seekCRIT: Detecting and characterizing differentially expressed circular RNAs using high-throughput sequencing data

Beyond traditional translation: ncRNA derived peptides as modulators of tumor behaviors

Within the intricate tapestry of molecular research, noncoding RNAs (ncRNAs) were historically overshadowed by a pervasive presumption of their inability to encode proteins or peptides. However, groundbreaking revelations have challenged this notion, unveiling select ncRNAs that surprisingly encode peptides specifically those nearing a succinct 100 amino acids. At the forefront of this epiphany stand lncRNAs and circRNAs, distinctively characterized by their embedded small open reading frames (sORFs). Increasing evidence has revealed different functions and mechanisms of peptides/proteins encoded by ncRNAs in cancer, including promotion or inhibition of cancer cell proliferation, cellular metabolism (glucose metabolism and lipid metabolism), and promotion or concerted metastasis of cancer cells. The discoveries not only accentuate the depth of ncRNA functionality but also open novel avenues for oncological research and therapeutic innovations. The main difficulties in the study of these ncRNA-derived peptides hinge crucially on precise peptide detection and sORFs identification. Here, we illuminate cutting-edge methodologies, essential instrumentation, and dedicated databases tailored for unearthing sORFs and peptides. In addition, we also conclude the potential of clinical applications in cancer therapy.

Circular RNAs in intracranial aneurysms: Emerging roles in pathogenesis, diagnosis and therapeutic intervention

Intracranial aneurysms (IAs) present a substantial health threat, given the potential for catastrophic ruptures and subarachnoid hemorrhages (SAH). Swift and effective measures for diagnosis and treatment are paramount to enhance patient outcomes and alleviate the associated healthcare burden. In this context, circular RNAs (circRNAs) have emerged as an intriguing area of investigation, offering promise as both diagnostic biomarkers and therapeutic targets for IAs. CircRNAs have demonstrated their influence on critical molecular and cellular processes underpinning IAs pathogenesis, revealing their pivotal role in understanding this complex ailment. Beyond their diagnostic potential, circRNAs hold great potential as prognostic markers, providing crucial insights into IAs rupture risk. The unique circular structure and their regulatory functions make circRNAs an enticing avenue for innovative therapeutic approaches. The ongoing study of circRNAs in the context of IAs is an exciting and rapidly evolving field that has the potential to revolutionize approaches to diagnosis, treatment, and prevention of this life-threatening condition. As research continues to unravel the intricate roles of circRNAs, they are poised to become invaluable tools in clinical practice, enhancing patient care and ultimately reducing the impact of cerebral aneurysms on both individuals and healthcare systems. This comprehensive review delves deeply into the world of circRNAs in the realm of IAs, elucidating their multifaceted roles in the onset and progression of this condition. Moreover, this review ventures into the diagnosis and therapeutic potential of circRNAs, exploring their possible applications in gene therapy and as targets for novel treatment modalities.

Circular RNA expression profile and functional analysis of circUvrag in light-induced photoreceptor degeneration

BACKGROUND

Circular RNAs (circRNAs) are implicated in retinal pathophysiology; however, their expression profiles and functions in photoreceptor apoptosis are largely unknown. We explored circRNA-expression profiles and circUvrag (host gene: Uvrag, ultraviolet radiation resistance associated gene) function in light-induced photoreceptor apoptosis.

METHODS

Sprague-Dawley rats and 661 W photoreceptor cells were exposed to blue light to establish light-induced photoreceptor degeneration. Differentially expressed circRNAs were identified using microarrays. Potential functions of dysregulated circRNAs were analysed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. CircUvrag expression and localization were evaluated using quantitative RT-PCR and fluorescence in situ hybridization, respectively. CircUvrag overexpression and knockdown were induced using a plasmid and a small interfering RNA, respectively, and retinal function and structure were assessed using scotopic electroretinography, haematoxylin-eosin staining, and TUNEL staining. Microglial migration was assessed using IBA1 immunostaining. The apoptosis ratio of photoreceptor cells in vitro was detected using flow cytometry.

