Diverse alternative back-splicing and alternative splicing landscape of circular RNAs

Circular RNAs in gynecological cancer: From molecular mechanisms to clinical applications (Review)

Circular RNAs (circRNAs) have emerged as promising biomarkers and therapeutic targets in gynecological cancer. The present review explored developments in circRNA research in ovarian, endometrial and cervical cancer. circRNA biogenesis, functions and roles in cancer pathogenesis have been discussed, focusing on their potential as diagnostic and prognostic markers. Furthermore, circRNAs mechanisms of action, including miRNA sponging, protein scaffolding and peptide encoding were examined, highlighting specific circRNAs implicated in each cancer type and their clinical significance. The unique properties of circRNAs, such as stability and tissue-specific expression, make them ideal candidates for biomarker development. By synthesizing the currently available literature and identifying future research directions, the present review underscored circRNAs potential to improve gynecological cancer management through novel diagnostic tools, prognostic markers and targeted therapies.

Identification of biomarkers of male infertility through the circRNA expression profiling of seminal plasma

Circular RNAs (circRNAs) are key regulators of reproductive biology. However, limited information is available regarding circRNA expression profiles in seminal plasma samples from individuals with male infertility. The present study aimed to identify circRNAs associated with infertility in seminal plasma samples and to clarify their potential as biomarkers, as well as the possible molecular mechanisms underlying their functions. Next-generation RNA sequencing was conducted to analyze circRNA profiles in seminal plasma from healthy controls, oligoasthenospermia (OAZ) patients, and non-obstructive azoospermia (NOA) patients. Bioinformatics analysis revealed that 637 circRNAs were differentially expressed between OAZ and control subjects, as well as 272 circRNAs that were differentially expressed between NOA and control subjects. The expression of key circRNAs ( hsa-SAP130_0002, hsa-TRPC1_0001, hsa-FBRS_0001, hsa-ACACA_0025, hsa-UTRN_0042, and hsa-ZNF532_0023) was then validated by qPCR, and their diagnostic accuracy for infertility was confirmed through ROC curve analysis. Additionally, possible circRNA-miRNA-mRNA regulatory networks were developed for these candidate biomarkers. Collectively, this study identifies a novel set of circRNAs with potential as diagnostic biomarkers for male infertility and provides molecular insights that may facilitate both diagnostic and therapeutic efforts.

Reciprocal regulation between m6 A modifications and non-coding RNAs: emerging roles in cancer therapeutic resistance

In recent years, the interplay between N6-methyladenosine (m6A) modifications and non-coding RNAs (ncRNAs) has emerged as a pivotal research area, owing to their crucial involvement in the pathophysiological mechanisms underlying various diseases. A significant hurdle in cancer therapy is therapeutic resistance, which frequently contributes to adverse patient outcomes. Recent investigations have underscored the vital role that interactions between m6A modifications and ncRNAs play in mediating cancer therapeutic resistance via the MAPK, PI3K/Akt/mTOR, Wnt/β-catenin, HIPPO, and NF-κB pathways. This review elucidates how these interactions drive tumor therapeutic resistance by modulating these pathways. By dissecting the regulatory dynamics between m6A and ncRNAs in the context of cancer therapeutic resistance, this review aims to deepen the understanding of m6A-ncRNA interaction in cancer therapeutic resistance and identify potential therapeutic targets to improve cancer treatment efficacy.

Circular RMST cooperates with lineage-driving transcription factors to govern neuroendocrine transdifferentiation

Circular RNA (circRNA) is a class of noncoding RNA with regulatory potentials. Its role in the transdifferentiation of prostate and lung adenocarcinoma into neuroendocrine prostate cancer (NEPC) and small cell lung cancer (SCLC) remains unexplored. Here, we identified circRMST as an exceptionally abundant circRNA predominantly expressed in NEPC and SCLC, with strong conservation between humans and mice. Functional studies using shRNA, siRNA, CRISPR-Cas13, and Cas9 consistently demonstrate that circRMST is essential for tumor growth and the expression of ASCL1, a master regulator of neuroendocrine fate. Genetic knockout of Rmst in NEPC genetic engineered mouse models prevents neuroendocrine transdifferentiation, maintaining tumors in an adenocarcinoma state. Mechanistically, circRMST physically interacts with lineage transcription factors NKX2-1 and SOX2. Loss of circRMST induces NKX2-1 protein degradation through autophagy-lysosomal pathway and alters the genomic binding of SOX2, collectively leading to the loss of ASCL1 transcription.

Transcriptome analysis reveals PTBP1 as a key regulator of circRNA biogenesis

BACKGROUND

Circular RNAs (circRNAs) are a class of non-coding RNAs generated through back splicing. High expression of circRNAs is often associated with numerous abnormal cellular biological processes. However, the regulatory factors of circRNAs are not fully understood.

RESULTS

In this study, we identified PTBP1 as a crucial regulator of circRNA biogenesis through a comprehensive analysis of the whole transcriptome profiles across 10 diverse cell lines. Knockdown of PTBP1 led to a significant decrease in circRNA expression, concomitant with a distinct reduction in cell proliferation. To investigate the regulatory mechanism of PTBP1 on circRNA biogenesis, we constructed a minigene reporter based on SPPL3 gene. The results showed that PTBP1 can bind to the flanking introns of circSPPL3, and the mutation of PTBP1 motif impedes the back splicing of circSPPL3. Subsequently, to demonstrate that this observation is not an exception, the comprehensive regulatory effects of PTBP1 on circRNAs were confirmed by miniGFP, reflecting the necessity of the binding site in the flanking introns. Analysis of data from clinical samples showed that both PTBP1 and circRNAs exhibited substantial upregulation in acute myeloid leukemia, further demonstrating a potential role for PTBP1 in promoting circRNA biogenesis under in vivo conditions. Competitive endogenous RNA (ceRNA) network revealed that PTBP1-associated circRNAs participated in biological processes associated with cell proliferation.

CONCLUSIONS

In summary, our study is the first to identify the regulatory effect of PTBP1 on circRNA biogenesis and indicates a possible link between PTBP1 and circRNA expression in leukemia.

circRNA/TLR interaction: key players in immune regulation and autoimmune diseases

Circular RNAs are a class of non-coding RNAs with covalently closed loops. They have been revealed to regulate immune responses by affecting gene expression. Although initially considered splicing byproducts, new studies have indicated their role in transcriptional and post-transcriptional control, especially with TLRs. TLRs start inflammatory signaling and let the innate immune system recognize PAMPs. circRNAs interact context-dependently with TLR pathways to influence immune homeostasis and inflammation in either pathogenic or protective roles. In autoimmune diseases, dysregulated circRNA expression can aggravate immune responses and damage tissue. CircRNAs can interact with RNA-binding proteins, function as molecular sponges for miRNAs, and change inflammatory pathways like the NF-κB signaling cascade, influencing immune responses. They control adaptive immunity, function of antigen-presenting cells, and cytokine generation. The stability and presence of circRNAs in many body fluids make them therapeutic targets and biomarkers for inflammatory and autoimmune diseases. The several immune control roles of circRNA-TLR interactions are discussed in this review, as well as their consequences for immunologically mediated disease diagnosis and treatment.

The biomarker potential of circPOLD1 and its binding protein YBX1 in cervical carcinogenesis

BACKGROUND

Cervical cancer progresses through distinct precancerous stages, making early screening and intervention crucial for prevention. However, conventional screening modalities, such as cytology and HPV testing, face challenges related to sensitivity, specificity, and resource dependency. Circular RNAs (circRNAs), owing to their high stability and tissue-specific expression, have emerged as promising biomarkers, though their role in cervical carcinogenesis remains underexplored. In particular, the clinical utility of circRNAs for optimizing cervical cancer screening and early diagnosis has yet to be established. This study aimed to investigate the dynamic expression profiles of circRNAs across various stages of cervical cancer progression and identify potential biomarkers to enhance early detection.

METHODS

CircRNA sequencing was performed on cervical tissues spanning normal cervical epithelium (NCE), high-grade squamous intraepithelial lesions (HSIL), and cervical squamous cell carcinoma (CSCC). Functional assays, including cell viability, colony formation, and apoptosis, were performed to assess the oncogenic potential of circPOLD1 and its interaction with YBX1 in cervical cancer cells. BaseScope and immunohistochemistry (IHC) were applied to tissue microarrays for clincial validation and ROC curve analysis evaluated the diagnostic performance of circPOLD1 in serum as a liquid biopsy marker.

