Drosophila melanogaster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA397882 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5925370.fastq.gz | Fastqsanger.gz | |||
| SRR5925380.fastq.gz | Fastqsanger.gz | |||
| SRR5925390.fastq.gz | Fastqsanger.gz | |||
| SRR5925400.fastq.gz | Fastqsanger.gz | |||
| SRR5925371.fastq.gz | Fastqsanger.gz |
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Project description:Circadian clocks coordinate time-of-day specific metabolic and physiological processes to maximize performance and fitness. In addition to light, which is considered the strongest time cue to entrain animal circadian clocks, metabolic input has emerged as an important signal for clock modulation and entrainment, especially in peripheral clocks. Circadian clock proteins have been to be substrates of O-GlcNAcylation, a nutrient sensitive post-translational modification (PTM), and the interplay between clock protein O-GlcNAcylation and other PTMs, like phosphorylation, is expected to facilitate the regulation of circadian physiology by metabolic signals. Here, we used mass spectrometry proteomics to identify PTMs on PERIOD, the key biochemical timer of the Drosophila clock, over the circadian cycle.
2017-11-23 | MSV000081736 | MassIVE
Project description:Circadian rhythms are daily oscillations in metabolism and physiology and are generated by the circadian clock. In fruit fly Drosophila, the circadian clock is generated by a transcription-translation feedback loop in which the positive arm components Clock and Cycle activate the expression of the Period and Timeless genes of negative arm, as well as other circadian clock-regulated genes. After being retained in the cytoplasm, the Period and Timeless proteins then migrate to the nucleus to inhibit the Clock/Cycle transactivity by protein-protein interactions (PPIs). The endogenous circadian clock is synchronized with the geological (solar) clock via photoreceptors. Drosophila Cryptochrome protein functions as a circadian photoreceptor. In the early morning, exposure of Cryptochrome to light causes a conformational change in it which results in the formation of new PPIs. Light-activated Cryptochrome interacts with the core clock protein Timeless and the E3 ubiquitin ligase-substrate adaptor protein Jetlag, which results in the ubiquitylation of Timeless by Jetlag-E3 ligase complex and then degradation of Timeless within minutes by proteasome system. Rapid degradation of Timeless and then its partner protein Period, because of its instability in the absence of Timeless, relieves the inhibition on the Clock/Cycle transcription factors suddenly. Therefore, Clock/Cycle-driven expression of circadian clock-regulated genes are induced again, which is the restart of the circadian oscillation or the resetting of the clock. Following Timeless degradation, Cryptochrome is also degraded so the photoreceptor mechanism does not start a new resetting signal until all the required factors are re-synthesized in a circadian manner. Light-dependent degradation of Drosophila Cryptochrome can be observed in Drosophila S2 cell line in culture. In this project, we aimed at finding the interactome of Cryptochrome protein in Drosophila S2 cell line under light and in the dark using proximity labeling method. Because of the fast kinetics of Cryptochrome degradation, we chose the enzymes that can saturate in less than one hour. TurboID (TID) and APEX2 enzymes label proteins with biotin in the proximity even though they work with different mechanisms. They were fused to Cryptochrome protein, and proximity labeling was performed in the dark or under light. We have identified novel light-dependent or -independent interactors of Drosophila Cryptochrome and confirmed some of them using classical coimmunoprecipitation technique.
2024-02-05 | PXD038052 | Pride
Project description:We report a large-scale transcriptomic analysis of several tissues of a reference Drosophila melanogaster strain as well as 141 Drosophila Genetic Reference Panel (DGRP) lines at high temporal resolution. Comprehensive data analysis has identified thousands of genes under clock- and tissue-specific control. By using a molecular time table approach, we uncovered that >20% of probed DGRP lines exhibit aberrant circadian expression, and the genetic dissection of one line (DGRP-796) revelled disrupted circadian gene expression in all analysed tissues, revealing a novel deletion in the cry gene. Together, this study revealed extensive variation in tissue-specific circadian expression, which acts upon tissue-specific regulatory networks to generate local oscillations in gene expression. Moreover, the many other lines identified here can be now used to better understand the mechanisms underlying the molecular clock, from tissue-specific to more central mechanisms.
