A memory transcriptome time course reveals essential long-term memory transcription factors in Drosophila [RNA-Seq]
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ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE282412 | GEO | 2025/08/14
REPOSITORIES: GEO
Similar Datasets
Project description:We have analyzed transcript level changes in nuclei isolated from the adult mushroom body (MB) of Drosophila melanogaster, as well from whole-head (WH) nuclear extracts. MB and WH nuclei were isolated at five time-points across a 24-hour period.
2025-07-31 | GSE274348 | GEO
Project description:Purpose: The formation and recall of long term memory (LTM) requires neuron activity induced gene expression. Transcriptome analysis has been used to identify genes that have altered expression after memory acquisition, however, we still have an incomplete picture of the transcriptional changes that are required for LTM formation. The complex spatial and temporal dynamics of memory formation creates significant challenges in defining memory-relevant gene expression changes. The mushroom body (MB) is a signaling hub in the insect brain that integrates sensory information to form memories. Our study looks to further elucidate the transcriptional mechanisms underlying LTM by profiling gene expression changes in nuclei of the MB during a time course of LTM formation. Methods: We isolated and sequenced fly RNA from biologically paired whole head (WH) and mushroom body (MB) nuclei. MB nuclei were isolated using INTACT (isolation of nuclei tagged in a specific cell type). LTM was induced using a seven-hour courtship conditioning protocol. Fly heads were collected one hour and 24-hours after this period of sexual rejection. Samples of naive, socially isolated males were also collected at the same age and time-of-day for comparison. Results and conclusions: We identified more transcriptional changes 1 hour after memory acquisition (WH = 322, MB = 305) than at 24 hours (WH = 20, MB = 24). WH samples showed downregulation of developmental genes and upregulation of sensory response genes. In contrast, MB samples showed vastly different gene expression changes affecting biological processes that are specifically related to LTM. MB-downregulated genes were highly enriched for metabolic function, consistent with the MB-specific energy influx that occurs during LTM formation. MB-upregulated genes were highly enriched for known learning and memory processes, including calcium mediated neurotransmitter release and cAMP signalling. The neuron activity inducible genes hr38 and sr were also specifically induced in the MB. These results highlight the importance of sampling time and cell type in capturing biologically relevant transcriptional changes involved in learning and memory. Our data suggests that MB cells transiently upregulate known memory related pathways after memory acquisition, and provides a critical frame of reference for further investigation into the role MB-specific gene regulation in memory.
2018-09-17 | GSE115718 | GEO
Project description:We have analyzed regions of accessible chromatin in adult mushroom body neurons of Drosophila melanogaster of a control genetic background using ATAC-seq.
2025-08-14 | GSE282413 | GEO
Project description:Disruption of learning and memory can occur for a number of reasons including chronic alcohol abuse, head injury, anoxia, and various neurodegenerative disorders such as Alzheimer's disease. An understanding of the basic mechanisms underlying learning and memory is essential for prevention and treatment of such brain disorders. Recent studies unequivocally demonstrated the astonishing similarities in the basic mechanisms of learning and memory between divergent species, indicating that studies of experimentally tractable model organisms with relatively simpler nervous systems are likely to produce valuable information that will facilitate our understanding of learning and memory in higher organisms. We are studying the experience-dependent modification in Drosophila male courtship as a physiologically relevant model of learning and memory. The genome-scale gene-profiling analysis in this model system should provide us the basic information about learning-induced changes in gene expression, which will be the foundation of our future studies to identify genes and genetic pathways specifically involved in the formation of long-term memory. The proposed gene-profiling experiment is designed to identify candidate genes and genetic pathways involved in the formation of long-term memory in the Drosophila courtship conditioning. The specific aims of this project are to: 1) compare gene expression profiles between the naive and trained wild type males using the GeneChip Drosophila Genome 2.0 Arrays and identify genes that are up- or down-regulated in the fly head immediately or 24-hr after the male fly is exposed to the condition where the long-term courtship memory is established (i.e., paired with a mated female for 7 hrs), 2) carry out the same analysis for the per null mutant males, 3) compare the identified genes between the 0 and 24-hr after training as well as the wild type and per mutant males, 4) identify candidate genes which might be involved in the long-term memory formation either upstream or downstream of per, 5) classify the candidate genes according to their putative cellular function and discern the possible genetic pathways necessary for the long-term memory formation. When a male fly is presented with a previously mated female, he will initially court her vigorously but his courtship activity is reduced over