RESULTS

CircRNA profiling revealed a progressive increase in circPOLD1 expression from NCE to HSIL and CSCC. Mechanistically, circPOLD1 functioned as an oncogene by binding to and phosphorylating YBX1, activating the AKT/mTOR/HIF-1α pathway to enhance glycolysis-driven tumorigenesis. BaseScope and IHC confirmed the stage-specific elevation of circPOLD1 and YBX1 in cervical lesions. The circPOLD1/YBX1 multi-marker panel demonstrated superior diagnostic performance, achieving an AUC of 0.951 for LSIL+ and 0.817 for HSIL+ detection. Furthermore, serum circPOLD1 levels exhibited a progressive increase across disease stages, underscoring its potential as a non-invasive biomarker.

CONCLUSION

circPOLD1 and YBX1 synergistically drive cervical carcinogenesis and exhibit stage-specific expression patterns. Their combined detection significantly enhanced the accuracy for cervical cancer screening and dynamic monitoring. The successful application of BaseScope and IHC highlights the immediate translational potential of these biomarkers, paving the way for refined risk stratification, improved therapeutic targeting, and reduced cervical cancer burden through early intervention.

circAFF2 promotes the development of AML by binding to PML mRNA

AML is a complex disease caused by multiple molecular mechanisms. As an important regulatory molecule, the role of circRNA in AML is not fully understood. By performing high-throughput sequencing on clinical samples, we systematically identified the differences in circRNA expression and distribution between AML and healthy donor samples. One circular RNA, circAFF2, was found to be significantly upregulated in AML patients. Functional studies showed that knockdown of circAFF2 could significantly inhibit the proliferation of AML cells and promote their apoptosis. Overexpression of circAFF2 can have opposite effects. In vivo experiments showed that transplantation of AML cells with circAFF2 knockdown slowed the proliferation and infiltration and prolonged the survival time of mice compared to controls. Further studies showed that circAFF2 can promote the degradation of PML mRNA by binding to the 3'UTR of PML mRNA, thereby affecting the proliferation and apoptosis of AML cells. In conclusion, our work demonstrates that circAFF2 can bind to PML mRNA to regulate AML cell function, providing new insights into the mechanism of AML development and potential targets for clinical diagnosis and treatment.

Circular RNA discovery with emerging sequencing and deep learning technologies

Circular RNA (circRNA) represents a type of RNA molecule characterized by a closed-loop structure that is distinct from linear RNA counterparts. Recent studies have revealed the emerging role of these circular transcripts in gene regulation and disease pathogenesis. However, their low expression levels and high sequence similarity to linear RNAs present substantial challenges for circRNA detection and characterization. Recent advances in long-read and single-cell RNA sequencing technologies, coupled with sophisticated deep learning-based algorithms, have revolutionized the investigation of circRNAs at unprecedented resolution and scale. This Review summarizes recent breakthroughs in circRNA discovery, characterization and functional analysis algorithms. We also discuss the challenges associated with integrating large-scale circRNA sequencing data and explore the potential future development of artificial intelligence (AI)-driven algorithms to unlock the full potential of circRNA research in biomedical applications.

Circular RNAs increase during vascular cell differentiation and are biomarkers for vascular disease

AIMS

The role of circular RNAs (circRNAs) and their regulation in health and disease are poorly understood. Here, we systematically investigated the temporally resolved transcriptomic expression of circRNAs during differentiation of human induced pluripotent stem cells (iPSCs) into vascular endothelial cells (ECs) and smooth muscle cells (SMCs) and explored their potential as biomarkers for human vascular disease.

METHODS AND RESULTS

Using high-throughput RNA sequencing and a de novo circRNA detection pipeline, we quantified the daily levels of 31 369 circRNAs in a 2-week differentiation trajectory from human stem cells to proliferating mesoderm progenitors to quiescent, differentiated EC and SMC. We detected a significant global increase in RNA circularization, with 397 and 214 circRNAs up-regulated greater than two-fold (adjusted P < 0.05) in mature EC and SMC, compared with undifferentiated progenitor cells. This global increase in circRNAs was associated with up-regulation of host genes and their promoters and a parallel down-regulation of splicing factors. Underlying this switch, the proliferation-regulating transcription factor MYC decreased as vascular cells matured, and inhibition of MYC led to down-regulation of splicing factors such as SRSF1 and SRSF2 and changes in vascular circRNA levels. Examining the identified circRNAs in arterial tissue samples and in peripheral blood mononuclear cells (PBMCs) from patients, we found that circRNA levels decreased in atherosclerotic disease, in contrast to their increase during iPSC maturation into EC and SMC. Using machine learning, we determined that a set of circRNAs derived from COL4A1, COL4A2, HSPG2, and YPEL2 discriminated atherosclerotic from healthy tissue with an area under the receiver operating characteristic curve (AUC) of 0.79. circRNAs from HSPG2 and YPEL2 in blood PBMC samples detected atherosclerosis with an AUC of 0.73.

CONCLUSION

Time-resolved transcriptional profiling of linear and circRNA species revealed that circRNAs provide granular molecular information for disease profiling. The identified circRNAs may serve as blood biomarkers for atherosclerotic vascular disease.

Transcriptome-scale analysis of functional alternative back-splicing events in colorectal cancer

BACKGROUND

Circular RNAs (circRNAs) are a class of non-polyadenylated RNAs generated from back-splicing of genes. Multiple circRNAs can be generated at a single gene locus through alternative back-splicing events (ABS), sharing the same 5' or 3' back-splice site. To date, how prevalent ABS events are and how they are participated in carcinogenesis of human colorectal cancer (CRC) remains unexplored.

METHODS

To explore the functional roles of ABS events in CRC carcinogenesis, we analyzed ribosomal RNA-depleted transcriptome sequencing data of 176 CRC samples and characterized the landscape of ABS events in CRC. CRC cancer-related ABS events were identified by comparing paired CRC tumor tissues and adjacent normal tissues. Then, univariate and multivariate Cox regression was used to find prognostic ABS events. Moreover, in vitro and in vivo assays were used to exploring the functional roles of circXPO1-1 and circXPO1-2 in CRC.

RESULTS

We totally identified 19,611 high confidence circRNAs in CRC, among which 17,874 (91·1%) of circRNAs were found recurrently. The number of ABS circRNAs accounted for 68.8% of all identified high confidence circRNAs, which suggested that ABS events are prevalent in CRC transcriptome. Particularly, 552 ABS circRNAs were found to be aberrantly expressed between paired CRC tumor tissues and adjacent normal tissues, and their parent genes are closely associated with cancer-related hallmarks. In addition, 13 differential ABS circRNAs were identified to be associated with CRC patient survival and could act as independent prognostic indicators. Furthermore, we identified two ABS circRNAs of XPO1 gene (circXPO1-1 and circXPO1-2). The result showed that overexpression of circXPO1-2 inhibited CRC cell proliferation, migration, and invasion in vitro and in vivo, whereas circXPO1-1 is not, indicating that the circularization isoforms of XPO1 gene have different functions in CRC.

CONCLUSIONS

In conclusion, our work provides the landscape of ABS events in CRC transcriptome and the close association of ABS circRNAs with tumorigenesis offers a new set of targets with potential clinical benefit.

Long Circulating RNAs Packaged in Extracellular Vesicles: Prospects for Improved Risk Assessment in Childhood B-Cell Acute Lymphoblastic Leukemia

Analysis of tumoral RNA from bone marrow (BM) biopsy is essential for diagnosing childhood B-cell acute lymphoblastic leukemia (B-ALL), risk stratification, and monitoring, by detecting fusions and gene expression patterns. However, frequent BM biopsies are invasive and traumatic for patients. Small extracellular vesicles (sEVs) circulating in blood contain a variety of biomolecules, including RNA, that may contribute to cancer progression, offering a promising source of non-invasive biomarkers from liquid biopsies. While most EV studies have focused on small RNAs like microRNAs (miRNAs), the role of longer RNA species, including messenger RNAs (mRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), remains underexplored despite their demonstrated potential for risk-based patient stratification when starting from BM biopsies. We used immuno-purification to isolate sEVs from peripheral blood at diagnosis in B-ALL patients and cell model-based conditioned culture medium (CCM) with ETV6::RUNX1 and TCF3::PBX1 fusions. Using whole-transcriptome sequencing targeting transcripts over 200 nt and a novel data analysis pipeline, we identified 102 RNA transcripts (67 mRNAs, 16 lncRNAs, 10 circRNAs, 4 pseudogenes, and 5 others) in patient-derived sEVs. These transcripts could serve as biomarkers for two distinct molecular subgroups of B-ALL, each with different risk profiles at diagnosis. This is the first study characterizing the long transcriptome in blood-derived sEVs for childhood B-ALL, highlighting the potential use of circulating RNAs for improved risk-based stratification.

