COL: a method for identifying putatively functional circular RNAs

Zheng Li; Bandhan Sarker; Fengyu Zhao; Tianjiao Zhou; Jianzhi Zhang; Chuan Xu

doi:10.1016/j.jgg.2024.08.007

Volume 51 Issue 11

Nov. 2024

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Article Navigation > Journal of Genetics and Genomics > 2024 > 51(11): 1338-1341

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COL: a method for identifying putatively functional circular RNAs

doi: 10.1016/j.jgg.2024.08.007

1. Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China;
2. Department of Statistics, George Washington University, Washington, DC 20052, USA;
3. Department of Otorhinolaryngology Head and Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China;
4. Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA;
5. Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China

Funds:

This study was supported by the National Natural Science Foundation of China (32270704, 32100518 and 32472630), National Science and Technology Innovation 2030 (2022ZD0214400), Engineering Shanghai Jiao Tong University (YG2022QN084), and the U.S. National Institutes of Health (R35GM139484 to J.Z.).

Received Date: 2024-08-25
Accepted Date: 2024-08-28
Rev Recd Date: 2024-08-27

Available Online: 2025-06-06

Publish Date: 2024-08-31

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References(20)

References

Ashwal-Fluss, R., Meyer, M., Pamudurti, N.R., Ivanov, A., Bartok, O., Hanan, M., Evantal, N., Memczak, S., Rajewsky, N.,Kadener, S., 2014. Circrna biogenesis competes with pre-mrna splicing. Mol. Cell 56, 55-66.

Chen, L.L., 2016. The biogenesis and emerging roles of circular rnas. Nat. Rev. Mol. Cell Biol. 17, 205-211.

Disotell, T.R.,Tosi, A.J., 2007. The monkey's perspective. Genome Biol. 8, 226.

Du, W.W., Yang, W., Liu, E., Yang, Z., Dhaliwal, P.,Yang, B.B., 2016. Foxo3 circular rna retards cell cycle progression via forming ternary complexes with p21 and cdk2. Nucleic Acids Res. 44, 2846-2858.

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, 384-388.

Hedges, S.B., Dudley, J.,Kumar, S., 2006. Timetree: a public knowledge-base of divergence times among organisms. Bioinformatics 22, 2971-2972.

Huang, M.G., Zhong, Z.Y., Lv, M.X., Shu, J., Tian, Q.,Chen, J.X., 2016. Comprehensive analysis of differentially expressed profiles of lncrnas and circrnas with associated co-expression and cerna networks in bladder carcinoma. Oncotarget 7, 47186-47200.

Huang, X., He, M., Huang, S., Lin, R.R., Zhan, M., Yang, D., Shen, H., Xu, S.W., Cheng, W., Yu, J.X., et al., 2019. Circular rna circerbb2 promotes gallbladder cancer progression by regulating pa2g4-dependent rdna transcription. Mol. Cancer 18.

Ji, P., Wu, W., Chen, S., Zheng, Y., Zhou, L., Zhang, J., Cheng, H., Yan, J., Zhang, S., Yang, P., et al., 2019. Expanded expression landscape and prioritization of circular rnas in mammals. Cell Rep. 26, 3444-3460 e3445.

Kolde, R., Laur, S., Adler, P.,Vilo, J., 2012. Robust rank aggregation for gene list integration and meta-analysis. Bioinformatics 28, 573-580.

Kristensen, L.S., Andersen, M.S., Stagsted, L.V.W., Ebbesen, K.K., Hansen, T.B.,Kjems, J., 2019. The biogenesis, biology and characterization of circular rnas. Nat. Rev. Genet. 20, 675-691.

Li, S., Li, X., Xue, W., Zhang, L., Yang, L.Z., Cao, S.M., Lei, Y.N., Liu, C.X., Guo, S.K., Shan, L., et al., 2021. Screening for functional circular rnas using the crispr-cas13 system. Nat. Methods 18, 51-59.

Liu, Z., Ran, Y., Tao, C., Li, S., Chen, J.,Yang, E., 2019. Detection of circular rna expression and related quantitative trait loci in the human dorsolateral prefrontal cortex. Genome Biol. 20, 99.

Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A., Maier, L., Mackowiak, S.D., Gregersen, L.H., Munschauer, M., et al., 2013. Circular rnas are a large class of animal rnas with regulatory potency. Nature 495, 333-338.

Okholm, T.L.H., Sathe, S., Park, S.S., Kamstrup, A.B., Rasmussen, A.M., Shankar, A., Chua, Z.M., Fristrup, N., Nielsen, M.M., Vang, S., et al., 2020. Transcriptome-wide profiles of circular rna and rna-binding protein interactions reveal effects on circular rna biogenesis and cancer pathway expression. Genome Med. 12, 112.

Pamudurti, N.R., Bartok, O., Jens, M., Ashwal-Fluss, R., Stottmeister, C., Ruhe, L., Hanan, M., Wyler, E., Perez-Hernandez, D., Ramberger, E., et al., 2017. Translation of circrnas. Mol. Cell 66, 9-21 e27.

Reiner, A., Yekutieli, D.,Benjamini, Y., 2003. Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics 19, 368-375.

Rybak-Wolf, A., Stottmeister, C., Glazar, P., Jens, M., Pino, N., Giusti, S., Hanan, M., Behm, M., Bartok, O., Ashwal-Fluss, R., et al., 2015. Circular rnas in the mammalian brain are highly abundant, conserved, and dynamically expressed. Mol. Cell 58, 870-885.

Suenkel, C., Cavalli, D., Massalini, S., Calegari, F.,Rajewsky, N., 2020. A highly conserved circular rna is required to keep neural cells in a progenitor state in the mammalian brain. Cell Rep. 30, 2170-2179.

Xu, C.,Zhang, J., 2021. Mammalian circular rnas result largely from splicing errors. Cell Rep. 36, 109439.

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