreceptor neurons. We show that the chromatin landscape of photoreceptors reflects the transcriptional state of these cells, demonstrating the quality and reproducibility of our approach for profiling the transcriptome and epigenome of specific cell types in Drosophila.
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Affiliation(s)
| | - Kimaya Bakhle
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Vikki M Weake
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA.,Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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12
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Zatsepina OG, Nikitina EA, Shilova VY, Chuvakova LN, Sorokina S, Vorontsova JE, Tokmacheva EV, Funikov SY, Rezvykh AP, Evgen'ev MB. Hsp70 affects memory formation and behaviorally relevant gene expression in Drosophila melanogaster. Cell Stress Chaperones 2021; 26:575-594. [PMID: 33829398 PMCID: PMC8065088 DOI: 10.1007/s12192-021-01203-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/20/2021] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
Heat shock proteins, in particular Hsp70, play a central role in proteostasis in eukaryotic cells. Due to its chaperone properties, Hsp70 is involved in various processes after stress and under normal physiological conditions. In contrast to mammals and many Diptera species, inducible members of the Hsp70 family in Drosophila are constitutively synthesized at a low level and undergo dramatic induction after temperature elevation or other forms of stress. In the courtship suppression paradigm used in this study, Drosophila males that have been repeatedly rejected by mated females during courtship are less likely than naive males to court other females. Although numerous genes with known function were identified to play important roles in long-term memory, there is, to the best of our knowledge, no direct evidence implicating Hsp70 in this process. To elucidate a possible role of Hsp70 in memory formation, we used D. melanogaster strains containing different hsp70 copy numbers, including strains carrying a deletion of all six hsp70 genes. Our investigations exploring the memory of courtship rejection paradigm demonstrated that a low constitutive level of Hsp70 is apparently required for learning and the formation of short and long-term memories in males. The performed transcriptomic studies demonstrate that males with different hsp70 copy numbers differ significantly in the expression of a few definite groups of genes involved in mating, reproduction, and immunity in response to rejection. Specifically, our analysis reveals several major pathways that depend on the presence of hsp70 in the genome and participate in memory formation and consolidation, including the cAMP signaling cascade.
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Affiliation(s)
- O G Zatsepina
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, Russia
| | - E A Nikitina
- Department of Neurogenetics, Pavlov Institute of Physiology, Russian Academy of Sciences, St. Petersburg, Russia
- Department of Human and Animal Anatomy and Physiology, Herzen State Pedagogical University, St. Petersburg, Russia
| | - V Y Shilova
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, Russia
| | - L N Chuvakova
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, Russia
| | - S Sorokina
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow, Russia
| | - J E Vorontsova
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow, Russia
| | - E V Tokmacheva
- Department of Neurogenetics, Pavlov Institute of Physiology, Russian Academy of Sciences, St. Petersburg, Russia
| | - S Y Funikov
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, Russia
| | - A P Rezvykh
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, Russia
| | - M B Evgen'ev
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, Russia.
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13
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Roselli C, Ramaswami M, Boto T, Cervantes-Sandoval I. The Making of Long-Lasting Memories: A Fruit Fly Perspective. Front Behav Neurosci 2021; 15:662129. [PMID: 33859556 PMCID: PMC8042140 DOI: 10.3389/fnbeh.2021.662129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 03/08/2021] [Indexed: 11/25/2022] Open
Abstract
Understanding the nature of the molecular mechanisms underlying memory formation, consolidation, and forgetting are some of the fascinating questions in modern neuroscience. The encoding, stabilization and elimination of memories, rely on the structural reorganization of synapses. These changes will enable the facilitation or depression of neural activity in response to the acquisition of new information. In other words, these changes affect the weight of specific nodes within a neural network. We know that these plastic reorganizations require de novo protein synthesis in the context of Long-term memory (LTM). This process depends on neural activity triggered by the learned experience. The use of model organisms like Drosophila melanogaster has been proven essential for advancing our knowledge in the field of neuroscience. Flies offer an optimal combination of a more straightforward nervous system, composed of a limited number of cells, and while still displaying complex behaviors. Studies in Drosophila neuroscience, which expanded over several decades, have been critical for understanding the cellular and molecular mechanisms leading to the synaptic and behavioral plasticity occurring in the context of learning and memory. This is possible thanks to sophisticated technical approaches that enable precise control of gene expression in the fruit fly as well as neural manipulation, like chemogenetics, thermogenetics, or optogenetics. The search for the identity of genes