RESULTS

We identified 764 differentially expressed circRNAs, which were potentially related with the development of retinal structures, including neurons, dendrites, and synapses, and might participate in nervous-system pathophysiology. Light exposure enriched circUvrag in the cytoplasm of photoreceptors in the outer nuclear layer (ONL). CircUvrag knockdown decreased photoreceptor apoptosis and microglial migration to the ONL after light exposure, preserving ONL thickness and a-wave amplitude. In vitro, circUvrag knockdown inhibited photoreceptor apoptosis, although circUvrag overexpression slightly promoted photoreceptor apoptosis.

CONCLUSIONS

CircUvrag knockdown attenuated light-induced photoreceptor apoptosis, and might be a potential target in retinal degeneration.

Identification of key genes and regulatory mechanisms in adult degenerative scoliosis

BACKGROUND

Adult degenerative scoliosis (ADS) is a spinal disorder, but its pathogenesis remain unclear. Therefore, in this study, we utilized data from the GEO database and explored the key genes and regulatory mechanisms involved in ADS.

METHODS

We performed bioinformatics analysis on the GSE209825 dataset of GEO database. Weighted gene co-expression network analysis (WGCNA) was used to identify ADS-related gene modules, and we performed gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. We constructed a protein-protein interaction (PPI) network using the STRING database. We validated the specificity of hub genes in ADS using the GSE34095 dataset and plotted ROC curves for the identification of different degenerative spinal diseases based on the hub genes expression RESULTS: We identified 113 differentially expressed lncRNAs. WGCNA identified the MEblack module had the strongest correlation to ADS. GO and KEGG analyses of target genes in lncRNAs revealed their involvement in immune responses, inflammation, cellular processes, and metabolic pathways. Through PPI and ROC analysis, 10 hub genes linked to ADS diseases with certain specificity were found: ELANE, LTF, DEFA1B, SLC2A4, DEFA1, FAXDC2, LCN2, CTSB, FDFT1, and AURKA.

CONCLUSIONS

We identified 10 potential hub genes associated with ADS and constructed a transcription factors (TFs)-lncRNAs-hub genes regulatory network. These findings provide a new direction and research basis for the targeted treatment and mechanism research of ADS.

PARP1 Regulates Circular RNA Biogenesis though Control of Transcriptional Dynamics

Circular RNAs (circRNAs) are a recently discovered class of RNAs derived from protein-coding genes that have important biological and pathological roles. They are formed through backsplicing during co-transcriptional alternative splicing; however, the unified mechanism that accounts for backsplicing decisions remains unclear. Factors that regulate the transcriptional timing and spatial organization of pre-mRNA, including RNAPII kinetics, the availability of splicing factors, and features of gene architecture, have been shown to influence backsplicing decisions. Poly (ADP-ribose) polymerase I (PARP1) regulates alternative splicing through both its presence on chromatin as well as its PARylation activity. However, no studies have investigated PARP1's possible role in regulating circRNA biogenesis. Here, we hypothesized that PARP1's role in splicing extends to circRNA biogenesis. Our results identify many unique circRNAs in PARP1 depletion and PARylation-inhibited conditions compared to the wild type. We found that while all genes producing circRNAs share gene architecture features common to circRNA host genes, genes producing circRNAs in PARP1 knockdown conditions had longer upstream introns than downstream introns, whereas flanking introns in wild type host genes were symmetrical. Interestingly, we found that the behavior of PARP1 in regulating RNAPII pausing is distinct between these two classes of host genes. We conclude that the PARP1 pausing of RNAPII works within the context of gene architecture to regulate transcriptional kinetics, and therefore circRNA biogenesis. Furthermore, this regulation of PARP1 within host genes acts to fine tune their transcriptional output with implications in gene function.

