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

An improved transcriptome annotation reveals asymmetric expression and distinct regulation patterns in allotetraploid common carp

In allotetraploid common carp, protein-coding homoeologs presented divergent expression levels between the two subgenomes. However, whether subgenome dominance occurs in other transcriptional and post-transcriptional events remains unknown. Using Illumina RNA sequencing and PacBio full-length sequencing, we refined the common carp transcriptome annotation and explored differences in four transcriptional and post-transcriptional events between the two subgenomes. The results revealed that the B subgenome presented more alternative splicing events, as did lncRNAs and circRNAs. However, the expression levels, tissue specificity, sequence features, and functions of lncRNAs and circRNAs did not significantly differ between the two subgenomes, suggesting a common regulatory mechanism shared by the two subgenomes. Furthermore, both the number and base substitution frequency of RNA editing events were greater in the B subgenome. Functional analyses of these transcriptional events also revealed subgenome bias. Genes that undergo alternative splicing in the A subgenome participate in more biological processes, and lncRNA targets show a preference between subgenomes. CircRNA host genes in the B subgenome were associated with more biological functions, and RNA editing preferentially occurred in noncoding regions or led to nonsynonymous mutations in the B subgenome. Taken together, the refined transcriptome annotation revealed complicated and imbalanced expression strategies in allotetraploid common carp.

Selection and Regulatory Network Analysis of Differential CircRNAs in the Hypothalamus of Goats with High and Low Reproductive Capacity

The objectives of this investigation were to identify differentially expressed circular RNAs (circRNAs) in the hypothalamus of goats with high and low prolificacy and construct a circRNA-mRNA regulatory network to uncover key potential circRNAs that influence goat prolificacy. Transcriptome analysis was performed on hypothalamus samples from low-prolificacy (n = 5) and high-prolificacy (n = 6) Chuanzhong black goats to identify circRNAs that influence prolificacy in these goats. Differential expression analysis identified a total of 205 differentially expressed circRNAs, comprising 100 upregulated and 105 downregulated circRNAs in the high-prolificacy group compared with the low-prolificacy group. Enrichment analysis of these differentially expressed circRNAs indicated significant enrichment in Gene Ontology terms associated with mammalian oogenesis, negative regulation of neurotransmitter secretion, reproductive developmental processes, hormone-mediated signaling pathways, and negative regulation of hormone secretion. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis highlighted significant enrichment in the oxytocin signaling pathway, GnRH signaling pathway, and hormone-mediated oocyte maturation. The hypothalamus of low- and high-prolificacy goats contains circular RNAs (circRNAs), including chicirc_063269, chicirc_097731, chicirc_017440, chicirc_049641, chicirc_008429, chicirc_145057, chicirc_030156, chicirc_109497, chicirc_030156, chicirc_176754, and chicirc_193363. Chuanzhong black goats have the potential to influence prolificacy by modulating the release of serum hormones from the hypothalamus. A circRNA-miRNA regulatory network was constructed, which determined that miR-135a, miR-188-3p, miR-101-3p, and miR-128-3p may interact with differentially expressed circRNAs, thereby regulating reproductive capacity through the hypothalamic-pituitary-gonadal axis. The results of this study enhance our knowledge of the molecular mechanisms that regulate prolificacy in Chuanzhong black goats at the hypothalamic level.

Circular RNAs: characteristics, functions, mechanisms, and potential applications in thyroid cancer

Thyroid cancer (TC) is one of the most common endocrine malignancies, and its incidence has increased globally. Despite extensive research, the underlying molecular mechanisms of TC remain partially understood, warranting continued exploration of molecular markers for diagnostic and prognostic applications. Circular RNAs (circRNAs) have recently garnered significant attention owing to their distinct roles in cancers. This review article introduced the classification and biological functions of circRNAs and summarized their potential as diagnostic and prognostic markers in TC. Further, the interplay of circRNAs with PI3K/Akt/mTOR, Wnt/β-catenin, MAPK/ERK, Notch, JAK/STAT, and AMPK pathways is elaborated upon. The article culminates with an examination of circRNA's role in drug resistance of TC and highlights the challenges in circRNA research in TC.

The Application of Genetic and Genomic Biotechnology in Aquaculture

This Special Issue, "The Application of Genetic and Genomic Biotechnology in Aquaculture," collates 14 published manuscripts covering different aspects of implementing advanced molecular genetics and genomic science in aquaculture [...].

CircRNA Identification and CircRNA-miRNA-mRNA Network in Cynoglossus semilaevis Sexual Size Dimorphism

Sexual size dimorphism (SSD), which is the sexual differences in body size, has been widely reported in various species including fishes. For Chinese tongue sole (Cynoglossus semilaevis), a flatfish exhibiting typically female-biased SSD, little is known for its epigenetic regulation mechanism, especially the role of circRNAs. Here, we identified the differently expressed abundances of circRNAs in females, males, and pseudo-males to explore the potential functions of circRNAs in Chinese tongue sole SSD. In total, 14,745 novel circRNAs were screened, among which 1461 DE circRNAs were identified from the brain, gonad, liver, and muscle in female, male, and pseudo-male individuals. The ceRNA network was subsequently constructed, including 10 circRNAs, 26 mRNAs, and 11 miRNAs. These DE mRNAs were mainly related to the mRNA surveillance pathway, metabolic pathways, and cellular senescence. Importantly, the ceRNA network has revealed that several circRNAs such as novel_circ_004374 and novel_circ_014597 may regulate homeodomain interacting protein kinase 2 (hipk2) expression by sponging miR-130-x. It is also worth exploring whether or how novel_circ_008696 regulates SET Domain Containing 2, histone lysine methyltransferase (setd2), which in turn affects the epigenetic patterns of different sexual individuals. The present study not only enriches the knowledge on the potential roles of circRNA in the physiological process, but also provides new clues for the explanation of fish SSD. In future studies, the precise function and involvement of circRNAs in female-biased SSD will require more efforts.

Potential Clinical Applications of Exosomal Circular RNAs: More than Diagnosis

Exosomes are small vesicles derived from cells used as cell-to-cell communication goods in numerous diseases including tumorigenesis, neurological diseases, cardiovascular diseases and other diseases. Circular RNAs (circRNAs) are an innovative constituent of non-coding endogenous RNAs generated through backsplicing, catalyzed by RNA polymerase Ⅱ. These non-coding RNAs have been suggested to control gene expression through miRNA sponging, RNA-binding protein regulation and translational capabilities. Genome-wide RNA sequence analyses observed that circRNAs were stably improved in exosomes in association to parental cells. Little attention has been dedicated to exosomal circRNAs (exo-circRNAs). However, research has demonstrated that exo-circRNAs may have important regulatory functions because of their stability in cells and within exosomes. If well understood, the precise roles and mechanisms of exo-circRNAs might surge the impending clinical applications of these molecules as markers in the identification, prediction and treatment of various diseases. In this review, we outline recent findings regarding exo-circRNAs which includes their functions and highlights their potential applications and therapeutic targets in human diseases.