Nonradioactive Northern Blot of circRNAs

A Mammalian Conserved Circular RNA CircLARP1B Regulates Hepatocellular Carcinoma Metastasis and Lipid Metabolism

Circular RNAs (circRNAs) have emerged as crucial regulators in physiology and human diseases. However, evolutionarily conserved circRNAs with potent functions in cancers are rarely reported. In this study, a mammalian conserved circRNA circLARP1B is identified to play critical roles in hepatocellular carcinoma (HCC). Patients with high circLARP1B levels have advanced prognostic stage and poor overall survival. CircLARP1B facilitates cellular metastatic properties and lipid accumulation through promoting fatty acid synthesis in HCC. CircLARP1B deficient mice exhibit reduced metastasis and less lipid accumulation in an induced HCC model. Multiple lines of evidence demonstrate that circLARP1B binds to heterogeneous nuclear ribonucleoprotein D (HNRNPD) in the cytoplasm, and thus affects the binding of HNRNPD to sensitive transcripts including liver kinase B1 (LKB1) mRNA. This regulation causes decreased LKB1 mRNA stability and lower LKB1 protein levels. Antisense oligodeoxynucleotide complementary to theHNRNPD binding sites in circLARP1B increases the HNRNPD binding to LKB1 mRNA. Through the HNRNPD-LKB1-AMPK pathway, circLARP1B promotes HCC metastasis and lipid accumulation. Results from AAV8-mediated hepatocyte-directed knockdown of circLARP1B or Lkb1 in mouse models also demonstrate critical roles of hepatocytic circLARP1B regulatory pathway in HCC metastasis and lipid accumulation, and indicate that circLARP1B may be potential target of HCC treatment.

Recent Progress on Circular RNAs in the Development of Skeletal Muscle and Adipose Tissues of Farm Animals

Circular RNAs (circRNAs) are a highly conserved and specifically expressed novel class of covalently closed non-coding RNAs. CircRNAs can function as miRNA sponges, protein scaffolds, and regulatory factors, and play various roles in development and other biological processes in mammals. With the rapid development of high-throughput sequencing technology, thousands of circRNAs have been discovered in farm animals; some reportedly play vital roles in skeletal muscle and adipose development. These are critical factors affecting meat yield and quality. In this review, we have highlighted the recent advances in circRNA-related studies of skeletal muscle and adipose in farm animals. We have also described the biogenesis, properties, and biological functions of circRNAs. Furthermore, we have comprehensively summarized the functions and regulatory mechanisms of circRNAs in skeletal muscle and adipose development in farm animals and their effects on economic traits such as meat yield and quality. Finally, we propose that circRNAs are putative novel targets to improve meat yield and quality traits during animal breeding.

Circular RNA detection methods: A minireview

Circular RNA (circRNA), a novel type of covalently closed RNA, is implicated in several developmental and metabolic disease processes. CircRNAs exhibit tissue-specific expression, and are stable, abundant, and highly conserved, making them ideal biomarkers for diagnosis and prognosis. Accurate profiling of circRNA, however, is a prerequisite for their clinical application. Traditional methods such as northern blotting, RT-qPCR, and microarray analysis provide useful but limited information. To address these issues, a number of novel assays have recently emerged, such as droplet digital PCR (ddPCR), isothermal exponential amplification, and rolling cycle amplification, which increase the sensitivity and specificity of circRNA detection. Herein, we summarize the advantages and limitations of the new detection methods and discuss the challenges as well as future directions.

Circular RNAs in cardiovascular diseases

In eukaryotes, precursor mRNAs (pre-mRNAs) produce a unique class of biologically active molecules namely circular RNAs (circRNAs) with a covalently closed-loop structure via back-splicing. Because of this unconventional circular form, circRNAs exhibit much higher stability than linear RNAs due to the resistance to exonuclease degradation and thereby play exclusive cellular regulatory roles. Recent studies have shown that circRNAs are widely expressed in eukaryotes and display tissue- and disease-specific expression patterns, including in the cardiovascular system. Although numerous circRNAs are discovered by in silico methods, a limited number of circRNAs have been studied. This review intends to summarize the current understanding of the characteristics, biogenesis, and functions of circRNAs and delineate the practical approaches for circRNAs investigation. Moreover, we discuss the emerging roles of circRNAs in cardiovascular diseases.

The Use of circRNAs as Biomarkers of Cancer

CircRNAs are a subclass of lncRNAs that have been found to be abundantly present in a wide range of species, including humans. CircRNAs are generally produced by a noncanonical splicing event called backsplicing that is dependent on the canonical splicing machinery, giving rise to circRNAs classified into three main categories: exonic circRNA, circular intronic RNA, and exon-intron circular RNA. Notably, circRNAs possess functional importance and display their functions through different mechanisms of action including sponging miRNAs, or even being translated into functional proteins. In addition, circRNAs also have great potential as biomarkers, particularly in cancer, thanks to their high stability, tissue type and developmental stage specificity, and their presence in biological fluids, which make them promising candidates as noninvasive biomarkers. In this chapter, we describe the most commonly used techniques for the study of circRNAs as cancer biomarkers, including high-throughput techniques such as RNA-Seq and microarrays, and other methods to analyze the presence of specific circRNAs in patient samples.