expressed as a result of memory acquisition has been an active interest since the origins of behavioral genetics. From screenings of more or less specific candidates to broader studies based on transcriptome analysis, our understanding of the genetic control behind LTM has expanded exponentially in the past years. Here we review recent literature regarding how the formation of memories induces a rapid, extensive and, in many cases, transient wave of transcriptional activity. After a consolidation period, transcriptome changes seem more stable and likely represent the synthesis of new proteins. The complexity of the circuitry involved in memory formation and consolidation is such that there are localized changes in neural activity, both regarding temporal dynamics and the nature of neurons and subcellular locations affected, hence inducing specific temporal and localized changes in protein expression. Different types of neurons are recruited at different times into memory traces. In LTM, the synthesis of new proteins is required in specific subsets of cells. This de novo translation can take place in the somatic cytoplasm and/or locally in distinct zones of compartmentalized synaptic activity, depending on the nature of the proteins and the plasticity-inducing processes that occur. We will also review recent advances in understanding how localized changes are confined to the relevant synapse. These recent studies have led to exciting discoveries regarding proteins that were not previously involved in learning and memory processes. This invaluable information will lead to future functional studies on the roles that hundreds of new molecular actors play in modulating neural activity.
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Affiliation(s)
- Camilla Roselli
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Mani Ramaswami
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin, Ireland.,National Centre for Biological Sciences, TIFR, Bengaluru, India
| | - Tamara Boto
- Trinity College Institute of Neuroscience, Department of Physiology, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Isaac Cervantes-Sandoval
- Department of Biology, Georgetown University, Washington, DC, United States.,Interdisciplinary Program in Neuroscience, Georgetown University, Washington, DC, United States
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14
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Brovero SG, Fortier JC, Hu H, Lovejoy PC, Newell NR, Palmateer CM, Tzeng RY, Lee PT, Zinn K, Arbeitman MN. Investigation of Drosophila fruitless neurons that express Dpr/DIP cell adhesion molecules. eLife 2021; 10:e63101. [PMID: 33616528 PMCID: PMC7972454 DOI: 10.7554/elife.63101] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/22/2021] [Indexed: 12/16/2022] Open
Abstract
Drosophila reproductive behaviors are directed by fruitless neurons. A reanalysis of genomic studies shows that genes encoding dpr and DIP immunoglobulin superfamily (IgSF) members are expressed in fru P1 neurons. We find that each fru P1 and dpr/DIP (fru P1 ∩ dpr/DIP) overlapping expression pattern is similar in both sexes, but there are dimorphisms in neuronal morphology and cell number. Behavioral studies of fru P1 ∩ dpr/DIP perturbation genotypes indicate that the mushroom body functions together with the lateral protocerebral complex to direct courtship behavior. A single-cell RNA-seq analysis of fru P1 neurons shows that many DIPs have high expression in a small set of neurons, whereas the dprs are often expressed in a larger set of neurons at intermediate levels, with a myriad of dpr/DIP expression combinations. Functionally, we find that perturbations of sex hierarchy genes and of DIP-ε change the sex-specific morphologies of fru P1 ∩ DIP-α neurons.
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Affiliation(s)
- Savannah G Brovero
- Department of Biomedical Sciences and Program of Neuroscience, Florida State University, College of MedicineTallahasseeUnited States
| | - Julia C Fortier
- Department of Biomedical Sciences and Program of Neuroscience, Florida State University, College of MedicineTallahasseeUnited States
| | - Hongru Hu
- Department of Biomedical Sciences and Program of Neuroscience, Florida State University, College of MedicineTallahasseeUnited States
| | - Pamela C Lovejoy
- Department of Biomedical Sciences and Program of Neuroscience, Florida State University, College of MedicineTallahasseeUnited States
| | - Nicole R Newell
- Department of Biomedical Sciences and Program of Neuroscience, Florida State University, College of MedicineTallahasseeUnited States
| | - Colleen M Palmateer
- Department of Biomedical Sciences and Program of Neuroscience, Florida State University, College of MedicineTallahasseeUnited States
| | - Ruei-Ying Tzeng
- Department of Biomedical Sciences and Program of Neuroscience, Florida State University, College of MedicineTallahasseeUnited States
| | - Pei-Tseng Lee
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
| | - Kai Zinn
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Michelle N Arbeitman
- Department of Biomedical Sciences and Program of Neuroscience, Florida State University, College of MedicineTallahasseeUnited States
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15
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Abstract
Drosophila melanogaster males reduce courtship behaviour after mating failure. In the lab, such conditioned courtship suppression, aka 'courtship conditioning', serves as a complex learning and memory assay. Interestingly, variations in the courtship conditioning assay can establish different types of memory. Here, we review research investigating the underlying cellular and molecular mechanisms that allow male flies to form memories of previous mating failures.