2020-12-10 | GSE126018 | GEO
Project description:Circadian rhythms are cell-autonomous biological oscillations with a period of about 24 hours. Current models propose that transcriptional feedback loops are the principal mechanism for the generation of circadian oscillations. In these models, Drosophila S2 cells are generally regarded as ‘non-rhythmic’ cells, as they do not express several canonical circadian components. Using an unbiased multi-omics approach, we made the surprising discovery that Drosophila S2 cells do in fact display widespread daily rhythms. Transcriptomics and proteomics analyses revealed that hundreds of genes and their products are rhythmically expressed in a 24-hour cycle. Metabolomics analyses extended these findings and illustrated that central carbon metabolism and amino acid metabolism are the main pathways regulated in a rhythmic fashion. We thus demonstrate that daily genome-wide oscillations, coupled to metabolic cycles, take place in eukaryotic cells without the contribution of known circadian regulators.
2018-07-31 | PXD007669 | Pride
Project description:Background. The transcriptional circuits of circadian clocks control physiological and behavioral rhythms. Light may affect such overt rhythms in two ways: (1) by entraining the clock circuits and (2) via clock-independent molecular pathways. In this study we examine the relationship between autonomous transcript oscillations and light-driven transcript responses Methodology/Principal Findings. Transcript profiles of wild-type and arrhythmic mutant Drosophila were recorded both in the presence of an environmental photocycle and in constant darkness. Systematic autonomous oscillations in the 12-48 hr period range were detectable only in wild-type flies and occurred preferentially at the circadian period length. However, an extensive program of light-driven expression was confirmed in arrhythmic mutant flies. Many lightresponsive transcripts are preferentially expressed in the adult compound eye and the phospholipase C component of phototransduction, NO RECEPTOR POTENTIAL (NORPA), is required for their light-dependent regulation. Conclusions/Significance. Although there is growing evidence for the existence of multiple molecular clock circuits in plants and fungi, Drosophila appears to possess only one such system. The sustained photic expression responses identified here are partially coupled to the circadian clock and may reflect a mechanism for flies to modulate functions such as visual sensitivity and synaptic transmission in response to seasonal changes in photoperiod. Keywords: Time course
2006-02-03 | GSE3831 | GEO
Project description:Background. The transcriptional circuits of circadian clocks control physiological and behavioral rhythms. Light may affect such overt rhythms in two ways: (1) by entraining the clock circuits and (2) via clock-independent molecular pathways. In this study we examine the relationship between autonomous transcript oscillations and light-driven transcript responses Methodology/Principal Findings. Transcript profiles of wild-type and arrhythmic mutant Drosophila were recorded both in the presence of an environmental photocycle and in constant darkness. Systematic autonomous oscillations in the 12-48 hr period range were detectable only in wild-type flies and occurred preferentially at the circadian period length. However, an extensive program of light-driven expression was confirmed in arrhythmic mutant flies. Many lightresponsive transcripts are preferentially expressed in the adult compound eye and the phospholipase C component of phototransduction, NO RECEPTOR POTENTIAL (NORPA), is required for their light-dependent regulation. Conclusions/Significance. Although there is growing evidence for the existence of multiple molecular clock circuits in plants and fungi, Drosophila appears to possess only one such system. The sustained photic expression responses identified here are partially coupled to the circadian clock and may reflect a mechanism for flies to modulate functions such as visual sensitivity and synaptic transmission in response to seasonal changes in photoperiod. Keywords: Time course
2006-02-03 | GSE3832 | GEO
