Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CircRNA sequencing facilitates quantitative analysis of CUS mice hippocampus and Control mice hippocampus

ABSTRACT: The goal of this study is to seek the potential circular RNAs (circRNAs), which express differently between control group and chronic unpredictable stress (CUS) group mouse hippocampus, involved in major dipresssion disorder (MDD) by high-throughput sequencing. QPCR was preformed to identify the circRNAs trend. CircRNAs are a class of RNAs in the eukaryotic transcriptome. The function and explicit downstream mechanisms of circRNA regulated in maior depression disorser remain unclear. To further investigate the potential role of circRNAs in MDD, we performed human and mouse homology screening on circRNA sequences using the Basic Local Alignment Search Tool on the NCBI website. CircSTAG1, a homologous human and mouse circRNA, was found downregulated in circRNA high-throughput sequencing. Our study represents the first detailed analysis of circRNA expressing differently in CUS mouse hippocampus by high-throughput sequencing.

ORGANISM(S): Mus musculus

PROVIDER: GSE135343 | GEO | 2022/08/02

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed

Project description:Circular RNAs (circRNAs) are an endogenous class of animal RNAs. Despite their abundance, their function and expression in the nervous system are unknown. Therefore, we sequenced RNA from different brain regions, primary neurons, isolated synapses, as well as during neuronal differentiation. Using these and other available data, we discovered and analyzed thousands of neuronal human and mouse circRNAs. circRNAs were extraordinarily enriched in the mammalian brain, well conserved in sequence, often expressed as circRNAs in both human and mouse, and sometimes even detected in Drosophila brains. circRNAs were overall upregulated during neuronal differentiation, highly enriched in synapses, and often differentially expressed compared to their mRNA isoforms. circRNA expression correlated negatively with expression of the RNA-editing enzyme ADAR1. Knockdown of ADAR1 induced elevated circRNA expression. Together, we provide a circRNA brain expression atlas and evidence for important circRNA functions and values as biomarkers. To assess circRNA expression in mammalian brain, we sequenced and analyzed mouse brain regions (hippocampus, cerebellum, prefrontal cortex and olfactory bulb), various neuronal differentiation (mouse P19 and human SH-SY5Y cells) and maturation (mouse cortical neurons) stages, and subcellular compartments in mouse (synaptoneurosomal fraction, cytoplasmic fraction, whole brain lysate).

2015-04-24 | E-GEOD-65926 | biostudies-arrayexpress

Total RNA sequencing in the hippocampus of wild type and APP/PS1 mice

Project description:Our study aimed to dissect differentially expressed circRNAs in the hippocampus of wild type and APP/PS1 mice and demonstrated the important role of circRNA in Alzheimer's disease.

2020-10-05 | GSE158995 | GEO

Structured elements drive circular RNA translation and expand the human proteome, part3

Project description:The human genome encodes tens of thousands circular RNAs (circRNAs) whose levels correlate with many disease states. While studies have focused on the non-coding functions of circRNAs, emerging evidence suggests that a handful of circRNAs encode proteins. Translation canonically starts by recognition of mRNA 5â€™cap and scanning to the start codon; how circRNA translation initiates remains unclear. Here, we developed a high-throughput screen to systematically identify and quantify RNA sequences that can direct circRNA translation. We identify and validate over 17,000 circRNA internal ribosome entry sites (IRES) and reveal that 18S rRNA complementarity and a structured RNA element on the IRES are important for facilitating circRNA cap-independent translation. With genomic and peptidomic analyses of the IRES, we identified nearly 1,000 putative endogenous protein-coding circRNAs and hundreds of translational units encoded by these circRNAs. We further characterized circFGFR1p, a protein encoded by circFGFR1, functions as a negative regulator of FGFR1 to suppress cell growth under stress conditions. The circRNA proteome may be important links among circRNA, biological control, and disease.

2021-08-25 | PXD025233 | Pride

Structured elements drive circular RNA translation and expand the human proteome part2

Project description:The human genome encodes tens of thousands circular RNAs (circRNAs) whose levels correlate with many disease states. While studies have focused on the non-coding functions of circRNAs, emerging evidence suggests that a handful of circRNAs encode proteins. Translation canonically starts by recognition of mRNA 5’cap and scanning to the start codon; how circRNA translation initiates remains unclear. Here, we developed a high-throughput screen to systematically identify and quantify RNA sequences that can direct circRNA translation. We identify and validate over 17,000 circRNA internal ribosome entry sites (IRES) and reveal that 18S rRNA complementarity and a structured RNA element on the IRES are important for facilitating circRNA cap-independent translation. With genomic and peptidomic analyses of the IRES, we identified nearly 1,000 putative endogenous protein-coding circRNAs and hundreds of translational units encoded by these circRNAs. We further characterized circFGFR1p, a protein encoded by circFGFR1, functions as a negative regulator of FGFR1 to suppress cell growth under stress conditions. The circRNA proteome may be important links among circRNA, biological control, and disease.