Degradation of circular RNA by the ribonuclease DIS3

Features of circular RNAs (circRNAs) produced by back-splicing of eukaryotic exon(s) make them resistant to degradation by linear RNA decay machineries. Thus, a general circRNA degradation pathway under normal conditions has remained largely elusive. Here, we report that the endonucleolytic enzyme DIS3 is responsible for the degradation of circRNAs. Depletion of DIS3 leads to the upregulation of more than 60% of circRNAs with little effect on their linear cognates. Such DIS3-mediated circRNA degradation is conserved, occurs in the cytoplasm, and relies on DIS3's endonucleolytic activity but is independent of the RNA exosome complex. Sequence enrichment analyses suggest that DIS3 prefers to degrade circRNAs containing U-rich motifs. Correspondingly, synthesized RNA circles with or without U-rich motifs exhibit decreased or increased stabilities, respectively. Together, these findings suggest a general regulation of circRNA turnover by DIS3.

Unveiling Pharmacogenomics Insights into Circular RNAs: Toward Precision Medicine in Cancer Therapy

Pharmacogenomics is revolutionizing precision medicine by enabling tailored therapeutic strategies based on an individual genetic and molecular profile. Circular RNAs (circRNAs), a distinct subclass of endogenous non-coding RNAs, have recently emerged as key regulators of drug resistance, tumor progression, and therapeutic responses. Their covalently closed circular structure provides exceptional stability and resistance to exonuclease degradation, positioning them as reliable biomarkers and novel therapeutic targets in cancer management. This review provides a comprehensive analysis of the interplay between circRNAs and pharmacogenomics, focusing on their role in modulating drug metabolism, therapeutic efficacy, and toxicity profiles. We examine how circRNA-mediated regulatory networks influence chemotherapy resistance, alter targeted therapy responses, and impact immunotherapy outcomes. Additionally, we discuss emerging experimental tools and bioinformatics techniques for studying circRNAs, including multi-omics integration, machine learning-driven biomarker discovery, and high-throughput sequencing technologies. Beyond their diagnostic potential, circRNAs are being actively explored as therapeutic agents and drug delivery vehicles. Recent advancements in circRNA-based vaccines, engineered CAR-T cells, and synthetic circRNA therapeutics highlight their transformative potential in oncology. Furthermore, we address the challenges of standardization, reproducibility, and clinical translation, emphasizing the need for rigorous biomarker validation and regulatory frameworks to facilitate their integration into clinical practice. By incorporating circRNA profiling into pharmacogenomic strategies, this review underscores a paradigm shift toward highly personalized cancer therapies. circRNAs hold immense potential to overcome drug resistance, enhance treatment efficacy, and optimize patient outcomes, marking a significant advancement in precision oncology.

Targeting Regulatory Noncoding RNAs in Human Cancer: The State of the Art in Clinical Trials

Noncoding RNAs (ncRNAs) are a heterogeneous group of RNA molecules whose classification is mainly based on arbitrary criteria such as the molecule length, secondary structures, and cellular functions. A large fraction of these ncRNAs play a regulatory role regarding messenger RNAs (mRNAs) or other ncRNAs, creating an intracellular network of cross-interactions that allow the fine and complex regulation of gene expression. Altering the balance between these interactions may be sufficient to cause a transition from health to disease and vice versa. This leads to the possibility of intervening in these mechanisms to re-establish health in patients. The regulatory role of ncRNAs is associated with all cancer hallmarks, such as proliferation, apoptosis, invasion, metastasis, and genomic instability. Based on the function performed in carcinogenesis, ncRNAs may behave either as oncogenes or tumor suppressors. However, this distinction is not rigid; some ncRNAs can fall into both classes depending on the tissue considered or the target molecule. Furthermore, some of them are also involved in regulating the response to traditional cancer-therapeutic approaches. In general, the regulation of molecular mechanisms by ncRNAs is very complex and still largely unclear, but it has enormous potential both for the development of new therapies, especially in cases where traditional methods fail, and for their use as novel and more efficient biomarkers. Overall, this review will provide a brief overview of ncRNAs in human cancer biology, with a specific focus on describing the most recent ongoing clinical trials (CT) in which ncRNAs have been tested for their potential as therapeutic agents or evaluated as biomarkers.

Circular RNAs in neurological conditions - computational identification, functional validation, and potential clinical applications

Non-coding RNAs (ncRNAs) have gained significant attention in recent years due to advancements in biotechnology, particularly high-throughput total RNA sequencing. These developments have led to new understandings of non-coding biology, revealing that approximately 80% of non-coding regions in the genome possesses biochemical functionality. Among ncRNAs, circular RNAs (circRNAs), first identified in 1976, have emerged as a prominent research field. CircRNAs are abundant in most human cell types, evolutionary conserved, highly stable, and formed by back-splicing events which generate covalently closed ends. Notably, circRNAs exhibit high expression levels in neural tissue and perform diverse biochemical functions, including acting as molecular sponges for microRNAs, interacting with RNA-binding proteins to regulate their availability and activity, modulating transcription and splicing, and even translating into functional peptides in some cases. Recent advancements in computational and experimental methods have enhanced our ability to identify and validate circRNAs, providing valuable insights into their biological roles. This review focuses on recent developments in circRNA research as they related to neuropsychiatric and neurodegenerative conditions. We also explore their potential applications in clinical diagnostics, therapeutics, and future research directions. CircRNAs remain a relatively underexplored area of non-coding biology, particularly in the context of neurological disorders. However, emerging evidence supports their role as critical players in the etiology and molecular mechanisms of conditions such as schizophrenia, bipolar disorder, major depressive disorder, Alzheimer's disease, and Parkinson's disease. These findings suggest that circRNAs may provide a novel framework contributing to the molecular dysfunctions underpinning these complex neurological conditions.

CircZmMED16 delays plant flowering by negatively regulating starch content through its binding to ZmAPS1

Circular RNAs (circRNAs), a type of head-to-tail closed RNA molecules, have been implicated in various aspects of plant development and stress responses through transcriptome sequencing; however, the precise functional roles of circRNAs in plants remain poorly understood. In this study, we identified a highly expressed circular RNA, circZmMED16, derived from exon 8 of the mediator complex subunit 16 (ZmMED16) across different maize (Zea mays L.) inbred lines using circRNA-seq analysis. This circRNA is predominantly expressed in maize tassels and functions in the cytoplasm. Overexpression of circZmMED16 resulted in increased expression of ZmMED16/AtMED16 and delayed flowering in both maize and Arabidopsis thaliana, compared with that in wild-type plants. In contrast, overexpression of the parent gene ZmMED16 did not alter the flowering time of transgenic plants in Arabidopsis, suggesting that circZmMED16 plays a specific role in regulating flowering, distinct from that of linear ZmMED16. To further understand the mechanisms underlying the regulation of flowering time by circZmMED16, we performed RNA pull-down, dual-luciferase, RNA interference (RNAi), and ribonuclease protection assays (RPA). These results indicate that circZmMED16 interacts with small subunit 1 of ADP-glucose pyrophosphorylase (APS1) mRNA in both maize and Arabidopsis. The knockdown of circZmMED16 increased the expression of ZmAPS1, whereas the overexpression of circZmMED16 led to the downregulation of ZmAPS1 RNA and protein. By affecting ZmAPS1 expression, circZmMED16 reduced ADP-glucose pyrophosphorylase (AGPase) activity and led to delayed flowering. These results revealed a novel regulatory mechanism for circRNAs in flowering time and shed light on their functional and regulatory roles in plants.

Overview of splicing variation in ovarian cancer

Ovarian cancer remains one of the deadliest gynecological malignancies, with a persistently high mortality rate despite promising advancements in immunotherapy. Aberrant splicing events play a crucial role in cancer heterogeneity and treatment resistance. Many splicing variants, especially those involving key molecular markers such as BRCA1/2, are closely linked to disease progression and treatment outcomes. These variants and related splicing factors hold significant clinical value as diagnostic and prognostic biomarkers and therapeutic targets. This review provides a comprehensive overview of splicing variants in ovarian cancer, emphasizing their role in metastasis and resistance, and offers insights to advance biomarker development and treatment strategies.

A novel peptide encoded by a rice circular RNA confers broad-spectrum disease resistance in rice plants

Circular RNAs (circRNAs) are a significant class of endogenous RNAs that exert crucial biological functions in human and animal systems, but little is currently understood regarding their roles in plants. Here, we identified a circRNA originating from the back-splicing of exon 4 and exon 5 of a rice gene, OsWRKY9, and named it circ-WRKY9. It is upregulated in rice stripe mosaic virus (RSMV)-infected rice plants. Notably, circ-WRKY9 contains two open reading frames with an internal ribosome entry site. We found that circ-WRKY9 encoded a peptide of 88 amino acids (aa) and named it WRKY9-88aa. Overexpression of WRKY9-88aa suppresses RSMV infection in rice plants, with increased reactive oxygen species production. Furthermore, WRKY9-88aa enhances resistance to blast disease and bacterial leaf blight, suggesting its potential to provide broad-spectrum disease resistance. Our findings provide the first evidence of a peptide encoded by a circRNA in planta and highlight its potential application to control a wide spectrum of plant diseases.