time. Subsequently, when paired with a virgin female, the male will display a reduced amount of courtship compared with naïve males with no prior courtship experience. This modification of courtship is called âcourtship conditioningâ. We found that this type of courtship memory lasts at least 5 days when a male is trained with a mated female for 7 hrs. We have also found that the period gene (per) that is involved in circadian rhythm regulation plays a critical role in the formation of long-term, but not short-term, courtship memory. Our hypotheses are 1) the long-lasting memory in 7 h-trained males is accompanied with characteristic temporal changes in gene expression in the brain, 2) per mutant males are defective in regulation of critical genes involved in long-term courtship memory, 3) the memoryârelated changes in gene expression can be detected by comparing total head transcript levels between trained and naïve as well as the wild type and the per mutant males using the Affymetrix microarray. Two fly strains, a wild type Oregon R (OR) and a null mutant allele of per (per01) with the OR background for the second and third chromosomes, will be used. Virgin males and females will be collected without anesthesia within 6 hrs after eclosion and maintained individually in vials until experiments. Mated wild type females will be prepared by crossing to the wild type males the night before they are used for conditioning males. All flies will be raised at 25oC in a 12 h light/12 h dark cycle and the following behavioral experiments will be carried out during daytime. For courtship conditioning, a 3 day-old virgin male (either OR or per01) will be placed with a mated OR female in a conditioning chamber (15 mm x 5 mm in depth) containing fly food. As a control, a virgin male will be introduced into another conditioning chamber without a mated female. Seven hours after the male is introduced into the chamber, he will be anesthetized under CO2 gas or transferred to a new vial. For the anesthetized male, the head will be immediately excised and frozen with liquid nitrogen. The male fly transferred to a new vial will be decapitated 24 hrs after the end of the 7-hr training. Approximately thirty fly heads will be pooled for each of the 8-genotype/treatment groups, i.e., Oregon R 0-hr and 24-hr after conditioning, per01 0-hr and 24-hr after conditioning, in addition to the corresponding four naïve controls. Total RNA will be extracted from the pooled heads using the TRIzol Reagent (Life Technologies) followed by an RNeasy (Qiagen) cleanup step and a DNAase I digestion step. After purification, the RNA will be resuspended in DEPC water and the absorbance will be checked at 260 and 280 nm for determination of sample purity and concentration. The GeneChip Drosophila Genome 2.0 Arrays will be used to quantify the levels of transcripts in each sample.
2008-03-13 | E-GEOD-4032 | biostudies-arrayexpress
Project description:Mushroom bodies (MBs) are the centers for olfactory associative learning and elementary cognitive functions in the Drosophila brain. To get insights of the repertoire of MB genes that control initiation and maintenance of neural differentiation as well as the repertoire of neural factors that may have functions in the synaptic plasticity of MB neurons during learning and memory, we compared the transcript profiles between wild type and MB-ablated brains using a Drosophila whole-genome microarray. Newly hatched larvae were briefly administered with a DNA-synthesis inhibitor, hydroxyurea, and raised to adults, from which total brain RNA was analyzed. Experiment Overall Design: Two conditions analyzed: Control Brains and Musroom Body-ablated brains. Experiment Overall Design: Each condition was analyzed in triplicate.
2007-11-01 | E-GEOD-3379 | biostudies-arrayexpress
Project description:Purpose: The goal of this study was to globally characterize the transcript levels of genes in Drosophila photoreceptor neurons. Using transcriptome profiling of isolated photoreceptor nuclei from day 10 flies, we identified genes with enriched or reduced transcript levels post nuclei isolation relative to the starting pre-isolation material (whole head RNA extracts).
2017-11-10 | GSE93128 | GEO
Project description:Utilizing a single nuclei multiomics approach, this study elucidates how enhancing histone lysine crotonylation regulates cell type specific gene expression and chromatin accessibility during memory consolidation.
2024-11-13 | GSE281007 | GEO
Project description:Lasting 24hr transcriptomic response of adult Drosophila mushroom body nuclei following odors only (odors) or odors+ethanol (trained) treatment.
2018-10-25 | GSE108525 | GEO
Project description:We performed mRNA-seq of dissected Drosophila mushroom bodies, comparing to whole brain and testis mRNA seq of MB, brain and testis
2012-02-01 | E-GEOD-33783 | biostudies-arrayexpress
Project description:Drosophila mushroom body (MB) γ neurons undergo axon pruning during metamorphosis through a process of localized degeneration of specific axon branches. Developmental axon degeneration is initiated at the onset of metamorphosis by the pre-pupal rise in the steroid hormone ecdysone. This study identifies genes that alter their expression in MB neurons at the onset and early steps of axon pruning. Experiment Overall Design: y,w animals were staged at -18, 0 and 5 hours relative to puparium formation. RNA was isolated from MB neurons labeled with mCD8::GFP driven by OK107-GAL4 by laser capture microdissection, labeled and hybridized to Affymetrix Drosophila Genome Arrays.
2008-06-18 | E-GEOD-10012 | biostudies-arrayexpress