The Biological Function of circRNA and Its Research Progress in Domestic Animals

doi:10.11924/j.issn.1000-6850.casb18090073

Abstract

Abstract:

circRNA is a kind of endogenous and circular non-coding RNAs. At present, the researches on circRNA mainly focus on cancer and tumor. There are fewer studies on circRNA in domestic animals, most of which are about the information mining of circRNA. In this paper, the generation way, classification, research methods, biological functions of circRNA are summed up. The research progress of circRNA on muscle development and fat deposition of domestic animals are summarized. Finally, the research problems of circRNAs in domestic animals are analyzed, and the future research direction of circRNA is discussed.

Key words: circRNA, generation way, research method, biological function, domestic animal

CLC Number:

S813.1

Li Jingjing, Qi Xiaolong, Wang Xiangguo, Xing Kai, Chang Di, Guo Yong, Ni Hemin, Sheng Xihui. The Biological Function of circRNA and Its Research Progress in Domestic Animals[J]. Chinese Agricultural Science Bulletin, 2020, 36(3): 142-146.

References 44

[1]	Nigro J M, Cho K R, Fearon E R , et al. Scrambled exons[J]. Cell, 1991,64(3):607. doi: 10.1016/0092-8674(91)90244-s URL pmid: 1991322
[2]	Werfel S, Nothjunge S, Schwarzmayr T , et al. Characterization of circular RNAs in human, mouse and rat hearts[J]. Journal of Molecular & Cellular Cardiology, 2016,98:103-107. doi: 10.1016/j.yjmcc.2016.07.007 URL pmid: 27476877
[3]	Jeck W R, Sorrentino J A, Wang K , et al. Circular RNAs are abundant, conserved, and associated with ALU repeats[J]. Rna-a Publication of the Rna Society, 2013,19(2):141-157. doi: 10.1261/rna.035667.112 URL
[4]	Salzman J, Gawad C, Wang P L , et al. Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types[J]. Plos One., 2012,7(2):e30733. doi: 10.1371/journal.pone.0030733 URL pmid: 22319583
[5]	Salzman J, Chen R E, Olsen M N , et al. Cell-type specific features of circular RNA expression[J]. Plos Genetics, 2013,9(9):e1003777. doi: 10.1371/journal.pgen.1003777 URL pmid: 24039610
[6]	Lei K, Bai H, Wei Z , et al. The mechanism and function of circular RNAs in human diseases[J]. Experimental Cell Research, 2018.
[7]	Venø M T, Hansen T B, Venø S T , et al. Spatio-temporal regulation of circular RNA expression during porcine embryonic brain development[J]. Genome Biology, 2015,16(1):245. doi: 10.1186/s13059-015-0801-3 URL pmid: 26541409
[8]	Ivanov A, Memczak S, Wyler E , et al. Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals[J]. Cell Reports, 2015,10(2):170-177. doi: 10.1016/j.celrep.2014.12.019 URL pmid: 25558066
[9]	Wang Y, Wang Z . Efficient backsplicing produces translatable circular mRNAs[J]. Rna-a Publication of the Rna Society, 2015,21(2):172-179. doi: 10.1261/rna.048272.114 URL pmid: 25449546
[10]	Starke S, Jost I, Rossbach O , et al. Exon circularization requires canonical splice signals[J]. Cell Reports, 2015,10(1):103-111. doi: 10.1016/j.celrep.2014.12.002 URL pmid: 25543144
[11]	Memczak S, Jens M, Elefsinioti A , et al. Circular RNAs are a large class of animal RNAs with regulatory potency[J]. Nature, 2013,495(7441):333-338. doi: 10.1038/nature11928 URL
[12]	Glaå Ar P, Papavasileiou P, Rajewsky N. circBase: a database for circular RNAs[J]. Rna-a Publication of the Rna Society, 2014,20(11):1666-1670. doi: 10.1261/rna.043687.113 URL
[13]	Li J H, Liu S, Zhou H , et al. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data[J]. Nucleic Acids Research, 2014,42(Database issue):D92. doi: 10.1093/nar/gkt1248 URL pmid: 24297251