Noncanonical circRNA biogenesis driven by alpha and gamma herpesviruses

Herpesviruses require the host transcriptional machinery, inducing significant changes in gene expression to prioritize viral transcripts. We examined alpha- and gamma-herpesvirus alterations to a type of alternative splicing, namely circular RNA (circRNA) synthesis. We developed "Circrnas in Host And viRuses anaLysis pIpEline" (CHARLIE) to facilitate viral profiling. This method identified thousands of back-splicing variants, including circRNA common to lytic and latent phases of infection. Ours is the first report of Herpes Simplex Virus-1 circRNAs, including species derived from ICP0 and the latency-associated transcript. We characterized back-splicing cis- and trans-elements, and found viral circRNAs resistant to spliceosome perturbation and lacking canonical splice donor-acceptors. Subsequent loss-of-function studies of host RNA ligases (RTCB, RLIG1) revealed instances of decreased viral back splicing. Using eCLIP and 4sU-Sequencing, we determined that the KSHV RNA-binding protein, ORF57, enhanced synthesis for a subset of viral and host circRNAs. Our work explores unique splicing mechanisms driven by lytic infection, and identifies a class of transcripts with the potential to function in replication, persistence, or tumorigenesis.

circ2LO: Identification of CircRNA Based on the LucaOne Large Model

Circular RNA is a type of noncoding RNA with a special covalent bond structure. As an endogenous RNA in animals and plants, it is formed through RNA splicing. The 5' and 3' ends of the exons form circular RNA at the back-splicing sites. Circular RNA plays an important regulatory role in diseases by interacting with the associated miRNAs. Accurate identification of circular RNA can enrich the data on circular RNA and provide new ideas for drug development. At present, mainstream circular RNA recognition algorithms are divided into two categories: those based on RNA sequence position information and those based on RNA sequence biometric information. Herein, we propose a method for the recognition of circular RNA, called circ2LO, which utilizes the LucaOne large model for feature embedding of the splicing sites of RNA sequences as well as their upstream and downstream sequences to prevent semantic information loss caused by the traditional one-hot encoding method. Subsequently, it employs a convolutional layer to extract features and a self-attention mechanism to extract interactive features to accurately capture the core features of the circular RNA at the splicing sites. Finally, it uses a fully connected layer to identify circular RNA. The accuracy of circ2LO on the human dataset reached 95.47%, which is higher than the values shown by existing methods. It also achieved accuracies of 97.04% and 72.04% on the Arabidopsis and mouse datasets, respectively, demonstrating good robustness. Through rigorous validation, the circ2LO model has proven its high-precision identification capability for circular RNAs, marking it as a potentially transformative analytical platform in the circRNA research field.

ASVirus: A Comprehensive Knowledgebase for the Viral Alternative Splicing

Viruses are significant human pathogens responsible for pandemic outbreaks and seasonal epidemics. Viral infectious diseases impose a devastating global burden and have a profound impact on public health systems. During viral infections, alternative splicing (AS) plays a crucial role in regulating immune responses, altering the host's cellular environment, expanding viral genetic material, and facilitating viral replication. As research on AS in viral infections expands, it is crucial to consolidate data on virus-related splicing changes to improve our understanding of these viruses and associated diseases. To address this need, we created ASVirus (https://bddg.hznu.edu.cn/asvirus/), a comprehensive database of virus-associated AS events and their regulatory factors. ASVirus uniquely combines high-confidence, experimentally validated splicing data and investigates upstream regulatory mechanisms through a gene-splicing factor interaction network. Its user-friendly web interface offers detailed information into AS events from various viral families and the resulting mis-splicing in host genes, aiding the exploration of novel viral infection mechanisms and the identification of critical therapeutic targets for viral diseases.

Intron-Derived Lariat RNAs Go Stable

During pre-mRNA splicing, introns are removed by the spliceosome, and the flanking exons are ligated to form mature mRNA, which is subsequently translated into protein. Traditionally, intronic RNAs have been regarded as "junk", presumed to be degraded for nucleotide turnover. Notably, after debranching, some linearized lariat RNAs can be further processed into snoRNAs, miRNAs, and other long non-coding RNAs. However, recent studies have shown that many intron-derived lariat RNAs can escape degradation and remain stable across various eukaryotic organisms, indicating they may play significant roles in cellular processes. Moreover, these naturally retained lariat RNAs are frequently observed in circular forms in vivo, suggesting that their linear tails are highly susceptible to degradation. This highlights lariat RNAs as an important source of circular RNAs. Furthermore, many lariat-derived circRNAs have been detected in the cytoplasm, implying active nuclear export and potential roles in cytoplasmic processes. In this review, we provide an overview of the life cycle of intron-derived lariat RNAs, focusing on their biogenesis, degradation, and retention. We also discuss the mechanisms that enable their resistance to degradation and the biological functions of stable lariat RNAs, shedding light on these seemingly "nonsense" yet inevitably produced non-coding intronic RNAs.

CircMETTL6 Suppresses Ovarian Cancer Cell Growth and Metastasis Through Inhibition of GDF15 Transcription by Disrupting the NONO-POLR2A Complex

Circular RNAs (circRNAs) are a distinctive class of non-coding RNAs with covalent closed-loop structure, lacking 5' caps and 3' poly(A) tails. These molecules are prevalent in eukaryotes and play key roles in cancer. Here, the function of a new circRNA, circMETTL6, in ovarian cancer is identified and investigated. The prognostic significance of circMETTL6 is assessed using RNA in situ hybridization. Functional studies involving circMETTL6 overexpression are performed both in vitro and in vivo. Mechanistic investigations are performed using RNA-seq, RNA pull-down, RNA immunoprecipitation, co-immunoprecipitation, chromatin immunoprecipitation, protein degradation assay and dual-luciferase reporter assays. circMETTL6 is significantly downregulated in ovarian cancer, and its lower expression correlates with worse prognosis. Overexpression of circMETTL6 significantly inhibited proliferation, migration, and invasion of ovarian cancer cell in vitro, as well as tumor growth and metastasis in vivo. Mechanistically, circMETTL6 recruited the non-POU domain containing octamer binding protein (NONO) by binding to its Coiled-coil domain and disrupted its binding with RNA polymerase II subunit A (POLR2A), and consequently inhibiting growth differentiation factor 15 (GDF15) transcription, thereby suppressing ovarian cancer progression. These findings establish circMETTL6 as a novel tumor suppressor in ovarian cancer. Targeting the circMETTL6/NONO/GDF15 axis presents a potential therapeutic avenue for ovarian cancer treatment.

Goose multi-omics database: A comprehensive multi-omics database for goose genomics

Multi-omics has helped elucidate the gene expression patterns and genomic variations closely associated with economically significant traits in geese. Despite the substantial genomic data generated through extensive goose studies, a unified platform for integrating these datasets is lacking. To address this gap, we introduced the Goose Multi-omics Database (GMD), which is accessible at http://goosedb.com/. The GMD is a comprehensive resource enabling streamlined search, analysis, and visualization of genetic information through a unified interface, providing insights into phenotypic traits, gene sequences, structures, expression profiles, genomic variations, gene families, homology, and collinearity. Equipped with robust analytical tools such as GBrowse and BLAST, the GMD facilitates rapid access to target gene information, significantly enhancing the efficiency and productivity of genomic research. By serving as a versatile and intuitive online repository, the GMD offers transformative potential for advancing goose biology, fostering multi-omics investigations, and integrating cutting-edge methodologies such as deep learning to accelerate discoveries in goose genomics.

