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Expression Profiling of Circular RNAs in Early Pregnant Jianghuai Buffaloes

ABSTRACT: Expression Profiling of Circular RNAs in Early Pregnant Jianghuai Buffaloes

PROVIDER: PRJNA859775 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR20281530_1.fastq.gz	Fastqsanger.gz
	SRR20281530_2.fastq.gz	Fastqsanger.gz
	SRR20281531_1.fastq.gz	Fastqsanger.gz
	SRR20281531_2.fastq.gz	Fastqsanger.gz
	SRR20281532_1.fastq.gz	Fastqsanger.gz

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Expression Profiling of Circular RNAs in Early Pregnant Jianghuai Buffaloes

Project description:The long reproductive cycle of buffalo is a key factor limiting the expansion of buffalo populations. Early and accurate pregnancy diagnosis in breeding heifers can shorten calving intervals and improve reproductive efficiency. Circular RNA (circRNA) is expressed in cells and tissues of several species. However, the expression of circRNAs in the blood of Jianghuai buffaloes during early pregnancy has not been reported. In this study, we identified the differentially expressed circRNAs (DECs) in the blood of Jianghuai buffaloes and annotated the functions of these DECs. The results showed that there were 890 differentially expressed circRNAs between the pregnant and non-pregnant groups, of which more than 80% were exon-derived circRNAs, including 323 up-regulated circRNAs and 567 down-regulated circRNAs. Enrichment analysis revealed that DECs were mainly enriched in the epidermal growth factor receptor signaling pathway important for embryonic development and pregnancy maintenance. In addition, most DECs have multiple miRNA targets, suggesting that these DECs have the potential to function as miRNA sponges. In conclusion, a number of DECs are present between pregnant and non-pregnant Jianghuai buffaloes, and these DECs are associated with embryo implantation and pregnancy establishment.

2022-07-21 | GSE208385 | GEO

Expression Profiling of Circular RNAs in Early Pregnant Jianghuai Buffaloes.

Project description:Circular RNA (circRNA) is expressed in cells and tissues of several species. However, the expression of circRNAs in the blood of Jianghuai buffaloes during early pregnancy has not been reported. In this study, we identified the DECs in the blood of Jianghuai buffaloes and annotated the functions of these DECs. The results showed that there were 890 DECs between the pregnant and non-pregnant groups, of which more than 80% were exon-derived circRNAs, including 323 up-regulated circRNAs and 567 down-regulated circRNAs. Enrichment analysis revealed that DECs were mainly enriched in the epidermal growth factor receptor-signaling pathway important for embryonic development and pregnancy maintenance. In addition, most DECs have multiple miRNA targets, suggesting that these DECs have the potential to function as miRNA sponges. In conclusion, several DECs are present between pregnant and non-pregnant Jianghuai buffaloes, and these DECs are associated with embryo implantation and pregnancy establishment.

| S-EPMC9597768 | biostudies-literature

Profiling circular RNAs in HeLa cell

Project description:Profiling circular RNAs in HeLa cell

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Circular DNA tumor viruses make circular RNAs

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Project description:We used RNA-seq to examine circular RNAs from RNase R treated ribo-zero RNAs in HeLa cells.

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Expression profiling of circular RNAs in human islet samples

Project description:There is already strong evidence indicating that different types of non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs, are key players in the regulation of β-cell functions and in the development of diabetes. However, the role of the newly discovered class of circular RNAs remains to be elucidated. We therefore analysed circular RNA expression in human islet samples.

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Project description:Purpose: We are using the illumina sequencing to compare the false positive and true positive circular RNA findings to confine the method to detect the true circular RNAs Methods: The testis whole transcriptome profiling was generated from 4-week mouse testis using illumina Nextseq, duplicated. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: our data suggest that circular RNAs identified based on junction sequences in the RNA-seq reads, especially those from Illumina Hiseq sequencing, mostly result from template-switching events during reverse transcription by MMLV-derived reverse transcriptases. It is critical to employ reverse transcriptases lacking terminal transferase activity (e.g., MonsterScript) to construct sequencing library or perform RT-PCR for identification and quantification of true circular RNAs. Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. The wild type mouse testis RNAs were constructed NGS library by two different enzyme, then parallel sequenced in illumina Nextseq

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Cytoplasmic DIS3 degrades circular RNAs independently of the exosome

Project description:Circular RNAs (circRNAs) are frequently generated during splicing. Their physiological roles, however, remain largely elusive. Some specific circRNAs function as microRNA (miRNA) or RNA binding protein (RBP) sponges or encode for proteins and are actively translated. Due to the lack of accessible ends, circRNAs are resistant to exonucleolytic cleavage and thus are more stable than linear RNAs. Nevertheless, circRNAs are most likely turned over by cellular degradation pathways. Here, we used a biochemical purification strategy to find nucleases that could degrade circRNAs. We identified the exosome-associated nuclease DIS3, which contains an endonucleolytic PIN domain and an exonuclease domain. We show that DIS3 can degrade circRNAs independently of the exosome in vitro. Although moderately, RNA-seq reveals that selected circRNAs are stabilized when DIS3 is reduced in vivo. Based on our data, we propose a model, in which cytoplasmic DIS3 contributes to the turnover of circRNAs in human cells.

2025-05-05 | PXD050442 | Pride

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