Systematic benchmarking of statistical methods to assess differential expression of circular RNAs

Circular RNAs (circRNAs) are covalently closed transcripts involved in critical regulatory axes, cancer pathways and disease mechanisms. CircRNA expression measured with RNA-seq has particular characteristics that might hamper the performance of standard biostatistical differential expression assessment methods (DEMs). We compared 38 DEM pipelines configured to fit circRNA expression data's statistical properties, including bulk RNA-seq, single-cell RNA-seq (scRNA-seq) and metagenomics DEMs. The DEMs performed poorly on data sets of typical size. Widely used DEMs, such as DESeq2, edgeR and Limma-Voom, gave scarce results, unreliable predictions or even contravened the expected behaviour with some parameter configurations. Limma-Voom achieved the most consistent performance throughout different benchmark data sets and, as well as SAMseq, reasonably balanced false discovery rate (FDR) and recall rate. Interestingly, a few scRNA-seq DEMs obtained results comparable with the best-performing bulk RNA-seq tools. Almost all DEMs' performance improved when increasing the number of replicates. CircRNA expression studies require careful design, choice of DEM and DEM configuration. This analysis can guide scientists in selecting the appropriate tools to investigate circRNA differential expression with RNA-seq experiments.

Identification and functional analysis of circRNAs in the skeletal muscle of juvenile and adult largemouth bass (Micropterus salmoides)

Circular RNA (circRNA) is a novel emerging type of endogenous regulatory non-coding RNA molecules with a covalent closed-loop configuration, which exerts important functions in multiple biological processes. CircRNAs are known to regulate gene expression as functional regulators interacting with miRNAs by sponge, which have been reported to regulate skeletal muscle development. Nevertheless, the information of circRNAs involved in regulating muscle growth and development in fish is largely unknown. Here, we first identified 312 and 511 circRNAs in skeletal muscle of juvenile and adult largemouth bass (LMB) using RNA sequencing, respectively. The differentially expressed circRNAs (DE-circRNAs) analysis showed that there are 44 DE-circRNAs at two different skeletal muscle growth stages. Six circRNAs were chosen randomly and their relative expression levels in juvenile and adult LMB were confirmed by real-time PCR, indicating that these circRNAs were existed authenticity. In addition, Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis showed that these hose genes (their linear mRNAs) of DE-circRNAs were mainly enriched in the regulation of actin cytoskeleton signaling pathways. The circRNA-miRNA interaction regulatory networks indicated that one circRNA can regulate one or more miRNA. For instance, more than 30 miRNAs were regulated by two circRNAs (circRNA389 and circRNA399). Of them, the muscle-related miRNAs including the let-7 family, miR-133 and miR-26 and so on were found acting as miRNAs sponge regulated by circRNAs, indicating the roles of circRNAs in regulating muscle growth-related genes expression. Overall, these findings will not only broaden our understanding of circRNAs regulation mechanisms underlying muscle growth and development in LMB but also provides a novel clue for further functional research in carnivorous fish genetic breeding.

Circ_0039960 regulates growth and Warburg effect of breast cancer cells via modulating miR-1178/PRMT7 axis

BACKGROUND

Breast cancer (BC) is a serious threat to women's life and healthy. Increasing evidence indicated that blocking Warburg effect could attenuate the development of BC. Circular RNAs (circRNAs) has been found to be dysregulated in various carcinomas, including BC. Our study aims to illustrate the role and regulatory mechanism of circ_0039960 in BC development.

METHODS

RT-qPCR and western blotting were utilized to evaluate the expression of circ_0039960 in tissues recruited from 32 cases of BC patients and also BC cell lines. Circ_0039960 shRNA was transfected into cells to explore its function on cell processes. CCK-8, flow cytometry and ELISA were used to measure cell viability, cell cycle and apoptosis. Warburg effect was detected by using commercial kits. Besides, bioinformatic prediction, RIP and luciferase reporter assays were performed to validate the interactions between circ_0039960, miR-1178 and PRMT7.