S100P is a core gene for diagnosing and predicting the prognosis of sepsis

Sepsis, characterized as a severe systemic inflammatory response syndrome, typically originates from an exaggerated immune response to infection that gives rise to organ dysfunction. Serving as one of the predominant causes of death among critically ill patients, it's pressing to acquire an in-depth understanding of its intricate pathological mechanisms to strengthen diagnostic and therapeutic strategies. By integrating genomic, transcriptomic, proteomic, and metabolomic data across multiple biological levels, multi-omics research analysis has emerged as a crucial tool for unveiling the complex interactions within biological systems and unraveling disease mechanisms in recent years. Samples were collected from 23 cases of sepsis patients and 10 healthy volunteers from January 2019 to December 2020. The protein components in the samples were explored by independent data acquisition (DIA) analysis method, while Circular RNA (circRNA) categories were usually identified by RNA sequencing (RNA-seq) technology. Subsequent to the above steps, data quality monitoring was performed by employing software, and unqualified sequences were excluded, and conditions were set for differential expression network analysis (protein group and circRNA group were separately used log2 |FC|≥ 1 and log2 |FC|≥ 2, P < 0.050). Gene Ontology (GO) enrichment analysis and gene set enrichment analysis (GSEA) analysis were performed on common differentially expressed proteins, followed by protein-protein interaction between common differentially expressed genes and cytoscape software enrichment analysis, and subsequently its association with associated diseases (Disease Ontology (DO)) was investigated in an all-round manner. Afterwards, the distribution distinction of common differentially expressed genes in sepsis group and healthy volunteer group was displayed by heat map after Meta-analysis. Subsequent to the above procedures, pivotal targets with noticeable survival curve distinctions in two states were screened out after Meta-analysis. At last, their potential value was verified by in vitro cell experiment, which provided reference for further discussion of the diagnostic value and prognostic effect of target gene. A total of 174 DEPs and 308 DEcircRNAs were identified in the proteomics analysis, while a total of 12 common differentially expressed genes were identified after joint analysis. The protein-protein interaction (PPI) network suggested the degree of interaction between the dissimilar genes, and the heat map demonstrated their specific distribution in distinct groups. Through enrichment analysis, these proteins predominantly participated in a sequence of crucial processes such as intracellular material synthesis and secretion, changes in inflammatory receptors and immune inflammatory response. The meta-analysis identified that S100P is highly expressed in sepsis. As illustrated by the ROC curve, this gene has high clinical diagnostic value, and utimately confirmed its expression in sepsis through in vitro cell experiments. In these two groups of healthy people and septic patients, S100P demonstrated a more obvious trend of differential expression; Cell experiments also proved its value in diagnosis and prognosis judgment in sepsis; As a result, they may become diagnostic and prognostic markers for sepsis in clinical practice.

m6A2Circ: A comprehensive database for decoding the regulatory relationship between m6A modification and circular RNA

Circular RNA (circRNA) is a class of noncoding RNAs derived from back-splicing of pre-mRNAs. Recent studies have increasingly highlighted the pivotal roles of N6-methyladenosine (m6A) in regulating various aspects of circRNA metabolism, including biogenesis, localization, stability, and translation. Despite the importance of m6A in circRNA metabolism, there remains a substantial gap in comprehensive resources dedicated to exploring m6A modification in circRNA. To bridge this significant gap, we present m6A2Circ (http://m6a2circ.canceromics.org/), a pioneering database designed to systematically explore the regulatory interactions between m6A modification and circRNA. The m6A2Circ database encompasses 198,804 m6A-circRNA associations derived from diverse human and mouse tissues. These associations are meticulously categorized into four levels of evidence supported either by experimental data or by high-throughput sequencing data. Moreover, the database offers extensive annotations, facilitating research into circRNA function and its potential disease implications. Overall, m6A2Circ aims to benefit the research community and bolster novel discoveries in terms of crosstalk between m6A and circRNA.

Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration

Newts have large genomes harboring many repeat elements. How these elements shape the genome and relate to newts' unique regeneration ability remains unknown. We present here the chromosome-scale assembly of the 20.3 Gb genome of the Iberian ribbed newt, Pleurodeles waltl, with a hitherto unprecedented contiguity and completeness among giant genomes. Utilizing this assembly, we demonstrate conserved synteny as well as genetic rearrangements, such as in the major histocompatibility complex locus. We provide evidence suggesting that intronic repeat elements drive newt-specific circular RNA (circRNA) biogenesis and show their regeneration-specific expression. We also present a comprehensive in-depth annotation and chromosomal mapping of microRNAs, highlighting genomic expansion profiles as well as a distinct regulatory pattern in the regenerating limb. These data reveal links between repeat elements, non-coding RNAs, and adult regeneration and provide key resources for addressing developmental, regenerative, and evolutionary principles.

Past, present, and future strategies for detecting and quantifying circular RNA variants

Circular RNAs (circRNAs) are a family of covalently closed RNA transcripts ubiquitous across the eukaryotic kingdom. CircRNAs are generated by a class of alternative splicing called backsplicing, with the resultant circularization of a part of parental RNA producing the characteristic backsplice junction (BSJ). Because of the noncontiguous sequence of the BSJ with respect to the DNA genome, circRNAs remained hidden in plain sight through over a decade of RNA next-generation sequencing, yet over 3 million unique circRNA transcripts have been illuminated in the past decade alone. CircRNAs are expressed in a cell type-specific manner, are highly stable, with many examples of circRNAs being evolutionarily conserved and/or functional in specific contexts. However, circRNAs can be very lowly expressed and predictions of the circRNA context from BSJ-spanning reads alone can confound extrapolation of the exact sequence composition of the circRNA transcript. For these reasons, specific and ultrasensitive detection, combined with enrichment, bespoke bioinformatics pipelines and, more recently, long-read, highly processive sequencing is becoming critical for complete characterization of all circRNA variants. Concomitantly, the need for targeted detection and quantification of specific circRNAs has sparked numerous laboratory-based and commercial approaches to visualize circRNAs in cells and quantify them in biological samples, including biospecimens. This review focuses on advancements in the detection and quantification of circRNAs, with a particular focus on recent next-generation sequencing approaches to bolster detection of circRNA variants and accurately normalize between sequencing libraries.

A novel protein encoded by porcine circANKRD17 activates the PPAR pathway to regulate intramuscular fat metabolism

BACKGROUND

Intramuscular fat is an important factor in evaluating pork quality and varies widely among different pig breeds. However, the regulatory mechanism of circular RNAs (circRNAs) in lipid metabolism remains largely unexplored.

RESULTS

We combined circRNA-seq and Ribo-seq data to screen a total of 18 circRNA candidates with coding potential, and circANKRD17 was found to be significantly elevated in the longissimus dorsi muscle of Lantang piglets, with a length of 1,844 nucleotides. Using single-cell sequencing, we identified 477 differentially expressed genes in IMF cells between Lantang and Landrace piglets, with enrichment in the PPAR signaling pathway. These genes included FABP4, FABP5, CPT1A, and UBC, consistent with the high levels of acylcarnitines observed in the longissimus dorsi muscles of the Lantang breed, as determined by lipidomic analysis. Further in vitro and in vivo experiments indicated that circANKRD17 can regulate lipid metabolism through various mechanisms involving the PPAR pathway, including promoting adipocyte differentiation, fatty acid transport and metabolism, triglyceride synthesis, and lipid droplet formation and maturation. In addition, we discovered that circANKRD17 has an open reading frame and can be translated into a novel 571-amino-acid protein that promotes lipid metabolism.

CONCLUSIONS

Our research provides new insights into the role of protein-coding circANKRD17, especially concerning the metabolic characteristics of pig breeds with higher intramuscular fat content.

Enhanced Oxidative Phosphorylation Driven by TACO1 Mitochondrial Translocation Promotes Stemness and Cisplatin Resistance in Bladder Cancer

Chemoresistance poses a critical obstacle in bladder cancer (BCa) treatment, and effective interventions are currently limited. Elevated oxidative phosphorylation (OXPHOS) has been linked to cancer stemness, a determinant of chemoresistance. However, the mechanisms underlying increased OXPHOS during cancer cell chemoresistance remain unclear. This study revealed that the mitochondrial translational activator of cytochrome oxidase subunit 1 (TACO1) is linked to stemness and cisplatin resistance in BCa cells. Mechanistically, mitochondrial TACO1 enhances the translation of the mitochondrial cytochrome c oxidase I (MTCO1), promoting mitochondrial reactive oxygen species (mtROS) by upregulating OXPHOS, consequently driving cancer stemness and cisplatin resistance. Intriguingly, the mitochondrial translocation of TACO1 is mediated by the heat shock protein 90 β (HSP90β), a process that requires circFOXK2 as a scaffold for the TACO1-HSP90β interaction. The mutations at the binding sites of TACO1-circFOXK2-HSP90β disturb the ternary complex and inhibit cancer stemness and cisplatin resistance in BCa cells by suppressing the MTCO1/OXPHOS/mtROS axis. Clinically, BCa patients with increased mitochondrial TACO1 expression respond poorly to cisplatin treatment. This study elucidates the mechanisms by which TACO1 promotes BCa stemness and cisplatin resistance, providing a potential target for mitigating cisplatin resistance for BCa and a biomarker for predicting cisplatin response.

CircRNA regulates lung cancer metastasis

Lung cancer stands prominently among the foremost contributors to human mortality, distinguished by its elevated fatality rate and the second-highest incidence rate among malignancies. The metastatic dissemination of lung cancer stands as a primary determinant of its elevated mortality and recurrence rates, underscoring the imperative for comprehensive investigation into its metastatic pathways. Circular RNAs (circRNAs), a subclass of non-coding RNA (ncRNA) molecules, have garnered attention for their pivotal involvement in the genesis and advancement of lung cancer. Emerging evidence highlights the indispensable functions of circRNAs in orchestrating the metastatic cascade of lung cancer. This review primarily discusses the mechanisms by which circRNAs act as competitive endogenous RNAs (ceRNAs) and modulate various signaling pathways to regulate lung cancer metastasis. CircRNAs influence critical cellular processes including angiogenesis, autophagy, and glycolysis, thereby exerting influence over the metastatic cascade in lung cancer. These discoveries offer innovative perspectives and therapeutic avenues for the diagnosis and management of lung cancer.

