Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Circadian rhythms of ribosome binding for Drosophila astrocyte RNAs

ABSTRACT: Circadian rhythms of ribosome binding for Drosophila astrocyte RNAs

PROVIDER: PRJNA759883 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR15702126.fastq.gz	Fastqsanger.gz
	SRR15702127.fastq.gz	Fastqsanger.gz
	SRR15702128.fastq.gz	Fastqsanger.gz
	SRR15702129.fastq.gz	Fastqsanger.gz
	SRR15702130.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 48

Similar Datasets

Circadian rhythms of ribosome binding for Drosophila astrocyte RNAs

Project description:Raw RNAseq data (fastq) files that were analyzed for circadian changes in RNA ribosome binding. The numbers in the file names (00 - 44) represent circadian time (0 to 44 hours in constant dark and constant temperature). Two separate sets of samples (independent biological replicates) were collected over a 44-hour period of time.

2021-09-06 | GSE183282 | GEO

"Cancersensor": Circadian Rhythms

Project description:Observational, non randomized study aimed at measuring the circadian rhythms in the urinary concentrations of physiological modified nucleosides in 30 patients with metastatic colorectal cancer and in 30 age and sex-matched healthy subjects.

| 2132582 | ecrin-mdr-crc

Circadian clock control of ribosome composition promotes rhythmic translation and termination fidelity

Project description:We describe circadian clock-dependent changes in ribosome composition in Neurospora crassa depending on cell type, stress, or developmental state. Mass spectrometry of ribosomes isolated at different circadian times identified six ribosomal proteins and one ribosome-associated protein with clock-controlled abundance. We confirmed clock control of eL31-HA abundance in purified ribosomes and found that deletion of eL31 altered and inhibited translation rhythms. We examined ribosome protected footprint (RPF)-seq reads mapping past stop codons over circadian time to reveal clock-dependent and eL31-enhanced rhythms in translation termination fidelity. We discovered that eL31 promotes proper ion homeostasis and translation elongation fidelity, and demonstrated that the circadian clock governs daily changes in ribosome composition that control rhythms in translation and impact translation fidelity, likely through changes in intracellular Mg2+ levels.

2024-10-15 | MSV000096101 | MassIVE

Circadian clock control of ribosome composition promotes rhythmic translation and termination fidelity [Ribo-Seq]

Project description:Ribosome composition can vary depending on cell type, stress or developmental state. Here we describe circadian clock-dependent changes in ribosome composition in Neurospora crassa. Mass spectrometry of ribosomes isolated at different circadian times identified six ribosomal proteins and one ribosome-associated protein with clock-controlled abundance. We confirmed clock control of eL31-HA abundance in purified ribosomes and found that deletion of eL31 altered translation of many mRNAs and inhibited translation rhythms for 42% of rhythmically translated mRNAs. Because eL31 homologs promote translation termination fidelity, we examined ribosome protected footprint (RPF)-seq reads mapping past stop codons over circadian time to reveal clock-dependent and eL31-enhanced rhythms in translation termination fidelity. We further discovered that eL31 promotes proper ion homeostasis and translation elongation fidelity. Taken together these studies demonstrated that the circadian clock governs daily changes in ribosome composition that control rhythms in translation and impact translation fidelity, likely through changes in intracellular Mg2+ levels.

2025-10-26 | GSE282318 | GEO

Circadian clock control of ribosome composition promotes rhythmic translation and termination fidelity [RNA-Seq]

2025-10-26 | GSE282317 | GEO

Circadian rhythms in plant roots

Project description:Circadian rhythms in plant roots

| PRJEB5695 | ENA

Dietary tryptophan and circadian rhythms

Project description:Dietary tryptophan and circadian rhythms

| PRJNA773065 | ENA

Maternal Circadian Rhythms during Pregnancy Dictate Metabolic Plasticity in Offspring

Project description:The circadian gene expression in peripheral tissue displays rhythmicity which is reprogrammed by feeding rhythms and dietary composition in mammals. In this study, circadian transcriptome was performed to investigate how maternal circadian rhythms during pregnancy influences circadian gene regulation in the mouse liver.

2025-01-15 | GSE236201 | GEO

Circadian ribosome profiling reveals a role for the Period2 upstream opening reading frame in sleep.

Project description:Many mammalian proteins have circadian cycles of production and degradation, and many of these rhythms are altered post-transcriptionally. We used ribosome profiling to examine post-transcriptional control of circadian rhythms by quantifying RNA translation in the liver over a 24-h period from circadian-entrained mice transferred to constant darkness conditions and by comparing ribosome binding levels to protein levels for 16 circadian proteins. We observed large differences in ribosome binding levels compared to protein levels, and we observed delays between peak ribosome binding and peak protein abundance. We found extensive binding of ribosomes to upstream open reading frames (uORFs) in circadian mRNAs, including the core clock gene Period2 (Per2). An increase in the number of uORFs in the 5'UTR was associated with a decrease in ribosome binding in the main coding sequence and a reduction in expression of synthetic reporter constructs. Mutation of the Per2 uORF increased luciferase and fluorescence reporter expression in 3T3 cells without altering the phase or period and increased luciferase expression in PER2:LUC MEF cells. Mutation of the Per2 uORF in mice increased PER2 protein levels and reduced total sleep time compared to that in wild-type mice. These results suggest that post-transcriptional processes shape translation of mRNA transcripts, which can impact physiological rhythms and sleep.

2023-09-13 | GSE231820 | GEO

Ribosome profiling reveals an important role for translational control in circadian gene expression

Project description:Physiological and behavioral circadian rhythms are driven by a conserved transcriptional/translational negative feedback loop in mammals. Although most core clock factors are transcription factors, post-transcriptional control introduces delays that are critical for circadian oscillations. Little work has been done on circadian regulation of translation, so to address this deficit we conducted ribosome profiling experiments in a human cell model for an autonomous clock. We found that most rhythmic gene expression occurs with little delay between transcription and translation, suggesting that the lag in the accumulation of some clock proteins relative to their mRNAs does not arise from regulated translation. Nevertheless, we found that translation occurs in a circadian fashion for many genes, sometimes imposing an additional level of control on rhythmically expressed mRNAs and, in other cases, conferring rhythms on non-cycling mRNAs. Most cyclically transcribed RNAs are translated at one of two major times in a 24h day, while rhythmic translation of most non-cyclic RNAs is phased to a single time of day. Unexpectedly, we found that the clock also regulates the formation of cytoplasmic processing (P) bodies, which control the fate of mRNAs, suggesting circadian coordination of mRNA metabolism and translation.

2015-08-19 | GSE56924 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data