Tanvi Sinha1
Kotb Abdelmohsen
Amaresh C. Panda- 1Institute of Life Sciences, Bhubaneswar, India
- 2National Institute on Aging, National Institutes of Health (NIH), Baltimore, MD, United States
Editorial on the Research Topic
Volume II: Structural and functional characterization of circular RNAs
Circular RNAs (circRNAs) are endogenously expressed covalently circularized RNA structures formed via non-canonical backsplicing of the primary transcript where the downstream donor site is ligated to the upstream acceptor site (Salzman et al., 2012; Jeck et al., 2013; Chen and Yang, 2015). Discovered more than 4 decades ago as “tiny circles” in plant viroids and later in eukaryotic cells, circRNAs were initially thought to be junk splicing byproducts (Sanger et al., 1976; Hsu and Coca-Prados, 1979; Nigro et al., 1991). However, later on, the identification and functional characterization of circRNAs gained momentum upon the advancements of transcriptome-wide RNA-sequencing technologies and novel circRNA annotation tools (Salzman et al., 2012; Memczak et al., 2013; Jakobi and Dieterich, 2019). Over the years, circRNAs have emerged as one of the most extensively studied RNA species across the eukaryotic tree of life. The unique chimeric closed loop form of circRNAs confers them with certain special properties such as enhanced tolerance to exonuclease attack rendering them stable compared to their linear isoforms (Salzman et al., 2012; Memczak et al., 2013). An ever-expanding body of research revealed that several circRNAs are conserved across species showing a nearly ubiquitous spatial- and temporal-expression pattern in myriads of mammalian cells and tissue types (Ji et al., 2019). Increasing evidence suggests that circRNAs can function as regulatory transcripts, which serve as microRNA and RNA-binding protein sponges, and directly act as translation templates (Panda, 2018; Das et al., 2021; Sinha et al., 2022).
Interestingly, the altered expression of circRNAs during development, disease progression, the presence in biofluids, and their extraordinary stability make them promising biomarkers for disease diagnosis and hence provide novel approaches for therapeutic intervention (Verduci et al., 2021; Chen et al., 2022). Understanding the unique structural and functional characteristics of circRNAs is essential to uncover gene regulatory systems in human development and disease progression (Chen et al., 2022). Although circRNAs have been established as important regulators of various pathophysiological processes, the molecular mechanisms of circRNAs in regulating gene expression remain to be explored. In addition, only a small fraction of circRNAs has been characterized for their biological functions from tens of thousands of circRNAs identified in humans and mice (Vromman et al., 2020). The goal of our Research Topic is to highlight the recent developments in circRNA research.
While it is crucial to elucidate circRNA function in normal cell physiology and biological processes, there is a rising interest in exploring the role of circRNA dysregulation in cancer, diabetes, neurological disorders, and other diseases. The review by Wang et al., provides a comprehensive summary of the biogenesis and functions of circRNAs, with a major emphasis on the potential molecular mechanisms and their therapeutic applications in urological cancers. This review article is instrumental in developing novel therapeutic strategies for urological cancers in the near future.
Recently thousands of circRNAs were identified in mouse and human skeletal muscle tissue. Moreover, a subset of highly abundant circRNAs was found in mouse skeletal muscle based on experimental validation by RNase R treatment, RT-qPCR analysis, and sequencing of the backsplice junctions. Examining plausible circRNA-miRNA-mRNA networks led to the discovery of conserved circular RNA Nfix (circNfix), which was found to interact with miR-204-5p miRNA, known to suppress myocyte enhancer factor 2c (MEF2C) expression, thereby promoting muscle cell differentiation, was reported by Das et al.
Major hurdles in circRNA research are their relatively low cellular abundance and the dependence of detection methods on input size and lacuna in downstream processing using conventional RNA-seq and computational methodologies. In this Research Topic, a targeted RNA sequencing approach known as Lexo-circSeq has been proposed by Naarmann-de Vries et al., which can detect nearly one hundred circRNAs and their linear counterparts in a single experiment as shown in total human heart RNA samples. Lexo-circSeq can be used to detect any specific circRNA in a large cohort of clinical samples, as demonstrated in hiPSC-derived cardiomyocytes, biopsies from patients diagnosed with hypertrophic cardiomyopathy and dilated cardiomyopathy. Thus, Lexo-circSeq is a cost-effective technique that can monitor circRNA expression patterns across large patient cohorts in terms of circular-to-linear ratios starting with a small input.
Another interesting article by Guria et al., demonstrated a novel template-dependent multiple displacement amplification (tdMDA)-NGS method. The improved-tdMDA-NGS method involves the typical rRNA depletion coupled with cDNA library preparation using H minus reverse transcriptase and RNase H treatment followed by tdMDA using Phi29 DNA polymerase. This cost-effective hybrid NGS approach improves the detection threshold to find even the marginally expressed circRNAs at lower NGS depths. Reportedly, there was a significant rise of nearly 11-fold in the total number of circular RNAs identified in rice plant and HeLa cell line using this improved-tdMDA-NGS method compared to the typical RNA-seq method of circRNA sequencing. Thus, the improved-tdMDA-NGS method can identify and characterize circRNAs in diverse biological samples.