CircUCK2(2,3) promotes cancer progression and enhances synergistic cytotoxicity of lenvatinib with EGFR inhibitors via activating CNIH4-TGFα-EGFR signaling

BACKGROUND

Circular (circ)RNAs have emerged as crucial contributors to cancer progression. Nonetheless, the expression regulation, biological functions, and underlying mechanisms of circRNAs in mediating hepatocellular carcinoma (HCC) progression remain insufficiently elucidated.

METHODS

We identified circUCK2(2,3) through circRNA sequencing, RT-PCR, and Sanger sequencing. CircUCK2(2,3) levels were measured in two independent HCC cohorts using quantitative real-time PCR (qRT-PCR). We explored the functions of circUCK2(2,3) using gain- and loss-of-function assays. Techniques such as RNA-sequencing, RNA immunoprecipitation (RIP), polysome fractionation, RNA pulldown, dual luciferase reporter assay, inhibitors of EGFR downstream signaling, CRISPR-Cas9, and medium transfer assays were employed to investigate the regulatory mechanisms and the protumoral activities of circUCK2(2,3). Additionally, in vitro cytotoxic assays and patient-derived xenograft (PDX) models assessed the effects of circUCK2(2,3) on the cytotoxic synergy of lenvatinib and EGFR inhibitors.

RESULTS

CircUCK2(2,3) is upregulated in HCC tissues and serves as an independent risk factor for poor recurrence-free survival. The expression of circUCK2(2,3) is independent on its host gene, UCK2, but is regulated by its upstream promoter and flanking inverted complementary sequences. Functionally, circUCK2(2,3) enhances HCC proliferation, migration, and invasion, both in vitro and in vivo. Mechanistically, by sponging miR-149-5p, circUCK2(2,3) increases CNIH4 levels, which in turn amplifies TGFα secretion, resulting in the activation of EGFR and downstream pAKT and pERK signaling pathways. Moreover, circUCK2(2,3) overexpression sensitizes HCC cells to EGFR inhibitors, and increases the synergistic cytotoxicity of combined lenvatinib and EGFR inhibitor treatment.

CONCLUSIONS

CircUCK2(2,3) regulates a novel oncogenic pathway, miR-149-5p-CNIH4-TGFα-EGFR, in HCC, presenting a viable therapeutic target and biomarker for the precision treatment of HCC.

Maize transcriptome profiling reveals low temperatures affect photosynthesis during the emergence stage

Introduction

Earlier sowing is a promising strategy of ensuring sufficiently high maize yields in the face of negative environmental factors caused by climate change. However, it leads to the low temperature exposure of maize plants during emergence, warranting a better understanding of their response and acclimation to suboptimal temperatures.

Materials and Methods

To achieve this goal, whole transcriptome sequencing was performed on two maize inbred lines - tolerant/susceptible to low temperatures, at the 5-day-old seedling stage. Sampling was performed after 6h and 24h of treatment (10/8°C). The data was filtered, mapped, and the identified mRNAs, lncRNAs, and circRNAs were quantified. Expression patterns of the RNAs, as well as the interactions between them, were analyzed to reveal the ones important for low-temperature response.

Results and Discussion

Genes involved in different steps of photosynthesis were downregulated in both genotypes: psa, psb, lhc, and cab genes important for photosystem I and II functioning, as well as rca, prk, rbcx1 genes necessary for the Calvin cycle. The difference in low-temperature tolerance between genotypes appeared to arise from their ability to mitigate damage caused by photoinhibition: ctpa2, grx, elip, UF3GT genes showed higher expression in the tolerant genotype. Certain identified lncRNAs also targeted these genes, creating an interaction network induced by the treatment (XLOC_016169-rca; XLOC_002167-XLOC_006091-elip2). These findings shed light on the potential mechanisms of low-temperature acclimation during emergence and lay the groundwork for subsequent analyses across diverse maize genotypes and developmental stages. As such, it offers valuable guidance for future research directions in the molecular breeding of low-temperature tolerant maize.

The Regulation of Messenger RNAs and Biological Pathways by Long Non-Coding RNAs and Circular RNAs in Ischemic Stroke

Our aim was to evaluate the regulation of messenger RNAs (mRNAs) and biological pathways by long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in ischemic stroke. We employed weighted gene co-expression network analysis (WGCNA) to construct two co-expression networks for mRNAs with circRNAs and lncRNAs, respectively, to investigate their association with ischemic stroke. We compared the overlap of mRNAs and biological pathways in the stroke-associated modules of the two networks. Furthermore, we validated the association of key non-coding RNAs with the risk of ischemic stroke and poor prognosis using quantitative real-time polymerase chain reaction. Ischemic stroke patients exhibited lower eigengene expression in the turquoise module associated with lncRNAs and mRNAs, as well as in the turquoise, red, and greenyellow modules associated with circRNAs and mRNAs in ischemic stroke. In the lncRNA-mRNA network and circRNA-mRNA network, we observed a significant overlap of the 5126 mRNAs (P < 0.001) and 51 biological pathways (P < 0.001), respectively. Among the ten key non-coding RNAs, lnc-TPRG1-AS1, lnc-GUK1, and hsa_circ_RELL1 were significantly increased (P < 0.05), while hsa_circ_ZBTB20 and hsa_circ_ERBB2 were significantly decreased (P < 0.05) in ischemic stroke. Additionally, ischemic stroke patients with poor functional outcome had significantly lower levels of hsa_circ_ZBTB20 and hsa_circ_ERBB2 compared to those with favorable prognosis (P < 0.05). Our findings suggest lncRNAs and circRNAs display similar biological functions in ischemic stroke. Key non-coding RNAs may be associated with the risk and clinical prognosis of ischemic stroke. These results warrant further validation in the future studies.

Genome-Wide Characterization of Extrachromosomal Circular DNA in the Midgut of BmCPV-Infected Silkworms and Its Potential Role in Antiviral Responses

Extrachromosomal circular DNAs (eccDNAs) has been found to be widespread and functional in various organisms. However, comparative analyses of pre- and post-infection of virus are rarely known. Herein, we investigated the changes in expression patterns of eccDNA following infection with Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) and explore the role of eccDNA in viral infection. Circle-seq was used to analyze eccDNAs in the midgut of BmCPV-infected and BmCPV-uninfected silkworms. A total of 5508 eccDNAs were identified, with sizes varying from 72 bp to 17 kb. Most of eccDNAs are between 100 to 1000 bp in size. EccDNA abundance in BmCPV-infected silkworms was significantly higher than in BmCPV-uninfected silkworms. GO and KEGG analysis of genes carried by eccDNAs reveals that most are involved in microtubule motor activity, phosphatidic acid binding, cAMP signaling pathway, and pancreatic secretion signaling pathways. Several eccDNAs contain sequences of the transcription factor SOX6, sem-2, sp8b, or Foxa2. Association analysis of eccDNA-mRNA/miRNA/circRNA revealed that some highly expressed genes are transcribed from relevant sequences of eccDNA and the transcription of protein coding genes influenced the frequency of eccDNA. BmCPV infection resulted in changes in the expression levels of six miRNAs, but no known miRNAs with altered expression levels due to changes in eccDNA abundance were identified. Moreover, it was found that 1287 and 924 sequences representing back-spliced junctions of circRNAs were shared by the junctions of eccDNAs in the BmCPV-infected and uninfected silkworms, respectively, and some eccDNAs loci were shared by circRNAs on Chromosomes 2, 7, 11, 14, and 24, suggesting some eccDNAs may exert its function by being transcribed into circRNAs. These findings suggest that BmCPV infection alter the expression pattern of eccDNAs, leading to changes in RNA transcription levels, which may play roles in regulating BmCPV replication. In the future, further experiments are needed to verify the association between eccDNA-mRNA/miRNA/circRNA and its function in BmCPV infection.

CeRNA profiling and the role in regulating gonadal development in gold pompano

BACKGROUND

The golden pompano (Trachinotus ovatus) is an economically significant warm-water aquaculture species in China. The time required for sexual maturity of T. ovatus is relatively long. Consequently, it has prompted researchers to investigate gonadal development process of this fish. To gain further insight into the function of competing endogenous RNA (ceRNA) in the gonads of T. ovatus and the regulatory mechanism of the ceRNA network, whole transcriptome libraries were constructed from the testes and ovaries.

