Function of Circular RNAs in Fish and Their Potential Application As Biomarkers

Overview

Journal Int J Mol Sci

Publisher MDPI

Specialties Biochemistry
Chemistry
Molecular Biology

Date 2021 Jul 20

PMID 34281172

Citations 8

Authors

Golam Rbbani

Artem Nedoluzhko

Jorge Galindo-Villegas

Jorge M O Fernandes

Affiliations

Soon will be listed here.

Abstract

Circular RNAs (circRNAs) are an emerging class of regulatory RNAs with a covalently closed-loop structure formed during pre-mRNA splicing. Recent advances in high-throughput RNA sequencing and circRNA-specific computational tools have driven the development of novel approaches to their identification and functional characterization. CircRNAs are stable, developmentally regulated, and show tissue- and cell-type-specific expression across different taxonomic groups. They play a crucial role in regulating various biological processes at post-transcriptional and translational levels. However, the involvement of circRNAs in fish immunity has only recently been recognized. There is also broad evidence in mammals that the timely expression of circRNAs in muscle plays an essential role in growth regulation but our understanding of their expression and function in teleosts is still very limited. Here, we discuss the available knowledge about circRNAs and their role in growth and immunity in vertebrates from a comparative perspective, with emphasis on cultured teleost fish. We expect that the interest in teleost circRNAs will increase substantially soon, and we propose that they may be used as biomarkers for selective breeding of farmed fish, thus contributing to the sustainability of the aquaculture sector.

Citing Articles

Transcriptome Analysis of Muscle Growth-Related circRNA in the Pacific Abalone .

Huang J, He J, She Z, Zhou M, Li D, Chen J Genes (Basel). 2025; 16(1).

PMID: 39858612 PMC: 11764893. DOI: 10.3390/genes16010065.

Endemic Radiation of African Moonfish, (Gill 1863), in the Eastern Atlantic: Mitogenomic Characterization and Phylogenetic Implications of Carangids (Teleostei: Carangiformes).

Ewusi E, Lee S, Kim A, Go Y, Htoo H, Chung S Biomolecules. 2024; 14(10).

PMID: 39456141 PMC: 11506752. DOI: 10.3390/biom14101208.

Embryonic temperature has long-term effects on muscle circRNA expression and somatic growth in Nile tilapia.

Rbbani G, Murshed R, Siriyappagouder P, Sharko F, Nedoluzhko A, Joshi R Front Cell Dev Biol. 2024; 12:1369758.

PMID: 39149515 PMC: 11324953. DOI: 10.3389/fcell.2024.1369758.

Circular RNAs are associated with the resistance to Newcastle disease virus infection in duck cells.

Fan L, Ren J, Wang Y, Chen Y, Chen Y, Chen L Front Vet Sci. 2023; 10:1181916.

PMID: 37841466 PMC: 10570413. DOI: 10.3389/fvets.2023.1181916.

Comprehensive RNA-Seq Analysis Pipeline for Non-Model Organisms and Its Application in .

Wang Y, Li S, Nong B, Zhou W, Xu S, Songyang Z Genes (Basel). 2023; 14(5).

PMID: 37239350 PMC: 10218480. DOI: 10.3390/genes14050989.

References

You X, Conrad T . Acfs: accurate circRNA identification and quantification from RNA-Seq data. Sci Rep. 2016; 6:38820. PMC: 5144000. DOI: 10.1038/srep38820. View

Yan X, Ding L, Li Y, Zhang X, Liang Y, Sun X . Identification and profiling of microRNAs from skeletal muscle of the common carp. PLoS One. 2012; 7(1):e30925. PMC: 3267759. DOI: 10.1371/journal.pone.0030925. View

Hansen T, Jensen T, Clausen B, Bramsen J, Finsen B, Damgaard C . Natural RNA circles function as efficient microRNA sponges. Nature. 2013; 495(7441):384-8. DOI: 10.1038/nature11993. View

Zuo L, Zhang L, Zu J, Wang Z, Han B, Chen B . Circulating Circular RNAs as Biomarkers for the Diagnosis and Prediction of Outcomes in Acute Ischemic Stroke. Stroke. 2019; 51(1):319-323. DOI: 10.1161/STROKEAHA.119.027348. View

Liu J, Zhang X, Yan M, Li H . Emerging Role of Circular RNAs in Cancer. Front Oncol. 2020; 10:663. PMC: 7326090. DOI: 10.3389/fonc.2020.00663. View