This Research Topic covers the most recent findings concerning the roles of circRNA in health and diseases, as well as articles discussing improved state-of-the-art techniques to aid in accurately detecting circRNAs in clinically challenging scenarios. We believe that the articles highlighted in this Research Topic will be useful for carrying out a study to advance this emerging field of research.
Author contributions
All authors listed have made a substantial, direct, and intellectual contribution to the work and approved it for publication.
Funding
AP was supported by the Intermediate Fellowship of the Wellcome Trust/DBT India Alliance (Grant Number: IA/I/18/2/504017). KA is supported by the National Institute on Aging Intramural Research Program, NIH. TS was supported by the DST-Inspire JRF fellowship.
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Publisher’s note
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References
Chen, L. L., and Yang, L. (2015). Regulation of circRNA biogenesis. RNA Biol. 12, 381–388. doi:10.1080/15476286.2015.1020271
Chen, X., Zhou, M., Yant, L., and Huang, C. (2022). Circular RNA in disease: Basic properties and biomedical relevance. Wiley Interdiscip. Rev. RNA 22, e1723. doi:10.1002/wrna.1723
Das, A., Sinha, T., Shyamal, S., and Panda, A. C. (2021). Emerging role of circular RNA-protein interactions. Noncoding. RNA 7, 48. doi:10.3390/ncrna7030048
Hsu, M. T., and Coca-Prados, M. (1979). Electron microscopic evidence for the circular form of RNA in the cytoplasm of eukaryotic cells. Nature 280, 339–340. doi:10.1038/280339a0
Jakobi, T., and Dieterich, C. (2019). Computational approaches for circular RNA analysis. Wiley Interdiscip. Rev. RNA 10, e1528. doi:10.1002/wrna.1528
Jeck, W. R., Sorrentino, J. A., Wang, K., Slevin, M. K., Burd, C. E., Liu, J., et al. (2013). Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA 19, 141–157. doi:10.1261/rna.035667.112
Ji, P., Wu, W., Chen, S., Zheng, Y., Zhou, L., Zhang, J., et al. (2019). Expanded expression landscape and prioritization of circular RNAs in mammals. Cell. Rep. 26, 3444–3460. doi:10.1016/j.celrep.2019.02.078
Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A., et al. (2013). Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495, 333–338. doi:10.1038/nature11928
Nigro, J. M., Cho, K. R., Fearon, E. R., Kern, S. E., Ruppert, J. M., Oliner, J. D., et al. (1991). Scrambled exons. Cell. 64, 607–613. doi:10.1016/0092-8674(91)90244-s
Panda, A. C. (2018). “Circular RNAs act as miRNA sponges,” in Circular RNAs: Biogenesis and functions. Editor J. Xiao (Singapore: Springer Singapore), 67–79.
Salzman, J., Gawad, C., Wang, P. L., Lacayo, N., and Brown, P. O. (2012). Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One 7, e30733. doi:10.1371/journal.pone.0030733
Sanger, H. L., Klotz, G., Riesner, D., Gross, H. J., and Kleinschmidt, A. K. (1976). Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proc. Natl. Acad. Sci. U. S. A. 73, 3852–3856. doi:10.1073/pnas.73.11.3852
Sinha, T., Panigrahi, C., Das, D., and Chandra Panda, A. (2022). Circular RNA translation, a path to hidden proteome. Wiley Interdiscip. Rev. RNA 13, e1685. doi:10.1002/wrna.1685
Verduci, L., Tarcitano, E., Strano, S., Yarden, Y., and Blandino, G. (2021). CircRNAs: Role in human diseases and potential use as biomarkers. Cell. Death Dis. 12, 468. doi:10.1038/s41419-021-03743-3
Keywords: circular RNA, RNA-sequencing, microRNA sponge, RNA-binding protein, gene regulation
Citation: Sinha T, Abdelmohsen K and Panda AC (2022) Editorial: Volume II: Structural and functional characterization of circular RNAs. Front. Mol. Biosci. 9:1015990. doi: 10.3389/fmolb.2022.1015990
Received: 10 August 2022; Accepted: 15 August 2022;
Published: 06 September 2022.
Edited and reviewed by:
André P. Gerber, University of Surrey, United KingdomCopyright © 2022 Sinha, Abdelmohsen and Panda. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Kotb Abdelmohsen, YWJkZWxtb2hzZW5rQGdyYy5uaWEubmloLmdvdg==; Amaresh C. Panda, YW1hcmVzaC5wYW5kYUBpbHMucmVzLmlu