RESULTS

Overall, a total of 96 differentially expressed microRNAs (DE-miRNAs), 2,338 differentially expressed messenger RNAs (DE-mRNAs), 973 differentially expressed long non-coding RNAs (DE-lncRNAs), and 94 differentially expressed circular RNAs (DE-circRNAs) were identified. Additionally, a ceRNA network was constructed, and enrichment analysis confirmed the involvement of numerous pathways in reproduction and gonadal development, including the TGF-β signaling pathway and GnRH signaling pathway. The ceRNA network analysis revealed that the oni-let-7d-1-p3 and PC-3p-112794_13 may play significant roles in T. ovatus gonadal development. And we have observed a possible relationship related to gonadal development involving R-spondin-1 (Rspo1), oni-let-7d-1-p3, and MSTRG.14909.1 (lnc-TGFβR). Dual-luciferase gene reporter system and fluorescence in situ hybridization analyses preliminary verified the regulation relationship between Rspo1 and oni-let-7d-1-p3, as well as lnc-TGFβR and oni-let-7d-1-p3 in the cytoplasm of sertoli cells.

CONCLUSION

It is hypothesized that the lnc-TGFβR functions as a sponge for oni-let-7d-1-p3, participating in regulating the process of testis development. These findings could enhance our understanding of ncRNAs in gonadal development. It also provides new insight into the function of ncRNAs and the regulatory relationship of ceRNA between males and females. These results might contribute to discussions on the regulation of ncRNA during gametogenesis.

Circular RNA Formation and Degradation Are Not Directed by Universal Pathways

Circular RNAs (circRNAs) are a class of unique transcripts characterized by a covalently closed loop structure, which differentiates them from conventional linear RNAs. The formation of circRNAs occurs co-transcriptionally and post-transcriptionally through a distinct type of splicing known as back-splicing, which involves the formation of a head-to-tail splice junction between a 5' splice donor and an upstream 3' splice acceptor. This process, along with exon skipping, intron retention, cryptic splice site utilization, and lariat-driven intron processing, results in the generation of three main types of circRNAs (exonic, intronic, and exonic-intronic) and their isoforms. The intricate biogenesis of circRNAs is regulated by the interplay of cis-regulatory elements and trans-acting factors, with intronic Alu repeats and RNA-binding proteins playing pivotal roles, at least in the formation of exonic circRNAs. Various hypotheses regarding pathways of circRNA turnover are forwarded, including endonucleolytic cleavage and exonuclease-mediated degradation; however, similarly to the inconclusive nature of circRNA biogenesis, the process of their degradation and the factors involved remain largely unclear. There is a knowledge gap regarding whether these processes are guided by universal pathways or whether each category of circRNAs requires special tools and particular mechanisms for their life cycles. Understanding these factors is pivotal for fully comprehending the biological significance of circRNAs. This review provides an overview of the various pathways involved in the biogenesis and degradation of different types of circRNAs and explores key factors that have beneficial or adverse effects on the formation and stability of these unique transcripts in higher eukaryotes.

Recent advances in investigation of circRNA/lncRNA-miRNA-mRNA networks through RNA sequencing data analysis

Non-coding RNAs (ncRNAs) are RNA molecules that are transcribed from DNA but are not translated into proteins. Studies over the past decades have revealed that ncRNAs can be classified into small RNAs, long non-coding RNAs and circular RNAs by genomic size and structure. Accumulated evidences have eludicated the critical roles of these non-coding transcripts in regulating gene expression through transcription and translation, thereby shaping cellular function and disease pathogenesis. Notably, recent studies have investigated the function of ncRNAs as competitive endogenous RNAs (ceRNAs) that sequester miRNAs and modulate mRNAs expression. The ceRNAs network emerges as a pivotal regulatory function, with significant implications in various diseases such as cancer and neurodegenerative disease. Therefore, we highlighted multiple bioinformatics tools and databases that aim to predict ceRNAs interaction. Furthermore, we discussed limitations of using current technologies and potential improvement for ceRNAs network detection. Understanding of the dynamic interplay within ceRNAs may advance the biological comprehension, as well as providing potential targets for therapeutic intervention.

Comparative analysis of the whole transcriptome landscapes of muscle and adipose tissue in Qinchuan beef cattle

BACKGROUND

Muscle and adipose tissue are the most critical indicators of beef quality, and their development and function are regulated by noncoding RNAs (ncRNAs). However, the differential regulatory mechanisms of ncRNAs in muscle and adipose tissue remain unclear.

RESULTS

In this study, 2,343 differentially expressed mRNAs (DEMs), 235 differentially expressed lncRNAs (DELs), 95 differentially expressed circRNAs (DECs) and 54 differentially expressed miRNAs (DEmiRs) were identified in longissimus dorsi muscle (LD), subcutaneous fat (SF) and perirenal fat (VF) in Qinchuan beef cattle. The results of functional enrichment analysis showed that DEMs, DELs, DECs and DEmiRs were enriched in biological processes related to development and function of muscle and fat deposition, including skeletal muscle contraction, muscle organ development, PPAR signaling pathway, fatty acid metabolism and MAPK signaling pathway. Based on the competing endogenous RNA (ceRNA) regulatory mechanism, we constructed a lncRNA/circRNA-miRNA-mRNA network consisting of 6 circRNAs, 5 lncRNAs, 6 miRNAs and 27 mRNAs. Among them, 55 ceRNA axes were involved, including circRNA12990 - bta-miR-133a_L-1R + 1 - MYO6/ZEB2, circRNA2893/MSTRG.28538.1/MSTRG.11613.4 - pma-miR-145-5p_R + 2 - EYA4 and MSTRG.26982.1 - bta-let-7e_R + 1 - RBM40.

CONCLUSIONS

This study identified a group of differentially expressed mRNAs, lncRNAs, circRNAs and miRNAs between muscle and adipose tissue and constructed a potential ceRNA regulatory network, which may serve as a foundation for studying the differential regulatory roles of ncRNAs in the development and function of muscle and adipose tissue.

PlantCircRNA: a comprehensive database for plant circular RNAs

Circular RNAs (circRNAs) represent recently discovered novel regulatory non-coding RNAs. While they are present in many eukaryotes, there has been limited research on plant circRNAs. We developed PlantCircRNA (https://plant.deepbiology.cn/PlantCircRNA/) to fill this gap. The two most important features of PlantCircRNA are (i) it incorporates circRNAs from 94 plant species based on 39 245 RNA-sequencing samples and (ii) it imports the original AtCircDB and CropCircDB databases. We manually curated all circRNAs from published articles, and imported them into the database. Furthermore, we added detailed information of tissue as well as abiotic stresses to the database. To help users understand these circRNAs, the database includes a detection score to measure their consistency and a naming system following the guidelines recently proposed for eukaryotes. Finally, we developed a comprehensive platform for users to visualize, analyze, and download data regarding specific circRNAs. This resource will serve as a home for plant circRNAs and provide the community with unprecedented insights into these mysterious molecule.

Research on curcumin mediating immunotherapy of colorectal cancer by regulating cancer associated fibroblasts

The objective was to investigate curcumin's (Cur) function and associated molecular mechanisms in regulating tumor immunity in colon cancer. Primary cancer-associated fibroblasts (CAFs) from mouse CT26 colon cancer tumors were isolated. Validation of primary CAFs using immunofluorescence assay was done. Cell Counting Kit-8 experiments, real-time quantitative PCR (qPCR), and enzyme linked immunosorbent assay experiments were conducted to investigate how curcumin affected the growth and cytokine secretion functions of CAFs. The effect of curcumin on regulating PD-L1 expression on CT26 cells through CAFs in vitro was explored through coculture of CAFs and tumor cells, qPCR, and western blot experiments. A mouse colon cancer cell model was established in Balb/c nude mice to explore the effect of curcumin on colon tumor cells. Changes in the tumor microenvironment were detected by flow cytometry to explore the synergistic effect of curcumin combined with anti-PD-1 monoclonal antibody in the treatment of mouse colon cancer. In vitro, curcumin prevented the growth and TGF-β secretion of CT26 cells. At the same time, curcumin inhibited the secretion of TGF-β by CAFs, thereby downregulating the PD-L1 expression of CT26 cells. In vivo, curcumin combined with anti-PD-1 antibodies can further enhance the inhibitory effect of PD-1 antibodies on tumors and increase the number of tumor-suppressing immune cells in the tumor microenvironment, such as M1 macrophages and CD8 T cells, thus inhibiting tumors. Immune M2 macrophages, regulatory T cells, and other cells were reduced. In conclusion, curcumin reduces the expression of PD-L1 in colon cancer cells and improves the tumor immune microenvironment by inhibiting the proliferation of CAFs and the secretion of TGF-β. Curcumin and anti-PD-1 treatment have synergistic inhibitory effects on colon cancer.

