Circular RNA profiling reveals chi_circ_0008219 function as microRNA sponges in pre-ovulatory ovarian follicles of goats (Capra hircus)

Tao, Hu; Xiong, Qi; Zhang, Feng; Zhang, Nian; Liu, Yang; Suo, Xiaojun; Li, Xiaofeng; Yang, Qianping; Chen, Mingxin

doi:10.1016/j.ygeno.2017.10.005

Cited by 46 publications

(47 citation statements)

References 46 publications

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“…This would significantly reduce false positives of candidate circRNAs identified in GSF samples or OV samples. Furthermore, we found that > 98% of circRNAs were ecirRNAs, which differs from Hu's finding in which 86% of circRNAs were ciRNAs while only 13% were ecircRNAs and 1% were exon-intron circRNAs derived from the pre-ovulatory ovarian follicles of goats (Tao et al 2017). These discrepancies further demonstrate that the expression patterns of circRNAs are tissue specific and cell specific.…”

Section: Discussioncontrasting

confidence: 97%

Peer Review #1 of "Genome-wide analysis of circular RNAs in goat skin fibroblast cells in response to Orf virus infection (v0.2)"

2019

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Orf, caused by Orf virus (ORFV), is a globally distributed zoonotic disease responsible for serious economic losses in the agricultural sector. However, the mechanism underlying ORFV infection remains largely unknown. Circular RNAs (circRNAs), a novel type of endogenous non-coding RNAs, play important roles in various pathological processes but their involvement in ORFV infection and host response is unclear. In the current study, whole transcriptome sequencing and small RNA sequencing were performed in ORFVinfected goat skin fibroblast cells and uninfected cells. A total of 151 circRNAs, 341 messenger RNAs (mRNAs), and 56 microRNAs (miRNAs) were differently expressed following ORFV infection. Four circRNAs: circRNA1001, circRNA1684, circRNA3127 and circRNA7880 were validated by qRT-PCR and Sanger sequencing. Gene ontology (GO) analysis indicated that host genes of differently expressed circRNAs were significantly enriched in regulation of inflammatory response, epithelial structure maintenance, positive regulation of cell migration, positive regulation of ubiquitin-protein transferase activity, regulation of ion transmembrane transport, etc. The constructed circRNA-miRNA-mRNA network suggested that circRNAs may function as miRNA sponges indirectly regulating gene expression following ORFV infection. Our study presented the first comprehensive profiles of circRNAs in response to ORFV infection, thus providing new clues for the mechanisms of interactions between ORFV and the host.

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Section: Discussioncontrasting

confidence: 97%

Peer Review #1 of "Genome-wide analysis of circular RNAs in goat skin fibroblast cells in response to Orf virus infection (v0.2)"

2019

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“…During the past few years, through high-throughput RNA sequencing and bioinformatics analysis, a great number of circRNAs have been discovered in different species and tissues. For example, 13,950 circRNAs were detected in pre-ovulatory ovarian follicles of goats, and 37 circRNAs were found to be differentially expressed 27 . Empirical Bayes sequencing analysis identified 11 down-regulated and 32 up-regulated circRNAs in embryos with black fur skin and white fur skin of mice, and these circRNAs may play a role in skin pigmentation 28 .…”

Section: Discussionmentioning

confidence: 99%

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

Zheng

Hui

Chang

et al. 2020

Sci Rep

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circular RnA (circRnA) is endogenous non-coding RnA (ncRnA) with a covalently closed circular structure. it is mainly generated through RnA alternative splicing or back-splicing. circRnA is known in the majority of eukaryotes and very stable. However, knowledge of the circRnA involved in regulating cashmere fineness is limited. Skin samples were collected from Liaoning cashmere goats (LCG) and Inner Mongolia cashmere goats (MCG) during the anagen period. For differentially expressed circRNAs, RNA sequencing was performed, and the analysis led to an identification of 17 up-regulated circRNAs and 15 down-regulated circRNAs in LCG compared with MCG skin samples. In order to find the differentially expressed circRNAs in LCG, we carried out qPCRs on 10 candidate circRNAs in coarse type skin of LCG (CT-LCG) and fine type skin of LCG (FT-LCG). Four circRNAs: ciRNA128, circRNA6854, circRNA4154 and circRNA3620 were confirmed to be significantly differential expression in LCG. Also, a regulatory network of circRNAs-miRNAs was bioinformatically deduced and may help to understand molecular mechanisms of potential circRnA involvement in regulating cashmere fineness.

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“…Recently, with the rapid development of bioinformatics techniques and deep sequencing, more functional circRNAs have been discovered in animal follicle development (Shen et al, 2019). Previous studies have shown that the circRNAs of follicles and GCs in goats, chicken, and humans were detected (J. Cheng et al, 2017; Shen et al, 2019; Tao et al, 2017). However, data associated with the function of circRNAs in ducks are still less reported, especially regarding follicle development.…”

Section: Introductionmentioning

confidence: 98%

“…Previous studies have shown that the circRNAs of follicles and GCs in goats, chicken, and humans were detected (J. Cheng et al, 2017;Tao et al, 2017). However, data associated with the function of circRNAs in ducks are still less reported, especially regarding follicle development.…”

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confidence: 99%

The circular RNA aplacirc_13267 upregulates duck granulosa cell apoptosis by the apla‐miR‐1‐13/THBS1 signaling pathway

Xiao

et al. 2020

Journal Cellular Physiology

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Follicle development is a key factor that determines the reproductive performance of poultry. The existing evidence suggests that circular RNAs (circRNAs) play an important role in a variety of biological processes, especially in posttranscriptional regulation, but the regulatory mechanism of circRNAs in duck follicle development has rarely been reported. To better explore the molecular mechanism of follicle development in ducks, we sequenced and analyzed the follicular circRNAs; 4,204 circRNAs were predicted in the duck follicles. Fourteen circRNAs were differentially expressed between the white follicles and yellow follicles. The results of our studies showed that aplacirc_013267 promoted cell apoptosis in duck GCs. Moreover, a bioinformatics prediction analysis demonstrated that aplacirc_013267 was involved in a circRNA‐miRNA‐mRNA coexpression network and was observed to sponge two follicle‐related miRNAs by a luciferase activity assay. Furthermore, we found that overexpression of aplacirc_013267 significantly increased thrombospondin‐1 (THBS1) expression and downregulated granulosa cell apoptosis. The mechanistic study showed that aplacirc_013267 directly binds to and inhibits apla‐mir‐1‐13; then, aplacirc_013267 increases the expression of THBS1 and upregulates granulosa cell apoptosis. Taken together, our findings demonstrate that circRNAs have potential effects in duck ovarian follicles and that circRNAs may represent a new avenue to understand follicular development.

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Circular RNA profiling reveals chi_circ_0008219 function as microRNA sponges in pre-ovulatory ovarian follicles of goats (Capra hircus)

Cited by 46 publications

References 46 publications

Peer Review #1 of "Genome-wide analysis of circular RNAs in goat skin fibroblast cells in response to Orf virus infection (v0.2)"

Peer Review #1 of "Genome-wide analysis of circular RNAs in goat skin fibroblast cells in response to Orf virus infection (v0.2)"

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

The circular RNA aplacirc_13267 upregulates duck granulosa cell apoptosis by the apla‐miR‐1‐13/THBS1 signaling pathway

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