Short Summary on Circular and Non-coding RNAs

I will share some level of background for circRNAs from the proposal I wrote for CDM5103: Advanced RNA Biology course.

Long non coding RNAs (lncRNAs), >200bp, and circular RNAs (circRNAs) are type of RNAs that are (mostly) not translated into proteins, however, they have vital regulation roles in variety of biological process including cancer in the cell such as interaction between protein and genes, sponging miRNAs, binding to enhancer region or closer loci to the enhancers so modulating the transcription (Mattick&Makunin, 2006; Guttman and Rinn, 2012; Winkle et al., 2015; Chen et al., 2016; Li et al., 2016; Song et al., 2017; Lu et al., 2018).

On the other hand, circRNAs are RNA species having loop structures have diverse roles such as competing with miRNAs to inhibit target genes, regulation of RNA-binding proteins, cell proliferation. They are also more stable compared to mRNAs , since they do not have 3’ and 5’ ends, so having resistance to RNAse-R digestion, having a potential biomarker role (Suzuki et al., 2006; Jeck et al., 2012; Stoffelen et al., 2012; Hansen et al., 2013; Qu et al., 2015; Bahmaycr-Heyda et al., 2015; Zhong Z. et al., 2016; Wang et. al., 2016; Li et al., 2017; Wang et al., 2017).

There are four distinct categories of circRNAs are available: exonic consisting only exons, intronic consisting only introns, exon-intronic consisting both exonic and intronic regions, and intergenic ones (Li et al., 2020). The full-length sequence analysis of circRNAs and their isoforms is important to understand its function especially in the presence of alternative splicing events such as exon skipping or retention of the introns (Dong et al.,2017; You et al., 2015; Zhang et al., 2016).

Nevertheless, there has been accumulating evidence on circRNAs not only originated from pre-miRNAs but also from long non-coding RNAs associated with different risk factors and distinct mediatory roles (Burd et al., 2010; Holdt et al., 2016; Huang et al., 2018; Zhang et al., 2019). Moreover, their abundance in the blood and wide distribution across tissues make them an ideal biomarker candidate (Provost, P., 2016; Chen et al., 2016; Zhao et al., 2017).

References

(Only some part of my proposal is shared here, so there might be more reference)

Bachmayr-Heyda, A., Reiner, A. T., Auer, K., Sukhbaatar, N., Aust, S., Bachleitner-Hofmann, T., Mesteri, I., Grunt, T. W., Zeillinger, R., & Pils, D. (2015). Correlation of circular RNA abundance with proliferation — exemplified with colorectal and ovarian cancer, idiopathic lung fibrosis and normal human tissues. Scientific Reports, 5(1), 8057. https://doi.org/10.1038/srep08057

Burd, C. E., Jeck, W. R., Liu, Y., Sanoff, H. K., Wang, Z., & Sharpless, N. E. (2010). Expression of Linear and Novel Circular Forms of an INK4/ARF-Associated Non-Coding RNA Correlates with Atherosclerosis Risk. PLOS Genetics, 6(12), e1001233. https://doi.org/10.1371/journal.pgen.1001233

Chen, L.-L. (2016). The biogenesis and emerging roles of circular RNAs. Nature Reviews Molecular Cell Biology, 17(4), 205–211. https://doi.org/10.1038/nrm.2015.32

Chen, Z., Huang, L., Wu, Y., Zhai, W., Zhu, P., & Gao, Y. (2016). LncSox4 promotes the self-renewal of liver tumour-initiating cells through Stat3-mediated Sox4 expression. Nature Communications, 7(1), 12598. https://doi.org/10.1038/ncomms12598

Chen — 2016 — The biogenesis and emerging roles of circular RNAs.pdf. (n.d.). Retrieved November 11, 2020, from https://www-nature-com.libproxy1.nus.edu.sg/articles/nrm.2015.32.pdf?origin=ppub

Circular RNAs are abundant, conserved, and associated with ALU repeats. (n.d.). Retrieved November 11, 2020, from https://rnajournal-cshlp-org.libproxy1.nus.edu.sg/content/19/2/141.short

Ding, Y., Gao, H., & Zhang, Q. (2017). The biomarkers of leukemia stem cells in acute myeloid leukemia. Stem Cell Investigation, 4. https://doi.org/10.21037/sci.2017.02.10

Dong, R., Ma, X.-K., Chen, L.-L., & Yang, L. (2017). Increased complexity of circRNA expression during species evolution. RNA Biology, 14(8), 1064–1074. https://doi.org/10.1080/15476286.2016.1269999

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Gao, Y., Wang, J., Zheng, Y., Zhang, J., Chen, S., & Zhao, F. (2016). Comprehensive identification of internal structure and alternative splicing events in circular RNAs. Nature Communications, 7(1), 12060. https://doi.org/10.1038/ncomms12060