RESULTS

The results showed that circ_0039960 and PRMT7 were both up-regulated, while miR-1178 was down-regulated, in BC tissues and cells. Silencing circ_0039960 effectively inhibited cell viability and Warburg effect of BC cells, also, induced cell cycle arrest and apoptosis. Moreover, we validated that circ_0039960 positively mediated PRMT7 expression via directly targeting to miR-1178. The inhibition of miR-1178 and overexpression of PRMT7 reversed the effect of circ_0039960 knockdown on BC cell growth and Warburg effect.

CONCLUSION

In general, our research demonstrated that circ_0039960 regulates cell growth and Warburg effect in BC cells via miR-1178/PRMT7 axis. This may provide new evidence for the exploration of BC diagnostic and therapeutic targets.

Genome wide expression analysis of circular RNAs in mammary epithelial cells of cattle revealed difference in milk synthesis

Milk is an excellent source of nutrients for humans. Therefore, in order to enhance the quality and production of milk in cattle, it is interesting to examine the underlying mechanisms. A number of new investigations and research have found that, circRNA; a specific class of non-coding RNAs, is linked with the development of mammary gland and lactation. In the present study, genome wide identification and expression of the circRNAs in mammary epithelial cells of two distinct cattle breeds viz Jersey and Kashmiri at peak lactation was conducted. We reported 1554 and 1286 circRNA in Jersey and Kashmiri cattle, respectively, with 21 circRNAs being differentially expressed in the two breeds. The developmental genes of the established differentially expressed circRNAs were found to be largely enriched in antioxidant activity, progesterone, estradiol, lipid, growth hormone, and drug response. Certain pathways like MAPK, IP3K and immune response pathways were found significantly enriched in KEGG analysis. These results add to our understanding of the controlling mechanisms connected with the lactation process, as well as the function of circRNAs in bovine milk synthesis. Additionally, the comparative analysis of differentially expressed circRNAs showed significant conservation across different species.

circ‑Grm1 promotes pulmonary artery smooth muscle cell proliferation and migration via suppression of GRM1 expression by FUS

Pulmonary arterial hypertension is a progressive and fatal disease. Recent studies suggest that circular RNA (circRNAs/circs) can regulate various biological processes, including cell proliferation. Therefore, it is possible that circRNA may have important roles in pulmonary artery smooth muscle cell proliferation in hypoxic pulmonary hypertension (HPH). The aim of the present study was to determine the role and mechanism of circRNA‑glutamate metabotropic receptor 1 (circ‑Grm1; mmu_circ_0001907) in pulmonary artery smooth muscle cell (PASMC) proliferation and migration in HPH. High‑throughput transcriptome sequencing was used to screen circRNAs and targeted genes involved in HPH. Cell Counting Kit‑8 (CCK‑8), 5‑ethynyl‑2‑deoxyuridine and wound healing assays were employed to assess cell viability and migration. Reverse transcription‑quantitative PCR and western blotting were used to detect target gene expression in different groups. Bioinformatical approaches were used to predict the interaction probabilities of circ‑Grm1 and Grm1 with FUS RNA binding protein (FUS). The interactions of circ‑Grm1, Grm1 and FUS were evaluated using RNA silencing and RNA immunoprecipitation assays. The results demonstrated that circ‑Grm1 was upregulated in hypoxic PASMCs. Further experiments revealed that the knockdown of circ‑Grm1 could suppress the proliferation and migration of hypoxic PASMCs. Transcriptome sequencing revealed that Grm1 could be the target gene of circ‑Grm1. It was found that circ‑Grm1 could competitively bind to FUS and consequently downregulate Grm1. Moreover, Grm1 could inhibit the function of circ‑Grm1 by promoting the proliferative and migratory abilities of hypoxic PASMCs. The results also demonstrated that circ‑Grm1 influenced the biological functions of PASMCs via the Rap1/ERK pathway by regulating Grm1. Overall, the current results suggested that circ‑Grm1 was associated with HPH and promoted the proliferation and migration of PASMCs via suppression of Grm1 expression through FUS.

