Comprehensive analysis of circRNAs from cashmere goat skin by next generation RNA sequencing (RNA-seq)

Zheng, Yuanyuan; Hui, Taiyu; Chang, Yue; Sun, Jiaming; Guo, Dan; Guo, Suling; Guo, Shu; Li, Bojiang; Wang, Zeying; Bai, Wenlin

doi:10.1038/s41598-019-57404-9

Cited by 29 publications

(27 citation statements)

References 74 publications

(75 reference statements)

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“…Zheng et al. (2020) identified 13,320 circRNAs from skin samples of Liaoning cashmere goats and Inner Mongolia cashmere goats during the anagen period and found 32 circRNAs of these identified were found to be differential expression. Result indicated some circRNAs might be involved in regulation of cashmere fineness.…”

Section: Methodsmentioning

confidence: 99%

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Biological functions of circRNAs and their progress in livestock and poultry

Huang

Wang

Zhang

et al. 2020

Reprod Domestic Animals

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CircRNAs are a class of newly discovered RNAs extensively expressed in eukaryotic cells (Jeck et al., 2013). Compared with conventional linear RNAs (containing 5′ and 3′ ends), circRNAs are covalently closed RNA molecules. It was recognized as a class of functional RNA that differs from miRNA, piRNA and lncRNA due to its character of circularity (Xu, Wu, Han, Zhao, & Song, 2017). CircRNAs were first found in RNA viruses as a viroid as early as in 1976 (Sanger, Klotz, Riesner, Gross, & Kleinschmidt, 1976). And then in 1986, it was also founded that the HDV, an animal virus, has a circRNA genome, which were considered to be a characteristic of viroids (Kos, Dijkema, Arnberg, van der Meide, & Schellekens, 1986). Due to limitation of technology at that time, circRNAs were less reported and were once considered as by-products of mis-splicing or regarded as a meaningless abnormally cut RNA, which never got any attention by some researchers because traditional molecular techniques employed in RNA analysis were not able to detect circRNAs because they did not have cap of 5′ end and tail of 3′ end (Jeck & Sharpless, 2014). It was not until 1991 that endogenous circRNAs were demonstrated in human cells, which originated from exons (Nigro et al., 1991). Since then, with advancement of bioinformatics analysis and RNA sequencing technologies, circRNA has attracted more and more attention of many scientists because it has been reported to be ubiquitously present in eukaryotic organisms and have longer half-lives than linear RNAs (Memczak et al., 2013;

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Section: Methodsmentioning

confidence: 99%

“…In another recent study, Zhao et al. (2020) detected the expression profiles of circRNAs in skin tissue from AFWS at embryonic day 90, embryonic day 120 and Birth. They identified 8,753 circRNAs, of which 918 were found to be differentially expressed.…”

Section: Methodsmentioning

confidence: 99%

Biological functions of circRNAs and their progress in livestock and poultry

Huang

Wang

Zhang

et al. 2020

Reprod Domestic Animals

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“…GO analysis (http://www.geneontology.org) was applied to understand the corresponding host genes of differentially expressed circRNAs. Likewise, following the annotation of the KEGG (http://www.kegg.jp/kegg), [20,21] we disclosed the significant pathways connected with differentially expressed circRNAs.…”

Section: Go Analysis and Kegg Pathway Analysis Of Host Genesmentioning

confidence: 99%

Comprehensive analysis of circular RNAs from steatotic livers after ischemia and reperfusion injury by next‐generation RNA sequencing

Zheng

Wang

et al. 2020

FEBS Letters

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Global organ shortage has led to the acceptance of steatotic livers for transplantation, taking the risk of graft dysfunction associated with the higher sensitivity of steatotic livers to ischemia and reperfusion injury (IRI). Data about circular RNAs (circRNAs) in steatotic livers following IRI are practically nonexistent. In our study, a high-fat diet-fed mouse model of hepatic steatosis was generated, and RNA sequencing was performed both on IRI and on sham liver tissues of these mice to screen for circRNAs with significant differential expression. To further validate our bioinformatics data, one upregulated circRNA and four downregulated circRNAs were examined. The circularity of these circRNAs was demonstrated using RNaseR digestion and Sanger sequencing. The expression of four stable circRNAs undigested by RNaseR was further validated by quantitative PCR. In summary, this study unearths several circRNAs as novel and potentially effective targets involved in the more severe damage of steatotic livers following IRI.

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“…Studies suggest that circRNA may be involved in mammalian growth and differentiation and cancer 13 . In the past, few studies have shown that circRNA regulates the fineness of cashmere, nowadays, there is new evidence that circRNA may regulate the growth of cashmere 14 .…”

Section: Introductionmentioning

confidence: 99%

Screening of cashmere fineness-related genes and their ceRNA network construction in cashmere goats

Hui

Zheng

Chang

et al. 2021

Sci Rep

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Competitive endogenous RNA (ceRNA) is a transcript that can be mutually regulated at the post-transcriptional level by competing shared miRNAs. The ceRNA network connects the function of protein-encoded mRNA with the function of non-coding RNA, such as microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA). However, compared with the ceRNA, the identification and combined analysis of lncRNAs, mRNAs, miRNAs, and circRNAs in the cashmere fineness have not been completed. Using RNA-seq technology, we first identified the miRNAs presented in Liaoning Cashmere Goat (LCG) skin, and then analyzed the mRNAs, lncRNAs, circRNAs expressed in LCG and Inner Mongolia cashmere goat (MCG) skin. As a result, 464 known and 45 new miRNAs were identified in LCG skin. In LCG and MCG skin, 1222 differentially expressed mRNAs were identified, 170 differentially expressed lncRNAs and 32 differentially expressed circRNAs were obtained. Then, qRT-PCR was used to confirm further the representative lncRNAs, mRNAs, circRNAs and miRNAs. In addition, miRanda predicted the relationships of ceRNA regulatory network among lncRNAs, circRNAs, miRNAs and mRNAs, the potential regulatory effects were investigated by Go and KEGG analysis. Through the screening and analysis of the results, the ceRNA network regulating cashmere fineness was constructed. LncRNA MSTRG14109.1 and circRNA452 were competed with miRNA-2330 to regulated the expression of TCHH, KRT35 and JUNB, which may provide a potential basis for further research on the process of regulating the cashmere fineness.

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Comprehensive analysis of circRNAs from cashmere goat skin by next generation RNA sequencing (RNA-seq)

Cited by 29 publications

References 74 publications

Biological functions of circRNAs and their progress in livestock and poultry

Biological functions of circRNAs and their progress in livestock and poultry

Comprehensive analysis of circular RNAs from steatotic livers after ischemia and reperfusion injury by next‐generation RNA sequencing

Screening of cashmere fineness-related genes and their ceRNA network construction in cashmere goats

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