2021-08-23 | PXD025235 | Pride

Structured elements drive circular RNA translation and expand the human proteome, part1

Project description:The human genome encodes tens of thousands circular RNAs (circRNAs) whose levels correlate with many disease states. While studies have focused on the non-coding functions of circRNAs, emerging evidence suggests that a handful of circRNAs encode proteins. Translation canonically starts by recognition of mRNA 5’cap and scanning to the start codon; how circRNA translation initiates remains unclear. Here, we developed a high-throughput screen to systematically identify and quantify RNA sequences that can direct circRNA translation. We identify and validate over 17,000 circRNA internal ribosome entry sites (IRES) and reveal that 18S rRNA complementarity and a structured RNA element on the IRES are important for facilitating circRNA cap-independent translation. With genomic and peptidomic analyses of the IRES, we identified nearly 1,000 putative endogenous protein-coding circRNAs and hundreds of translational units encoded by these circRNAs. We further characterized circFGFR1p, a protein encoded by circFGFR1, functions as a negative regulator of FGFR1 to suppress cell growth under stress conditions. The circRNA proteome may be important links among circRNA, biological control, and disease.

2021-08-23 | PXD024993 | Pride

Structured elements drive circular RNA translation and expand the human proteome, part4

Project description:The human genome encodes tens of thousands circular RNAs (circRNAs) whose levels correlate with many disease states. While studies have focused on the non-coding functions of circRNAs, emerging evidence suggests that a handful of circRNAs encode proteins. Translation canonically starts by recognition of mRNA 5’cap and scanning to the start codon; how circRNA translation initiates remains unclear. Here, we developed a high-throughput screen to systematically identify and quantify RNA sequences that can direct circRNA translation. We identify and validate over 17,000 circRNA internal ribosome entry sites (IRES) and reveal that 18S rRNA complementarity and a structured RNA element on the IRES are important for facilitating circRNA cap-independent translation. With genomic and peptidomic analyses of the IRES, we identified nearly 1,000 putative endogenous protein-coding circRNAs and hundreds of translational units encoded by these circRNAs. We further characterized circFGFR1p, a protein encoded by circFGFR1, functions as a negative regulator of FGFR1 to suppress cell growth under stress conditions. The circRNA proteome may be important links among circRNA, biological control, and disease.

2021-08-26 | PXD025203 | Pride

The expression profiles of circRNAs in hippocampus from mice with prenatal glyphosate exposure

Project description:In this study, the circRNAs expression pattern in hippocampus of postnatal day (PND) 28 mice offsprings which were exposured by glyphosate-based herbicide (GBH) during pregnancy and lactation was investigated. CircRNA microarray had detected 330 upregulated and 333 downregulated miRNAs in the PND28 mice offsprings' hippocampus

2018-03-13 | GSE111670 | GEO

circRNA Microarray analysis of hippocampus from mouse treated by HFD

Project description:To explore the potential mechanism linking circRNAs in Obesity-associated cognitive impairment induced by a longtime high-fat diet. The male mouse was treated by HFD up to16 weeks . Then the hippocaum tissues was isloated and circRNA Microarray analysis was applied. The expression profiles of hippocaum from mouse treated with HFD changed and 2 circRNA (mmu-circRNA-004797,mmu-circRNA-21040) from this signature was quantified by real-time PCR, confirming high-fat diet can change the profiles of circRNAs of hippocaum from mouse and may participated in the obesity associated cognitive impairment.

2022-09-07 | GSE208344 | GEO

Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals

Project description:Circular RNAs (circRNAs) are a large class of animal RNAs. To investigate possible circRNA functions, it is important to understand circRNA biogenesis. Besides human Alu repeats, sequence features that promote exon circularization are largely unknown. We experimentally identified new circRNAs in C. elegans. Reverse complementary sequences between introns bracketing circRNAs were significantly enriched compared to linear controls. By scoring the presence of reverse complementary sequences in human introns we predicted and experimentally validated novel circRNAs. We show that introns bracketing circRNAs are highly enriched in RNA editing or hyper-editing events. Knockdown of the double-strand RNA editing ADAR1 enzyme significantly and specifically up-regulated circRNA expression. Together, our data support a model of animal circRNA biogenesis in which competing RNA:RNA interactions of introns form larger structures which promote circularization of embedded exons, while ADAR1 antagonizes circRNA expression by melting stems within these interactions. Thus, we assign a new function to ADAR1. Examination of 12 samples in different stages of C.elegans development.

2015-01-06 | E-GEOD-63823 | biostudies-arrayexpress

Circular RNAs in cattle muscle: developmental stage-dependent changes

Project description:Circular RNAs (circRNAs) have been identified in various tissues and cell types from human, monkey, porcine and mouse. However, expression profile of circRNAs across cattle muscle development has never been investigated. Here, we examine the expression of circRNA in cattle skeletal muscle at embryonic stage and adult stage, exhibiting the first report of circRNA in the cattle muscle development of a large animal. 12,981 circRNAs are identified and annotated in Qinchuan cattle muscle tissues, including 530 circular intronic RNAs (ciRNAs). We discovered that one parental gene could generate multiple circRNA isoforms with only one or two circRNA isoforms being expressed at higher levels, and several host genes produced different alternative circularization numbers between different muscle development stages. The most circRNA candidates contained two to seven exons, and the genomic distance of the back-splicing site was generally no more than 50 kb. The flanking intron length of most circRNAs was not more than 105 nt and the mean length of upstream or downstream flanking intron was about 11,000 nt. Real-time quantitative PCR (qPCR) analysis confirmed the expression profile of these circRNAs, including several highly abundant circRNAs, and a subset of differently expressed circRNAs according to the high-throughput RNA sequencing (RNA-seq) data. These results display that an abundant circRNAs are dynamically expressed in a spatio-temporal manner in cattle muscle, indicating important and diverse functions during mammalian muscle development.

2018-10-10 | GSE87908 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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