CircRNA expression profile of bovine placentas in late gestation with aberrant SCNT fetus

Abstract

BackgroundsOne of the limitations of somatic cell nuclear transfer (SCNT) strategy to generate genetically modified offspring is the low birth rate. Placental dysfunction is one of the causes of abortion. Circular RNA (circRNA) is noncoding RNA which functions as microRNA (miRNA) sponges in biological processes.MethodsTwo aberrant pregnant placenta (aberrant group, AG) and three normal pregnant placenta (normal group, NG) during late gestation (180‐210 days) with bovine SCNT fetus were collected for high‐throughput sequencing and analyzed. The host genes of differentially expressed (DE) circRNAs were predicted. And the microRNAs (miRNAs) which could interact with DE circRNAs were analyzed. Then, the expressional level of partial DE circRNAs and corresponding host genes was verified through qRT‐PCR. At last, the function of host genes was analyzed through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG).ResultsAltogether 123 differentially expressed circRNAs between two groups were identified, which were found related to 60 host genes and 32 miRNAs. The top 10 upregulated circRNAs were bta_circ_0012985, bta_circ_0013071, bta_circ_0013074, bta_circ_0016024, bta_circ_0013068, bta_circ_0008816, bta_circ_0012982, bta_circ_0013072, bta_circ_0019285, and bta_circ_0013067. The top 10 downregulated circRNAs were bta_circ_0024234, bta_circ_0017528, bta_circ_0008077, bta_circ_0003222, bta_circ_0007500, bta_circ_0020328, bta_circ_0011001, bta_circ_0016364, bta_circ_0008839, and bta_circ_0016049. The qRT‐PCR results showed consistent trend with sequencing analysis result, while host genes had no statistic difference. The GO and KEGG analyses of the host genes suggested that abnormal circRNA expression may play multiple roles in placental structure and dysfunction.ConclusionThe abnormal circRNA expression may be one of reasons of placental dysfunction, leads to abortion of bovine SCNT fetus.

CircRNA Profiling Reveals CircPPARγ Modulates Adipogenic Differentiation via Sponging miR-92a-3p

“…Increasing evidence suggests that circRNAs could serve as developmental biomarkers and may act as proliferation, differentiation or apoptosis regulators in the animal cell . Recently, circRNAs have been reported to act as sponges for miRNAs and proteins in the cytoplasm for biological regulation and also in the nucleus for regulation of gene expression, with some circRNAs functioning as translation templates and as scaffolds for circRNA–protein complexes . Ju et al found that the main function of circRNAs is to act as “sponges” to absorb miRNAs, thus providing positive control of downstream proteins.…”

Differentially Expressed Circular RNAs in Stenosed Arteriovenous Fistula Tissues of Uremia Patients

“…To further dissect the potential DE circRNA functions in AVF dysfunction development and progression, the miRNA-binding sites of four DE circRNAs (hsa_circ_015036, hsa_circ_005718, hsa_circ_017814, and hsa_circ_007293) were predicted via using miRanda software, which were validated by qRT-PCR. A perfect seed matching between miRNA and target circRNA was considered for a MiRanda score of 140 or higher [14]. The interaction network between the four candidate circRNAs and their corresponding target miRNAs was constructed using Cytoscape 3.6.1.…”

“…We further predicted miRNA binding sites on four candidate circRNAs (hsa_circ_015036, hsa_circ_005718, hsa_circ_017814, and hsa_circ_007293) through miRanda software, which included three downregulated circRNAs and one upregulated circRNA. Based on the criteria of max score ≥ 140 and max energy ≤ -25 [14], a total of 134 miRNA were paired with four DE circRNAs after discarding the repeated values. For each candidate circRNA, top 10 target miRNAs with the highest degree of correlation were considered (a lower max energy is indicative of a stronger correlation) [14], then we acquired 38 miRNAs after discarding repeating target miRNAs.…”

“…Based on the criteria of max score ≥ 140 and max energy ≤ -25 [14], a total of 134 miRNA were paired with four DE circRNAs after discarding the repeated values. For each candidate circRNA, top 10 target miRNAs with the highest degree of correlation were considered (a lower max energy is indicative of a stronger correlation) [14], then we acquired 38 miRNAs after discarding repeating target miRNAs. Figure 5 illustrates the miRNA-circRNA interaction network regarding the four candidate circRNAs.…”

Genetic Basis of Follicle Development in Dazu Black Goat by Whole-Transcriptome Sequencing

“…In particular, the advent of next-generation, high-throughput technology has led to the identification of specific functional noncoding RNAs (ncRNAs) with roles in biological development and/or physiological responses [ 9 , 10 , 11 ]. Several studies have suggested that ncRNAs including microRNA (miRNAs), long noncoding RNA (lncRNAs), and circular RNA (circRNAs) play crucial roles in various biological processes in domestic animals [ 12 , 13 , 14 ]. Moreover, some studies have provided evidence supporting that lncRNA/circRNA–miRNA–messenger RNA (mRNA) interactions are important mechanisms underlying mammalian physiological development and diseases [ 15 , 16 , 17 ].…”