CircURI1 interacts with hnRNPM to inhibit metastasis by modulating alternative splicing in gastric cancer

Circular RNAs (circRNAs) have emerged as key regulators of human cancers, yet their modes of action in gastric cancer (GC) remain largely unknown. Here, we identified circURI1 back-spliced from exons 3 and 4 of unconventional prefoldin RPB5 interactor 1 (URI1) from circRNA profiling of five-paired human gastric and the corresponding nontumor adjacent specimens (paraGC). CircURI1 exhibits the significantly higher expression in GC compared with paraGC and inhibitory effects on cell migration and invasion in vitro and GC metastasis in vivo. Mechanistically, circURI1 directly interacts with heterogeneous nuclear ribonucleoprotein M (hnRNPM) to modulate alternative splicing of genes, involved in the process of cell migration, thus suppressing GC metastasis. Collectively, our study expands the current knowledge regarding the molecular mechanism of circRNA-mediated cancer metastasis via modulating alternative splicing.

Identification and detection of mecciRNAs

Mitochondria participate in series of metabolic processes and cellular events. It is widely known that only 13 proteins are encoded by the mammalian mitochondria genome. However, it is not acknowledged until recently that mitochondrial genomes encode hundreds of circular RNAs, named as mecciRNAs. Some of these mecciRNAs can serve as molecular chaperones to help folding nuclear-encoded proteins and facilitating their mitochondrial entrance. As a novel type of circular RNAs, functions and characteristics of mecciRNAs are waiting for further exploration and methods for mecciRNA studies need to be improved. Here, we describe detailed methods for mitochondrial RNA isolation and mecciRNA detection. In addition, we present effective mecciRNA overexpression and knockdown strategies for future functional studies of mecciRNAs.

Circular RNA in renal diseases

Circular RNA (circRNA) is a newly described type of non-coding RNA. Active research is greatly enriching the current understanding of the expression and role of circRNA, and a large amount of evidence has implicated circRNA in the pathogenesis of certain renal diseases, such as renal cell carcinoma, acute kidney injury, diabetic nephropathy and lupus nephritis. Studies have found evidence that circRNAs regulate programmed cell death, invasion, and metastasis and serve as biomarkers in renal diseases. Recently, circRNAs were identified in exosomes secreted by the kidneys. Nevertheless, the function of circRNA in renal diseases remains ambiguous. Given that circRNAs are regulators of gene expression, they may be involved in the pathology of multiple renal diseases. Additionally, emerging evidence is showing that circulating circRNAs may serve as novel biomarkers for renal disease. In this review, we have summarized the identification, biogenesis, degradation, and functions of circRNA and have evaluated the roles of circRNA in renal diseases.

Identification of mecciRNAs and their roles in the mitochondrial entry of proteins

Mammalian mitochondria have small genomes encoding very limited numbers of proteins. Over one thousand proteins and noncoding RNAs encoded by the nuclear genome must be imported from the cytosol into the mitochondria. Here, we report the identification of hundreds of circular RNAs (mecciRNAs) encoded by the mitochondrial genome. We provide both in vitro and in vivo evidence to show that mecciRNAs facilitate the mitochondrial entry of nuclear-encoded proteins by serving as molecular chaperones in the folding of imported proteins. Known components involved in mitochondrial protein and RNA importation, such as TOM40 and PNPASE, interact with mecciRNAs and regulate protein entry. The expression of mecciRNAs is regulated, and these transcripts are critical for the adaption of mitochondria to physiological conditions and diseases such as stresses and cancers by modulating mitochondrial protein importation. mecciRNAs and their associated physiological roles add categories and functions to the known eukaryotic circular RNAs and shed novel light on the communication between mitochondria and the nucleus.

SplintQuant: a method for accurately quantifying circular RNA transcript abundance without reverse transcription bias

Reverse transcription of RNA is fallible, introducing biases and confounding the quantification of transcript abundance. We demonstrate that circular RNAs (circRNAs) are more subjective to overestimation of transcript abundance than cognate linear RNAs due to their covalently closed, circular form, producing multiple concatameric products from a single priming of reverse transcriptase. We developed SplintQuant, where custom DNA oligonucleotides are ligated by PBCV-1 DNA ligase only when bound to their target RNA. These circRNA-specific DNA oligonucleotides are terminally tagged with universal primers, allowing SplintQuant to accurately quantify even lowly abundant circRNAs through highly specific quantitative PCR (qPCR) in the absence of reverse transcription. SplintQuant is sensitive, specific, highly reproducible, and applicable to the quantification of canonical and noncanonical RNA transcripts including alternative splice variants, gene fusions, and offers a gold-standard approach for accurately quantifying circRNAs.