Advances in Non-Coding RNA Sequencing

Non-coding RNAs (ncRNAs) comprise a set of abundant and functionally diverse RNA molecules. Since the discovery of the first ncRNA in the 1960s, ncRNAs have been shown to be involved in nearly all steps of the central dogma of molecular biology. In recent years, the pace of discovery of novel ncRNAs and their cellular roles has been greatly accelerated by high-throughput sequencing. Advances in sequencing technology, library preparation protocols as well as computational biology helped to greatly expand our knowledge of which ncRNAs exist throughout the kingdoms of life. Moreover, RNA sequencing revealed crucial roles of many ncRNAs in human health and disease. In this review, we discuss the most recent methodological advancements in the rapidly evolving field of high-throughput sequencing and how it has greatly expanded our understanding of ncRNA biology across a large number of different organisms.

AQUARIUM: accurate quantification of circular isoforms using model-based strategy

SUMMARY

Currently, most computational methods estimate the expression of circular RNAs (circRNAs) using the number of sequencing reads that support back-splicing junctions (BSJ) in RNA-seq data, which may introduce biased estimation of circRNA expression due to the uneven distribution of sequencing reads. To overcome this, we previously developed a model-based strategy for circRNA quantification, enabling consideration of sequencing reads from the entire transcript. Yet, the lack of exact transcript structure of circRNAs may limit its accuracy. Here, we proposed a substantially improved circRNA quantification tool, AQUARIUM, by introducing the full-length RNA structure of circular isoforms. We assessed its performance in circRNA quantification using both biological and simulated rRNA-depleted RNA-seq datasets, and demonstrated its superior performance at both BSJ and isoform level.

AVAILABILITY AND IMPLEMENTATION

AQUARIUM is freely available at https://github.com/wanjun-group-seu/AQUARIUM.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Role and mechanism of action of circular RNA and laryngeal cancer

Laryngeal squamous cell carcinoma (LSCC), is the second most common malignant cancer of the head and neck after oral cavity cancer. Laryngeal cancer is associated with huge socio-economic burden worldwide. Studies have widely explored the role of non-coding RNAs, especially microRNAs and long non-coding RNAs in pathogenesis of laryngeal cancer. In addition, several studies have explored the mechanism and function of circRNAs. CircRNAs has higher stability and more extensive function models, including combining miRNA as sponge, modifying transcription, and even regulating protein translation have been developed. Therefore, circRNAs is applied as an excellent diagnostic tool and a promising candidate for development of cancer therapies. This study reviews the biogenesis and function of circRNAs, explores potential mechanism of circRNAs in LSCC, and implications and challenges in LSCC research.

Regulatory mechanisms, functions, and clinical significance of CircRNAs in triple-negative breast cancer

Circular RNAs (circRNAs) are a new class of endogenous regulatory RNAs characterized by covalently closed cyclic structure lacking poly-adenylated tails, and are capable of regulating gene expression at transcription or post-transcription levels. Recently, plentiful circRNAs have been discovered in breast cancer and some circRNAs expression profiles are specifically involved in the triple-negative breast cancer (TNBC). TNBC is a type of malignant tumor defined by the lack of estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 expression. Considering its clinical characteristics of high invasion, metastasis, poor prognosis, and lack of effective response to conventional chemotherapies or targeted therapies, it could be a promosing option to discover specific circRNAs as new targets for TNBC treatment. Meanwhile, accumulating evidence has demonstrated that circRNAs are dysregulated in TNBC tissues and are correlated with clinicopathological features and prognosis of TNBC patients. Furthermore, looking for circRNAs with high specificity and sensitivity will provide a new opportunity for the early diagnosis, clinical treatment, and prognosis monitoring of TNBC. Herein, we reviewed the biogenesis, regulatory mechanisms, and biological functions of circRNAs in TNBC and summarized the relationship between circRNAs expression and the clinicopathology, diagnosis, and prognosis of patients with TNBC.