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Affiliation(s)
- Nicholas Raun
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Spencer Jones
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jamie M Kramer
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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16
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Kaldun JC, Sprecher SG. Initiated by CREB: Resolving Gene Regulatory Programs in Learning and Memory. Bioessays 2019; 41:e1900045. [DOI: 10.1002/bies.201900045] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/29/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Jenifer C. Kaldun
- Department of BiologyUniversity of Fribourg1700 Fribourg Switzerland
| | - Simon G. Sprecher
- Department of BiologyUniversity of Fribourg1700 Fribourg Switzerland
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17
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Hosseini M, Larti F, Fattahi Z, Najmabadi H, Kahrizi K. A splice-altering variant in LARP7 gene leads to exon exclusion. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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Nixon KC, Rousseau J, Stone MH, Sarikahya M, Ehresmann S, Mizuno S, Matsumoto N, Miyake N, Baralle D, McKee S, Izumi K, Ritter AL, Heide S, Héron D, Depienne C, Titheradge H, Kramer JM, Campeau PM, Campeau PM. A Syndromic Neurodevelopmental Disorder Caused by Mutations in SMARCD1, a Core SWI/SNF Subunit Needed for Context-Dependent Neuronal Gene Regulation in Flies. Am J Hum Genet 2019; 104:596-610. [PMID: 30879640 DOI: 10.1016/j.ajhg.2019.02.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/31/2019] [Indexed: 12/22/2022] Open
Abstract
Mutations in several genes encoding components of the SWI/SNF chromatin remodeling complex cause neurodevelopmental disorders (NDDs). Here, we report on five individuals with mutations in SMARCD1; the individuals present with developmental delay, intellectual disability, hypotonia, feeding difficulties, and small hands and feet. Trio exome sequencing proved the mutations to be de novo in four of the five individuals. Mutations in other SWI/SNF components cause Coffin-Siris syndrome, Nicolaides-Baraitser syndrome, or other syndromic and non-syndromic NDDs. Although the individuals presented here have dysmorphisms and some clinical overlap with these syndromes, they lack their typical facial dysmorphisms. To gain insight into the function of SMARCD1 in neurons, we investigated the Drosophila ortholog Bap60 in postmitotic memory-forming neurons of the adult Drosophila mushroom body (MB). Targeted knockdown of Bap60 in the MB of adult flies causes defects in long-term memory. Mushroom-body-specific transcriptome analysis revealed that Bap60 is required for context-dependent expression of genes involved in neuron function and development in juvenile flies when synaptic connections are actively being formed in response to experience. Taken together, we identify an NDD caused by SMARCD1 mutations and establish a role for the SMARCD1 ortholog Bap60 in the regulation of neurodevelopmental genes during a critical time window of juvenile adult brain development when neuronal circuits that are required for learning and memory are formed.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Philippe M Campeau
- Centre Hospitalier Universitaire Sainte-Justine Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada; Department of Pediatrics, University of Montreal, Montreal, QC H4A 3J1, Canada.
