Biology:Circular RNA databases and resources

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In molecular biology, Circular RNAs (circRNAs) refer to a class of circular RNA molecules found across all kingdoms of life.[1][2][3] Studies in 2013 have suggested that circRNAs play important regulatory roles in miRNA activity. Researchers found that CDR1as circRNA acts as a miR-7 super-sponge that contains about 70 target sites from the same miR-7 at the same transcript.[4][5] The other testis-specific circRNA, sex-determining region Y (Sry), also was found as a miR-138 sponge.[6] About-mentioned examples suggesting that miRNA sponge effects achieved by circRNA formation may be a general phenomenon. As miR-7 modulates the expression of several oncogenes, ciRS-7/miR-7 interactions may play an important roles in cancer-related pathways.[7] circRNA has also been shown in viral infection where it sequesters anti-viral protein to enhance viral replication.[8][9]

This Circular RNA (circRNA) databases and resources is a compilation of databases and web portals and servers used for circRNAs.

Name Description type References
circRNABase circRNABase is designed for decoding miRNA-circRNA interaction networks from thousands of circRNAs and 108 CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) datasets. database [10]
circBase circBase explore public circRNA datasets and download the custom python scripts needed to discover circRNAs in your own (ribominus) RNA-seq data. database [11]
CircNet CircNet records public and novel circRNAs and putative circRNA-miRNA interactions. All the information is presented in an interactive user interface and available for download. database [12]
Circ2Traits Circ2Traits a comprehensive database for circular RNA potentially associated with disease and traits. database [13]
Gokool et al. 2019 The Landscape of Circular RNA Expression in the Human Brain resource [14]

References

  1. ↑ Memczak, S; Jens, M; Elefsinioti, A; Torti, F; Krueger, J; Rybak, A; Maier, L; Mackowiak, SD et al. (Mar 21, 2013). "Circular RNAs are a large class of animal RNAs with regulatory potency". Nature 495 (7441): 333–338. doi:10.1038/nature11928. PMID 23446348. Bibcode: 2013Natur.495..333M. 
  2. ↑ Hansen, TB; Jensen, TI; Clausen, BH; Bramsen, JB; Finsen, B; Damgaard, CK; Kjems, J (Mar 21, 2013). "Natural RNA circles function as efficient microRNA sponges.". Nature 495 (7441): 384–388. doi:10.1038/nature11993. PMID 23446346. Bibcode: 2013Natur.495..384H. 
  3. ↑ Kosik, KS (Mar 21, 2013). "Molecular biology: Circles reshape the RNA world.". Nature 495 (7441): 322–324. doi:10.1038/nature11956. PMID 23446351. Bibcode: 2013Natur.495..322K. 
  4. ↑ Memczak, S; Jens, M; Elefsinioti, A; Torti, F; Krueger, J; Rybak, A; Maier, L; Mackowiak, SD et al. (Mar 21, 2013). "Circular RNAs are a large class of animal RNAs with regulatory potency". Nature 495 (7441): 333–338. doi:10.1038/nature11928. PMID 23446348. Bibcode: 2013Natur.495..333M. 
  5. ↑ Hansen, TB; Jensen, TI; Clausen, BH; Bramsen, JB; Finsen, B; Damgaard, CK; Kjems, J (Mar 21, 2013). "Natural RNA circles function as efficient microRNA sponges.". Nature 495 (7441): 384–388. doi:10.1038/nature11993. PMID 23446346. Bibcode: 2013Natur.495..384H. 
  6. ↑ Hansen, TB; Jensen, TI; Clausen, BH; Bramsen, JB; Finsen, B; Damgaard, CK; Kjems, J (Mar 21, 2013). "Natural RNA circles function as efficient microRNA sponges.". Nature 495 (7441): 384–388. doi:10.1038/nature11993. PMID 23446346. Bibcode: 2013Natur.495..384H. 
  7. ↑ Hansen, TB; Kjems, J; Damgaard, CK (Sep 15, 2013). "Circular RNA and miR-7 in Cancer.". Cancer Research 73 (18): 5609–5612. doi:10.1158/0008-5472.CAN-13-1568. PMID 24014594. 
  8. ↑ Bhardwaj, Vipin; Singh, Aman; Dalavi, Rishikesh; Ralte, Lalchhanhima; Chawngthu, Richard L.; Kumar, Nachimuthu Senthil; Vijay, Nagarjun; Chande, Ajit (2022-11-04) (in en). HIV-1 Vpr induces ciTRAN to prevent transcriptional silencing of the provirus. pp. 2022.11.04.515166. doi:10.1101/2022.11.04.515166. https://www.biorxiv.org/content/10.1101/2022.11.04.515166v1. 
  9. ↑ Chen, Tzu-Chun; Tallo-Parra, Marc; Cao, Qian M.; Kadener, Sebastian; Böttcher, René; Pérez-Vilaró, Gemma; Boonchuen, Pakpoom; Somboonwiwat, Kunlaya et al. (2020-08-07). "Host-derived circular RNAs display proviral activities in Hepatitis C virus-infected cells". PLOS Pathogens 16 (8): e1008346. doi:10.1371/journal.ppat.1008346. ISSN 1553-7366. PMID 32764824. 
  10. ↑ Li, JH; Liu, S; Zhou, H; Qu, LH; Yang, JH (Jan 1, 2014). "starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data.". Nucleic Acids Research 42 (1): D92–7. doi:10.1093/nar/gkt1248. PMID 24297251. 
  11. ↑ Memczak, S; Jens, M; Elefsinioti, A; Torti, F; Krueger, J; Rybak, A; Maier, L; Mackowiak, SD et al. (Mar 21, 2013). "Circular RNAs are a large class of animal RNAs with regulatory potency". Nature 495 (7441): 333–338. doi:10.1038/nature11928. PMID 23446348. Bibcode: 2013Natur.495..333M. 
  12. ↑ Liu, Yu-Chen; Li, Jian-Rong; Sun, Chuan-Hu; Andrews, Erik; Chao, Rou-Fang; Lin, Feng-Mao; Weng, Shun-Long; Hsu, Sheng-Da et al. (2016-01-04). "CircNet: a database of circular RNAs derived from transcriptome sequencing data". Nucleic Acids Research 44 (D1): D209–215. doi:10.1093/nar/gkv940. ISSN 1362-4962. PMID 26450965. 
  13. ↑ Ghosal, S; Das, S; Sen, R; Basak, P; Chakrabarti, J (2013). "Circ2Traits: a comprehensive database for circular RNA potentially associated with disease and traits.". Frontiers in Genetics 4: 283. doi:10.3389/fgene.2013.00283. PMID 24339831. 
  14. ↑ Gokool, A; Anwar, F; Voineagu, I (2019). "The Landscape of Circular RNA Expression in the Human Brain". Biological Psychiatry 87 (3): 294–304. doi:10.1016/j.biopsych.2019.07.029. PMID 31570194. 



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