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

Abstract

Circular RNAs (circRNAs) are a new class of non-coding RNAs in animals and are a novel target of non-coding RNA (ncRNA) regulation. The mechanism and function of circRNAs have been reported in some species and tissues. However, there is little available information on the functions of circRNAs in the goat reproductive system. In the present study, we deeply sequenced and analyzed circRNAs through bioinformatics to reveal the expression profiles, and predicted 13,950 circRNAs in the pre-ovulatory ovarian follicles of goats for the first time. Thirty-seven circRNAs were differentially expressed in the Boer goat compared with the Macheng black goat. The chi_circ_0008219 was involved in a vast circRNA-miRNA-mRNA co-expression network. Via a luciferase activity assay, chi_circ_0008219 is observed to sponge to 3 ovarian follicle-related miRNAs. These findings demonstrate that circRNAs have potential effects in the ovarian follicles of ewes and may represent a promising new research field in ovarian follicular development.

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

“…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.…”

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

“…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.…”

Comprehensive CircRNA Profiling and Selection of Key CircRNAs Reveal the Potential Regulatory Roles of CircRNAs throughout Ovarian Development and Maturation in Cynoglossus semilaevis

“…One parental gene can produce one or more circRNA, which implies the vital function of circRNA temporal regulation. This is consistent with the research results of goats ( Capra hircus ) [ 17 ]. Thus, the most possible relationship of the expression between the circRNAs and their parent genes in fishes seems complexity and merits further investigation.…”

Characterization of Circular RNAs in Chinese Buffalo (Bubalus bubalis) Adipose Tissue: A Focus on Circular RNAs Involved in Fat Deposition

“…The RNA library construction by removing rRNAs and linear RNAs is more effective for circRNA identification [36]. In the present study, the RNA library was constructed and 5141 circRNAs were identified which was comparable with previous studies constructing libraries by removing rRNAs and linear RNAs [18,20]. Most of the circRNAs identified were exon type (Figure 1C), and ~98% of junctions reflected the classical GT-AG splicing mode (Figure 1D).…”

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

“…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.…”

Comprehensive CircRNA Profiling and Selection of Key CircRNAs Reveal the Potential Regulatory Roles of CircRNAs throughout Ovarian Development and Maturation in Cynoglossus semilaevis

“…One parental gene can produce one or more circRNA, which implies the vital function of circRNA temporal regulation. This is consistent with the research results of goats ( Capra hircus ) [ 17 ]. Thus, the most possible relationship of the expression between the circRNAs and their parent genes in fishes seems complexity and merits further investigation.…”

Characterization of Circular RNAs in Chinese Buffalo (Bubalus bubalis) Adipose Tissue: A Focus on Circular RNAs Involved in Fat Deposition

“…The RNA library construction by removing rRNAs and linear RNAs is more effective for circRNA identification [36]. In the present study, the RNA library was constructed and 5141 circRNAs were identified which was comparable with previous studies constructing libraries by removing rRNAs and linear RNAs [18,20]. Most of the circRNAs identified were exon type (Figure 1C), and ~98% of junctions reflected the classical GT-AG splicing mode (Figure 1D).…”

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

“…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.…”

Comprehensive CircRNA Profiling and Selection of Key CircRNAs Reveal the Potential Regulatory Roles of CircRNAs throughout Ovarian Development and Maturation in Cynoglossus semilaevis

“…One parental gene can produce one or more circRNA, which implies the vital function of circRNA temporal regulation. This is consistent with the research results of goats ( Capra hircus ) [ 17 ]. Thus, the most possible relationship of the expression between the circRNAs and their parent genes in fishes seems complexity and merits further investigation.…”

Characterization of Circular RNAs in Chinese Buffalo (Bubalus bubalis) Adipose Tissue: A Focus on Circular RNAs Involved in Fat Deposition

“…The RNA library construction by removing rRNAs and linear RNAs is more effective for circRNA identification [36]. In the present study, the RNA library was constructed and 5141 circRNAs were identified which was comparable with previous studies constructing libraries by removing rRNAs and linear RNAs [18,20]. Most of the circRNAs identified were exon type (Figure 1C), and ~98% of junctions reflected the classical GT-AG splicing mode (Figure 1D).…”