Yue B, Wang J, Ru W, Wu J, Cao X, Yang H . The Circular RNA circHUWE1 Sponges the miR-29b-AKT3 Axis to Regulate Myoblast Development. Mol Ther Nucleic Acids. 2020; 19:1086-1097. PMC: 7015828. DOI: 10.1016/j.omtn.2019.12.039. View

Hu X, Dai Y, Zhang X, Dai K, Liu B, Yuan R . Identification and characterization of novel type of RNAs, circRNAs in crucian carp Carassius auratus gibelio. Fish Shellfish Immunol. 2019; 94:50-57. DOI: 10.1016/j.fsi.2019.08.070. View

Wu T, Shi L, Lowe A, Nicolls M, Kao P . Inducible expression of immediate early genes is regulated through dynamic chromatin association by NF45/ILF2 and NF90/NF110/ILF3. PLoS One. 2019; 14(4):e0216042. PMC: 6483252. DOI: 10.1371/journal.pone.0216042. View

Liu H, Hu Y, Yin J, Yan X, Chen W, Jiang C . Profiles analysis reveals circular RNAs involving zebrafish physiological development. J Cell Physiol. 2019; 234(9):15922-15933. DOI: 10.1002/jcp.28250. View

10.

Rossi G, Messina G . Comparative myogenesis in teleosts and mammals. Cell Mol Life Sci. 2014; 71(16):3081-99. PMC: 4111864. DOI: 10.1007/s00018-014-1604-5. View

11.

Li C, Li X, Yao Y, Ma Q, Ni W, Zhang X . Genome-wide analysis of circular RNAs in prenatal and postnatal muscle of sheep. Oncotarget. 2017; 8(57):97165-97177. PMC: 5722553. DOI: 10.18632/oncotarget.21835. View

12.

Chen L, Yang L . Regulation of circRNA biogenesis. RNA Biol. 2015; 12(4):381-8. PMC: 4615371. DOI: 10.1080/15476286.2015.1020271. View

13.

Zeng K, Chen X, Xu M, Liu X, Hu X, Xu T . CircHIPK3 promotes colorectal cancer growth and metastasis by sponging miR-7. Cell Death Dis. 2018; 9(4):417. PMC: 5856798. DOI: 10.1038/s41419-018-0454-8. View

14.

Nakajima T, Hudson M, Uchiyama J, Makibayashi K, Zhang J . Common carp aquaculture in Neolithic China dates back 8,000 years. Nat Ecol Evol. 2019; 3(10):1415-1418. DOI: 10.1038/s41559-019-0974-3. View

15.

Ashwal-Fluss R, Meyer M, Pamudurti N, Ivanov A, Bartok O, Hanan M . circRNA biogenesis competes with pre-mRNA splicing. Mol Cell. 2014; 56(1):55-66. DOI: 10.1016/j.molcel.2014.08.019. View

16.

Li Z, Huang C, Bao C, Chen L, Lin M, Wang X . Exon-intron circular RNAs regulate transcription in the nucleus. Nat Struct Mol Biol. 2015; 22(3):256-64. DOI: 10.1038/nsmb.2959. View

17.

Shen X, Liu Z, Cao X, He H, Han S, Chen Y . Circular RNA profiling identified an abundant circular RNA circTMTC1 that inhibits chicken skeletal muscle satellite cell differentiation by sponging miR-128-3p. Int J Biol Sci. 2019; 15(10):2265-2281. PMC: 6775300. DOI: 10.7150/ijbs.36412. View

18.

Shen X, Zhang X, Ru W, Huang Y, Lan X, Lei C . circINSR Promotes Proliferation and Reduces Apoptosis of Embryonic Myoblasts by Sponging miR-34a. Mol Ther Nucleic Acids. 2020; 19:986-999. PMC: 7013137. DOI: 10.1016/j.omtn.2019.12.032. View

19.

Zhou D, Dong L, Yang L, Ma Q, Liu F, Li Y . Identification and analysis of circRNA-miRNA-mRNA regulatory network in hepatocellular carcinoma. IET Syst Biol. 2021; 14(6):391-398. PMC: 8687197. DOI: 10.1049/iet-syb.2020.0061. View

20.

Feng J, Xiang Y, Xia S, Liu H, Wang J, Ozguc F . CircView: a visualization and exploration tool for circular RNAs. Brief Bioinform. 2017; 19(6):1310-1316. DOI: 10.1093/bib/bbx070. View