Circular RNA regulatory role in pathological cardiac remodelling

Cardiac remodelling involves structural, cellular and molecular alterations in the heart after injury, resulting in progressive loss of heart function and ultimately leading to heart failure. Circular RNAs (circRNAs) are a recently rediscovered class of non-coding RNAs that play regulatory roles in the pathogenesis of cardiovascular diseases, including heart failure. Thus, a more comprehensive understanding of the role of circRNAs in the processes governing cardiac remodelling may set the ground for the development of circRNA-based diagnostic and therapeutic strategies. In this review, the current knowledge about circRNA origin, conservation, characteristics and function is summarized. Bioinformatics and wet-lab methods used in circRNA research are discussed. The regulatory function of circRNAs in cardiac remodelling mechanisms such as cell death, cardiomyocyte hypertrophy, inflammation, fibrosis and metabolism is highlighted. Finally, key challenges and opportunities in circRNA research are discussed, and orientations for future work to address the pharmacological potential of circRNAs in heart failure are proposed. LINKED ARTICLES: This article is part of a themed issue Non-coding RNA Therapeutics. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v182.2/issuetoc.

The Emerging Roles of CircPVT1 in Cancer Progression

CircRNA is stable due to its ring structure and is abundant in humans, which not only exists in various tissues and biofluids steadily but also plays a significant role in the physiology and pathology of human beings. CircPVT1, an endogenous circRNA, has recently been identified from the PVT1 gene located in the cancer risk region 8q24. CircPVT1 is reported to be highly expressed in many different tumors, where it affects tumor cell proliferation, apoptosis, invasion, and migration. We summarize the biosynthesis and biological functions of circPVT1 and analyze the relationship between circPVT1 and tumors as well as its significance to tumors. Further, it's noteworthy for the diagnosis, treatment, and prognosis of cancer patients. Therefore, circPVT1 is likely to become an innovative tumor marker.

Circular RNAs as a novel class of potential therapeutic and diagnostic biomarkers in reproductive biology/diseases

Infertility is a prevalent problem among 10% of people within their reproductive years. Sometimes, even advanced treatment options like assisted reproduction technology have the potential to result in failed implantation. Because of the expected changes in gene expression during both in vitro and in vivo fertilization processes, these methods of assisting fertility have also been associated with undesirable pregnancy outcomes related to infertility. In this aspect, Circular RNAs (circRNAs) play a crucial role as epigenetic modifiers in a wide range of biological and pathological activities, including problems with fertility. CircRNAs are integral pieces in multiple cellular functions, including moving substances within the nucleus, silencing one X chromosome, cell death, the ability of stem cells to differentiate into different cell types, and the process of gene expression inherited from parental genes. Due to the progress made in high-speed gene sequencing, a large amount of circRNA molecules have been detected, revealing their significant functions in diverse biological functions like enhancing testicular development, preserving the differentiation and renewal of spermatogonial cells, and controlling spermatocyte meiosis. Moreover, these non-coding RNAs contribute in different aspects of female reproductive system including pregnancy-related diseases, gynecologic cancers, and endometriosis. In conclusion, there is no denying that circRNAs have immense potential to be used as biomarkers and treatments for reproductive disorders in males and females. In this research, we provide a comprehensive analysis of the multiple circRNAs associated with women's infertility.

CircMIB1 inhibits glioma development and progression through a competing endogenous RNA interaction network

Introduction

The critical role of circular RNAs as non-coding RNAs in glioma has been extensively investigated. Therefore, we aimed to explore the role and potential molecular mechanisms of circRNA-mind bomb homolog 1 (circMIB1) in gliomas.

Methods

RNA sequencing was used to analyze the expression profiles of circRNAs in glioma tissues and normal brain tissues. Quantitative real-time polymerase chain reaction was implemented to examine the levels of circMIB1 in glioma cells and tissues. The circMIB1 was identified as a cyclic RNA molecule by DNA nucleic acid electrophoresis and ribonuclease R assay. The relationship between circMIB1 expression and the prognosis of glioma patients and its potential as a biomarker were analysed using Kaplan-Meier, Receiver operating characteristic curves, and Principal component analysis. Bioinformatics analysis predicted the miRNAs that bind to circMIB1 and their downstream targets, and analysed the functions of these genes.

Results

Firstly, a novel circRNA molecule termed circMIB1 was identified and validated by RNA sequencing. The expression of circMIB1 was significantly downregulated in glioma cells and tissues, and was closely associated with the tumor grade and survival prognosis of patients with glioma. Hence, it may be useful as a biomarker for glioma. Secondly, it was predicted that circMIB1 binds to hsa-miR-1290 based on bioinformatics analysis, which was significantly upregulated in glioma cells and tissues, and correlated with the tumor grade and overall survival of patients. Thirdly, through a series of bioinformatics analyses identified six genes downstream of hsa-miR-1290 that were significantly associated with glioma expression and prognosis, these genes are associated with cell cycle, cell necrosis and cell circadian rhythms.

Discussion

CircMIB1 may play a role in inhibiting glioma development through the hsa-miR-1290 competitive endogenous RNA interaction network, these findings provide new ideas and directions for the diagnosis and treatment of glioma.

A previously unidentified circRNA inhibits virus replication by regulating the miR-24-3p/KEAP1 axis

Circular RNAs (circRNAs) exert diverse biological functions in different processes. However, the role of circRNAs during virus infection is mostly unknown. Herein, we explored the characteristics of host circRNAs using alphaherpesvirus pseudorabies virus (PRV) as a model. PRV infection upregulated the expression of circRNA circ29164, which does not encode a protein. RNA pulldown assays identified that circ29164 interacts with the microRNA ssc-miRNA-24-3p. Further analysis indicated that ssc-miR-24-3p targets the mRNA encoding kelch-like ECH-associated protein 1 (KEAP1), and circ29164 competitively binds to ssc-miR-24-3p to prevent it binding to Keap1. Apoptosis detection demonstrated that circ29164 or Keap1 overexpression, but not knockdown, induced caspase 3 activity and the release of cytochrome C from mitochondria, and inhibited PRV replication. Taken together, these data identified a previously undiscovered circRNA, circ29164, which inhibits PRV replication by competitively binding to ssc-24-3p to maintain KEAP1 levels.

Epigenetic Modulations of Non-Coding RNAs: A Novel Therapeutic Perspective in Sjӧgren's Syndrome

Sjögren's syndrome (SS) is an autoimmune disease that can be classified as an epithelitis based on the immune-mediated attack directed specifically at epithelial cells. SS predominantly affects women, is characterized by the production of highly specific circulating autoantibodies, and the major targets are the salivary and lachrymal glands. Although a genetic predisposition has been amply demonstrated for SS, the etiology remains unclear. The recent integration of epigenetic data relating to autoimmune diseases opens new therapeutic perspectives based on a better understanding of the molecular processes implicated. In the autoimmune field, non-coding RNA molecules (nc-RNA), which regulate gene expression by binding to mRNAs and could have a therapeutic value, have aroused great interest. The focus of this review is to summarize the biological functions of nc-RNAs in the pathogenesis of SS and decode molecular pathways implicated in the disease, in order to identify new therapeutic strategies.

Mbnl1-mediated alternative splicing of circMlxipl regulates Rbbp6-involved ChREBP turnover to inhibit lipotoxicity-induced β-cell damage

BACKGROUND

Diabetes, a global epidemic, is the leading cause of mortality globally. The aim of this study is to get better understanding of pathophysiology of diabetes.

METHODS

Palmitic acid (PA)-treated β-cells, db/db mice and high fat diet (HFD)-fed mouse model of type 2 diabetes were established. H&E was used to assess the histological changes of pancreas. IHC, FISH, western blot or qRT-PCR was employed to detect the expression of key molecules in primary islets or lipotoxic β-cells. Cell behaviors were detected by MTT, EdU incorporation assay, TUNEL assay and glucose-induced insulin secretion (GSIS). The associations among circMlxipl, Mbnl1 and Rbbp6 were validated by RIP and RNA pull-down assays, and the direct binding between Hdac3 and Mbnl1 promoter was examined by ChIP and luciferase assays. Co-IP was employed to assess the interaction between ChREBP and Rbbp6, as well as the ubiquitination of ChREBP.

RESULTS

Hdac3 and ChREBP were upregulated, but Mbnl1 and circMlxipl were downregulated in islets from diabetic mice and lipotoxic β-cells. Mbnl1 overexpression protected against PA-induced impairments in lipotoxic β-cells through modulating back-splicing of circMlxipl and suppressing ChREBP. Hdac3 served as a transcriptional repressor of Mbnl1, and it was implicated in circMlxipl-mediated protection via regulating ChREBP expression in lipotoxic β-cells. Lack of circMlxipl inhibited Rbbp6-mediated ubiquitin-proteasomal degradation of ChREBP in lipotoxic β-cells. In vivo studies revealed that Hdac3 knockdown or Mbnl1 overexpression alleviated diabetes symptoms through circMlxipl-regulated ChREBP in diabetic mice.

CONCLUSION

Mbnl1-mediated alternative splicing of circMlxipl regulates Rbbp6-involved ChREBP turnover to inhibit lipotoxicity-induced β-cell damage.

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.