Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Circadian rhythms in mouse choroid plexus identified by time-resolved RNAseq require clock in the suprachiasmatic nucleus

ABSTRACT: The aim of our study was to investigate the circadian regulation of cellular processes in mouse choroid plexus (ChP) and to determine their dependence on signals from the clock in the suprachiasmatic nuclei (SCN). We performed time-resolved transcriptomics of ChP samples from C57Bl6J mice with intact (Ctrl) or surgically removed SCN (SCNx) collected every 4 h over 2 days in constant darkness and from FoxJ1-ERT2-Cre+/-; Bmal1fl/fl mice with ChP-specific clock disruption (Bmal1-KO) collected at 2 time points. We found widespread circadian gene expression in Ctrl mice that was not present in SCNx mice, and the SCNx day/night ratios were reduced similarly to Bmal1-KO.

ORGANISM(S): Mus musculus

PROVIDER: GSE243858 | GEO | 2023/09/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Circadian transcriptome of fast tibialis anterior (TA) and slow soleus (SOL) skeletal muscles from muscle-specific Bmal1 KO and control Cre- littermates

2014-01-01 | GSE43071 | GEO

Timed Exercise and Clocks: Does a Minimally Functional Suprachiasmatic Clock Support 24h Behavioral Rhythms?

Project description:The brain’s suprachiasmatic nucleus (SCN) is the master clock driving circadian rhythms in mammals. Vasoactive intestinal polypeptide (VIP) and its cognate receptor, VPAC2, are expressed in SCN neurons and mice with genetically targeted deletion of VPAC2 (Vipr2 -/-animals) show aberrant resetting to light, abnormal behavioral rhythms, and diminished SCN clock gene expression. Timed daily access to a running-wheel (scheduled voluntary exercise; SVE) promotes Vipr2 -/- SCN clock cell synchrony and 24h behavioral rhythms. We hypothesized that timed exercise alters the SCN transcriptome. Here, in control (Vipr2+/+) and Vipr2-/- mice under freely exercising and SVE conditions, RNAseq and qRT-PCR were used to measured gene expression of laser-dissected SCN. Compared to Vipr2+/+ mice, hundreds of genes were differentially expressed in the SCN from Vipr2-/- mice rhythmic in the freely exercising condition. Unexpectedly, SVE did not promote a Vipr2+/+-like SCN transcriptome in Vipr2-/- mice and many transcripts involved in SCN function including Avp, C1ql3, Gpr176, Prok2, Sst, Per2, and Nr1d1 remained dysregulated in the SVE condition. By contrast, circadian oscillators in the liver and lung were mostly intact in Vipr2-/- mice. This study indicates that marked molecular deficits in the SCN are sustained in behaviorally rhythmic Vipr2-/- mice, raising the possibility that a minimal functional SCN circadian clock can underpin whole animal rhythms.

2023-01-20 | GSE207992 | GEO

Circadian transcriptome of fast tibialis anterior (TA) and slow soleus (SOL) skeletal muscles from muscle-specific Bmal1 KO and control Cre- littermates

Project description:To investigate the role of the circadian clock gene Bmal1 in skeletal muscle, we compared the circadian transcriptomes of fast tibialis anterior (TA) and slow soleus (SOL) skeletal muscles from muscle-specific Bmal1 KO (mKO) and their control Cre- littermates (Ctrl). Keyword: Circadian Transcriptome, time course 72 samples were analyzed, comprised of 4 experimental groups (Ctrl SOL, mKO SOL, Ctrl TA, mKO TA), with 3 biological replicates for each time point sampled every 4 hours for 24 hours. SOL and TA muscles were collected from the same animals, as indicated by Source Animal ID data column

2014-01-01 | E-GEOD-43071 | biostudies-arrayexpress

Comprehensive and cell-type-based analysis of microRNA profiles and functions in mouse suprachiasmatic nucleus

Project description:Circadian rhythm governs a variety of biological processes in essentially all living organisms and microRNAs have been found to play important roles in the post-transcriptional regulation of circadian clocks. However, the microRNA expression profile in mouse central circadian clock – suprachiasmatic nucleus (SCN) is lacking. In this study, we systematically profiled microRNAs in mouse SCN and SCN subtype neurons by high sensitive small RNA sequencing and examined their potential circadian functions. We found that a large fraction of known microRNAs are SCN-specific and 20 of them are also oscillated significantly. Predicted targets of these 20 microRNAs were enriched in circadian rhythm pathway as well. Integrated analysis of microRNA and mRNA revealed 3 clock-related functional modules, demonstrating the regulation roles of miR-24, miR-30, miR-7a, miR-7b, miR125a and miR125b in SCN. Furthermore, we observed distinct microRNA profiles in SCN subtype neurons with divergent regulatory functions, which correlated with their differential spatial distribution. In addition, we also identified a proportion of light-response microRNAs in SCN, one of which was miR-7a. Further experiments showed that miR-7a directly target fos and regulated its translation in SCN. All these observations indicate important circadian regulation roles of microRNA in central circadian clock.