Project description:Background. The transcriptional circuits of circadian clocks control physiological and behavioral rhythms. Light may affect such overt rhythms in two ways: (1) by entraining the clock circuits and (2) via clock-independent molecular pathways. In this study we examine the relationship between autonomous transcript oscillations and light-driven transcript responses Methodology/Principal Findings. Transcript profiles of wild-type and arrhythmic mutant Drosophila were recorded both in the presence of an environmental photocycle and in constant darkness. Systematic autonomous oscillations in the 12-48 hr period range were detectable only in wild-type flies and occurred preferentially at the circadian period length. However, an extensive program of light-driven expression was confirmed in arrhythmic mutant flies. Many lightresponsive transcripts are preferentially expressed in the adult compound eye and the phospholipase C component of phototransduction, NO RECEPTOR POTENTIAL (NORPA), is required for their light-dependent regulation. Conclusions/Significance. Although there is growing evidence for the existence of multiple molecular clock circuits in plants and fungi, Drosophila appears to possess only one such system. The sustained photic expression responses identified here are partially coupled to the circadian clock and may reflect a mechanism for flies to modulate functions such as visual sensitivity and synaptic transmission in response to seasonal changes in photoperiod. For more information see also http://biorhythm.rockefeller.edu. Keywords: Time course
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Project description:Circadian expression profiling of purified clock neurons in adult Drosophila
| PRJNA127387 | ENA
Project description:Mechanisms composing Drosophila's clock are conserved within the animal kingdom. To learn how such clocks influence behavioral and physiological rhythms, we determined the complement of circadian transcripts in adult Drosophila heads. High-density oligonucleotide arrays were used to collect data in the form of three 12-point time course experiments spanning a total of 6 days. Analyses of 24 hr Fourier components of the expression patterns revealed significant oscillations for 400 transcripts. Based on secondary filters and experimental verifications, a subset of 158 genes showed particularly robust cycling and many oscillatory phases. Circadian expression was associated with genes involved in diverse biological processes, including learning and memory/synapse function, vision, olfaction, locomotion, detoxification, and areas of metabolism. Data collected from three different clock mutants (per0, tim01, and ClkJrk), are consistent with both known and novel regulatory mechanisms controlling circadian transcription (Claridge-Chang et al., Neuron. 2001 Nov 20;32(4):657-71). For more information see also http://biorhythm.rockefeller.edu Keywords: Time course
2006-02-03 | GSE3829 | GEO
Project description:Eukaryotic circadian clocks include transcriptional/translational feedback loops that drive 24-hour rhythms of transcription.These transcriptional rhythms underlie oscillations of protein abundance, thereby mediating circadian rhythms of behavior, physiology, and metabolism. Numerous studies over the last decade have employed microarrays to profile circadian transcriptional rhythms in various organisms and tissues. Here we use RNA sequencing (RNA-Seq) to profile the circadian transcriptome of *Drosophila melanogaster* brain from wild-type and *period*-null clock-defective animals. We identify several hundred transcripts whose abundance oscillates with 24-hour periods, including a number of non-coding RNAs (ncRNAs) that were not identified in previous microarray studies. Of particular interest are *U snoRNA host genes* (*Uhgs*), a family of cycling ncRNAs that encode the precursors of over 50 box C/D snoRNAs, key regulators of ribosomal biogenesis. Transcriptional profiling at the level of individual exons reveals alternative splice isoforms for many genes whose relative abundances are regulated by either *period* or circadian time, although the effect of circadian time is muted in comparison to that of *period*. Interestingly, *period* loss-of-function significantly alters the frequency of RNA editing at a number of editing sites, suggesting an unexpected link between a key circadian gene and RNA editing. We also identify tens of thousands of novel splicing events beyond those previously annotated by the modENCODE consortium, including several that affect key circadian genes. These studies demonstrate extensive circadian control of ncRNA expression, reveal the extent of clock control of alternative splicing and RNA editing, and provide a novel, genome-wide map of splicing in *Drosophila* brain. RNA-Seq transcriptional profiling of Drosophila brains from wildtype and period loss-of-function (per0) flies with time points taken over two days in constant darkness. Time points at CT24, 28, 32, 36, 40, 44, 48, 52, 56, 60, 64, and 68. 10-12 brains per time point.
2012-03-27 | E-GEOD-36108 | biostudies-arrayexpress