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19
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Chubak MC, Nixon KCJ, Stone MH, Raun N, Rice SL, Sarikahya M, Jones SG, Lyons TA, Jakub TE, Mainland RLM, Knip MJ, Edwards TN, Kramer JM. Individual components of the SWI/SNF chromatin remodelling complex have distinct roles in memory neurons of the Drosophila mushroom body. Dis Model Mech 2019; 12:12/3/dmm037325. [PMID: 30923190 PMCID: PMC6451433 DOI: 10.1242/dmm.037325] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 02/23/2019] [Indexed: 12/13/2022] Open
Abstract
Technology has led to rapid progress in the identification of genes involved in neurodevelopmental disorders such as intellectual disability (ID), but our functional understanding of the causative genes is lagging. Here, we show that the SWI/SNF chromatin remodelling complex is one of the most over-represented cellular components disrupted in ID. We investigated the role of individual subunits of this large protein complex using targeted RNA interference in post-mitotic memory-forming neurons of the Drosophila mushroom body (MB). Knockdown flies were tested for defects in MB morphology, short-term memory and long-term memory. Using this approach, we identified distinct roles for individual subunits of the Drosophila SWI/SNF complex. Bap60, Snr1 and E(y)3 are required for pruning of the MBγ neurons during pupal morphogenesis, while Brm and Osa are required for survival of MBγ axons during ageing. We used the courtship conditioning assay to test the effect of MB-specific SWI/SNF knockdown on short- and long-term memory. Several subunits, including Brm, Bap60, Snr1 and E(y)3, were required in the MB for both short- and long-term memory. In contrast, Osa knockdown only reduced long-term memory. Our results suggest that individual components of the SWI/SNF complex have different roles in the regulation of structural plasticity, survival and functionality of post-mitotic MB neurons. This study highlights the many possible processes that might be disrupted in SWI/SNF-related ID disorders. Our broad phenotypic characterization provides a starting point for understanding SWI/SNF-mediated gene regulatory mechanisms that are important for development and function of post-mitotic neurons. Summary: The SWI/SNF chromatin remodelling complex is the most over-represented protein complex in the intellectual disability. Different components of this complex have distinct roles in development and function of memory-forming neurons in the Drosophila mushroom body.
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Affiliation(s)
- Melissa C Chubak
- Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada
| | - Kevin C J Nixon
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Max H Stone
- Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada.,Division of Genetics and Development, Children's Health Research Institute, London, ON N6C 2V5, Canada
| | - Nicholas Raun
- Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada.,Division of Genetics and Development, Children's Health Research Institute, London, ON N6C 2V5, Canada
| | - Shelby L Rice
- Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada
| | - Mohammed Sarikahya
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Spencer G Jones
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Taylor A Lyons
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Taryn E Jakub
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Roslyn L M Mainland
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Maria J Knip
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Tara N Edwards
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Jamie M Kramer
- Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada .,Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada.,Division of Genetics and Development, Children's Health Research Institute, London, ON N6C 2V5, Canada
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20
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Shih MFM, Davis FP, Henry GL, Dubnau J. Nuclear Transcriptomes of the Seven Neuronal Cell Types That Constitute the Drosophila Mushroom Bodies. G3 (BETHESDA, MD.) 2019; 9:81-94. [PMID: 30397017 PMCID: PMC6325895 DOI: 10.1534/g3.118.200726] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/02/2018] [Indexed: 11/18/2022]
Abstract
The insect mushroom body (MB) is a conserved brain structure that plays key roles in a diverse array of behaviors. The Drosophila melanogaster MB is the primary invertebrate model of neural circuits related to memory formation and storage, and its development, morphology, wiring, and function has been extensively studied. MBs consist of intrinsic Kenyon Cells that are divided into three major neuron classes (γ, α'/β' and α/β) and 7 cell subtypes (γd, γm, α'/β'ap, α'/β'm, α/βp, α/βs and α/βc) based on their birth order, morphology, and connectivity. These subtypes play distinct roles in memory processing, however the underlying transcriptional differences are unknown. Here, we used RNA sequencing (RNA-seq) to profile the nuclear transcriptomes of each MB neuronal cell subtypes. We identified 350 MB class- or subtype-specific genes, including the widely used α/β class marker Fas2 and the α'/β' class marker trio Immunostaining corroborates the RNA-seq measurements at the protein level for several cases. Importantly, our data provide a full accounting of the neurotransmitter receptors, transporters, neurotransmitter biosynthetic enzymes, neuropeptides, and neuropeptide receptors expressed within each of these cell types. This high-quality, cell type-level transcriptome catalog for the Drosophila MB provides a valuable resource for the fly neuroscience community.
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Affiliation(s)
| | - Fred Pejman Davis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA; National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD
| | - Gilbert Lee Henry
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Josh Dubnau
- Department of Anesthesiology, Stony Brook School of Medicine; Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY
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