Guttman, M., & Rinn, J. L. (2012). Modular regulatory principles of large non-coding RNAs. Nature, 482(7385), 339–346. https://doi.org/10.1038/nature10887

Hansen, T. B., Jensen, T. I., Clausen, B. H., Bramsen, J. B., Finsen, B., Damgaard, C. K., & Kjems, J. (2013). Natural RNA circles function as efficient microRNA sponges. Nature, 495(7441), 384–388. https://doi.org/10.1038/nature11993

Huang, M.-S., Zhu, T., Li, L., Xie, P., Li, X., Zhou, H.-H., & Liu, Z.-Q. (2018). LncRNAs and CircRNAs from the same gene: Masterpieces of RNA splicing. Cancer Letters, 415, 49–57. https://doi.org/10.1016/j.canlet.2017.11.034

Jeck, W. R., & Sharpless, N. E. (2014). Detecting and characterizing circular RNAs. Nature Biotechnology, 32(5), 453–461. https://doi.org/10.1038/nbt.2890

Lee, C., & Roy, M. (2004). Analysis of alternative splicing with microarrays: Successes and challenges. Genome Biology, 5(7), 1–4. https://doi.org/10.1186/gb-2004-5-7-231

Li, D., Liu, X., Zhou, J., Hu, J., Zhang, D., Liu, J., Qiao, Y., & Zhan, Q. (2017). Long noncoding RNA HULC modulates the phosphorylation of YB-1 through serving as a scaffold of extracellular signal–regulated kinase and YB-1 to enhance hepatocarcinogenesis. Hepatology, 65(5), 1612–1627. https://doi.org/10.1002/hep.29010

Li et al. — 2020 — The mechanism and detection of alternative splicin.pdf. (n.d.). Retrieved November 11, 2020, from https://peerj.com/articles/10032.pdf

Li, M., Zhao, L., Li, S., Li, J., Gao, B., Wang, F., Wang, S., Hu, X., Cao, J., & Wang, G. (2018). Differentially expressed lncRNAs and mRNAs identified by NGS analysis in colorectal cancer patients. Cancer Medicine, 7(9), 4650–4664. https://doi.org/10.1002/cam4.1696

Li, Xiang, Liu, C.-X., Xue, W., Zhang, Y., Jiang, S., Yin, Q.-F., Wei, J., Yao, R.-W., Yang, L., & Chen, L.-L. (2017). Coordinated circRNA Biogenesis and Function with NF90/NF110 in Viral Infection. Molecular Cell, 67(2), 214–227.e7. https://doi.org/10.1016/j.molcel.2017.05.023

Li, Xiaohan, Zhang, B., Li, F., Yu, K., & Bai, Y. (2020). The mechanism and detection of alternative splicing events in circular RNAs. PeerJ, 8, e10032. https://doi.org/10.7717/peerj.10032

Long noncoding RNA SNHG1 promotes non‐small cell lung cancer progression by up‐regulating MTDH via sponging miR‐145–5p — Lu — 2018 — The FASEB Journal — Wiley Online Library. (n.d.). Retrieved November 11, 2020, from https://faseb.onlinelibrary.wiley.com/doi/full/10.1096/fj.201701237RR

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Provost, P. (2016). Platelets enrich their transcriptome circle. Blood, 127(9), 1080–1081. https://doi.org/10.1182/blood-2015-12-687723

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Song, Y., Sun, J., Zhao, J., Yang, Y., Shi, J., Wu, Z., Chen, X., Gao, P., Miao, Z., & Wang, Z. (2017). Non-coding RNAs participate in the regulatory network of CLDN4 via ceRNA mediated miRNA evasion. Nature Communications, 8(1), 289. https://doi.org/10.1038/s41467-017-00304-1

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Wang, F., Nazarali, A. J., & Ji, S. (2016). Circular RNAs as potential biomarkers for cancer diagnosis and therapy. American Journal of Cancer Research, 6(6), 1167–1176.

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Zhang, L., Hu, J., Li, J., Yang, Q., Hao, M., & Bu, L. (2019). Long noncoding RNA LINC-PINT inhibits non-small cell lung cancer progression through sponging miR-218–5p/PDCD4. Artificial Cells, Nanomedicine, and Biotechnology, 47(1), 1595–1602. https://doi.org/10.1080/21691401.2019.1605371

Zhao, Z., Li, X., Gao, C., Jian, D., Hao, P., Rao, L., & Li, M. (2017). Peripheral blood circular RNA hsa_circ_0124644 can be used as a diagnostic biomarker of coronary artery disease. Scientific Reports, 7(1), 39918. https://doi.org/10.1038/srep39918

Zhong, Z., Lv, M., & Chen, J. (2016). Screening differential circular RNA expression profiles reveals the regulatory role of circTCF25-miR-103a-3p/miR-107-CDK6 pathway in bladder carcinoma. Scientific Reports, 6(1), 30919. https://doi.org/10.1038/srep30919