2021-08-18 | GSE133051 | GEO

Transcriptome profiling of circadian day and night gene expression in the suprachiasmatic nucleus of hypophysectomized (HPX) and control (non-HPX) mice

Project description:HPX mice show enhanced re-entrainment after jet lag; it isimportant to investigate whether HPX affects gene expression in the SCN, the center of the circadian clock. We used microarrays to study the effects of HPX on gene expression in the SCN.

2023-10-16 | GSE226929 | GEO

REV-ERB nuclear receptors in the suprachiasmatic nucleus control circadian period and restrict diet-induced obesity

Project description:Circadian disruption, as shift work, is associated with metabolic diseases, including obesity and fatty liver, often attributed to discordance between internal clocks and environmental timekeepers1-5. However, this desynchrony hypothesis has not been rigorously tested. The body’s master clock, located in the suprachiasmatic nucleus (SCN), synchronizes peripheral clocks and ultimately metabolism2,6. Molecular clocks are comprised of transcriptional translational feedback loops involving gene activation by BMAL1, which is rhythmically repressed by separate mechanisms involving PER/CRY and REV-ERB nuclear receptors. Mice harboring whole body deletion of REV-ERBa/b have been reported to be arrhythmic7. However, we report here that mice lacking REV-ERBs specifically in the SCN maintain free-running and metabolic rhythms, but these are strikingly shortened by nearly 3 hours. When housed under a 24 hours light-dark cycle and fed an obesogenic diet, these mice gained excess weight and accrued more liver fat than controls. Remarkably, these metabolic disturbances were corrected by matching environmental lighting to the shortened endogenous clock period. Thus, SCN REV-ERBs are not required to maintain rhythmicity but powerfully control the free-running period. Moreover, these results support the hypothesis that dissonance between environmental conditions and endogenous period causes metabolic disruption. This has important implications for chronotherapy of metabolic and behavioral disorders.

2021-07-15 | GSE152919 | GEO

Mouse SCN in LC-MSMS - The suprachiasmatic nucleus (SCN) acts as the central clock to coordinate circadian oscillations in mammalian behavior, physiology and gene expression. Despite our knowledge of the circadian transcriptome of the SCN, how it impacts genome-wide protein expression is not well understood. Here, we interrogated the murine SCN proteome across the circadian cycle using SILAC-based quantitative mass spectrometry.

Project description:The suprachiasmatic nucleus (SCN) acts as the central clock to coordinate circadian oscillations in mammalian behavior, physiology and gene expression. Despite our knowledge of the circadian transcriptome of the SCN, how it impacts genome-wide protein expression is not well understood. Here, we interrogated the murine SCN proteome across the circadian cycle using SILAC-based quantitative mass spectrometry.

2014-09-10 | PXD000778 | Pride

Expression data in inguinal adipose tissue at different circadian times

Project description:Peripheral circadian clocks regulate many aspects of physiology. In this study we deleted the core circadian clock component Bmal1 specifically in mouse adipocytes in order to study the role of the adipocyte clock in energy homeostasis and body weight. We used microarrays to indentify changes in gene expression in the adipose tissue of mice lacking a functional adipocyte circadian clock and identified a small number of up- and down- regulated genes. Adipose tissues were isolated from inguinal adipose fat pads at four different times of the diurnal cycle under constant darkness (circadian time, CT) for RNA extraction and hybridization on Affymetrix microarrays. Adipocyte-specific Bmal1 KO (Ad-Bmal1-/-) and control mice were used for isolation of tissues at CT0, CT6, CT12, CT18 where CT0 the beginning of the subjective day.

2012-10-21 | E-GEOD-35026 | biostudies-arrayexpress

Defining the Independence of the Liver Circadian Clock

Project description:Mammals rely on a network of circadian clocks to control daily systemic metabolism and physiology. The central pacemaker in the suprachiasmatic nucleus (SCN) is considered hierarchically dominant over peripheral clocks, whose degree of independence, or tissue-level autonomy, has never been ascertained in vivo. Using arrhythmic Bmal1-null mice, we generated animals with reconstituted circadian expression of BMAL1 exclusively in the liver (Liver-RE). High-throughput transcriptomics and metabolomics show that the liver has independent circadian functions specific for metabolic processes such as the NAD+ salvage pathway and glycogen turnover. However, although BMAL1 occupies chromatin at most genomic targets in Liver-RE mice, circadian expression is restricted to ∼10% of normally rhythmic transcripts. Finally, rhythmic clock gene expression is lost in Liver-RE mice under constant darkness. Hence, full circadian function in the liver depends on signals emanating from other clocks, and light contributes to tissue-autonomous clock function.

2019-06-13 | GSE132659 | GEO

RNA-seq of neuronal SOX2-ablated murine suprachiasmatic nuclei against wild-type littermate controls

Project description:Mice lacking the stem/progenitor cell transcription factor, Sex determining region Y-box 2 (SOX2), in neurons of the suprachiasmatic nuclei display imprecise, poorly consolidated behavioral rhythms that do not entrain efficiently to environmental light cycles. RNA sequencing revealed that Sox2 deficiency alters the circadian transcriptome of the SCN, reducing the expression of many core clock genes and neuropeptide-receptor systems.

2019-03-18 | E-MTAB-7496 | biostudies-arrayexpress

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