[14]	Yang J H, Qu L H . DeepBase: annotation and discovery of microRNAs and other noncoding RNAs from deep-sequencing data[J]. Methods in Molecular Biology, 2012,822(822):233. doi: 10.1007/978-1-61779-427-8_16 URL pmid: 22144203
[15]	Liu Y C, Li J R, Sun C H , et al. CircNet: a database of circular RNAs derived from transcriptome sequencing data[J]. Nucleic Acids Research, 2016,44(Database issue):D209-D215. doi: 10.1093/nar/gkv940 URL pmid: 26450965
[16]	Dudekula D B, Panda A C, Grammatikakis I , et al. CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs[J]. Rna Biology, 2016,13(1):34-42. doi: 10.1080/15476286.2015.1128065 URL pmid: 26669964
[17]	Liang G, Yang Y, Niu G , et al. Genome-wide profiling ofSus scrofacircular RNAs across nine organs and three developmental stages[J]. Dna Research An International Journal for Rapid Publication of Reports on Genes & Genomes, 2017,24(5):523-535. doi: 10.1093/dnares/dsx022 URL pmid: 28575165
[18]	Jeck W R, Sharpless N E . Detecting and characterizing circular RNAs[J]. Nature Biotechnology, 2014,32(5):453-461. doi: 10.1038/nbt.2890 URL
[19]	Suzuki H, Zuo Y, Wang J , et al. Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing[J]. Nucleic Acids Research, 2006,34(8):e63. doi: 10.1093/nar/gkl151 URL pmid: 16682442
[20]	Tabak H F, Van D H G, Smit J , et al. Discrimination between RNA circles, interlocked RNA circles and lariats using two-dimensional polyacrylamide gel electrophoresis[J]. Nucleic Acids Research, 1988,16(14A):6597-6605. doi: 10.1093/nar/16.14.6597 URL pmid: 2456529
[21]	Li Z, Huang C, Bao C , et al. Exon-intron circular RNAs regulate transcription in the nucleus[J]. Nature Structural & Molecular Biology, 2015,22(3):256-264. doi: 10.1038/nsmb.2959 URL pmid: 25664725
[22]	Zhang Y, Zhang X O, Chen T , et al. Circular intronic long noncoding RNAs[J]. Molecular Cell, 2013,51(6):792-806. doi: 10.1016/j.molcel.2013.08.017 URL
[23]	Hoffmann S, Otto C, Doose G , et al. A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection[J]. Genome Biology, 2014,15(2):1-11. doi: 10.1186/gb-2014-15-2-r34 URL pmid: 24512684
[24]	Wang K, Singh D, Zeng Z , et al. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery[J]. Nucleic Acids Research, 2010,38(18):e178. doi: 10.1093/nar/gkq622 URL pmid: 20802226
[25]	Gao Y, Wang J, Zhao F . CIRI: an efficient and unbiased algorithm for de novo circular RNA identification[J]. Genome Biology, 2015,16(1):4. doi: 10.1186/s13059-014-0571-3 URL pmid: 25583365
[26]	Zhang X O, Wang H B, Zhang Y , et al. Complementary sequence-mediated exon circularization[J]. Cell, 2014,159(1):134-147. doi: 10.1016/j.cell.2014.09.001 URL
[27]	Ebbesen K K, Kjems J, Hansen T B . Circular RNAs: Identification, biogenesis and function ☆[J]. Biochimica Et Biophysica Acta, 2016,1859(1):163.
[28]	Hansen T B, Jensen T I, Clausen B H , et al. Natural RNA circles function as efficient microRNA sponges[J]. Nature, 2013,495(7441):384-388. doi: 10.1038/nature11993 URL
[29]	Wang X, Zhu X, Zhang H , et al. Increased circular RNA hsa_circ_0012673 acts as a sponge of miR-22 to promote lung adenocarcinoma proliferation[J]. Biochemical & Biophysical Research Communications, 2018,496(4):1069-1075. doi: 10.1016/j.bbrc.2018.01.126 URL pmid: 29366790
[30]	Deng N, Li L, Gao J , et al. Hsa_circ_0009910 promotes carcinogenesis by promoting the expression of miR-449a target IL6R in osteosarcoma[J]. Biochem Biophys Res Commun, 2017,495(1). doi: 10.1016/j.bbrc.2017.11.028 URL pmid: 29117539
[31]	Ashwal-Fluss R, Meyer M, Pamudurti N R , et al. circRNA Biogenesis Competes with Pre-mRNA Splicing[J]. Molecular Cell, 2014,56(1):55-66. doi: 10.1016/j.molcel.2014.08.019 URL
[32]	Du W W, Ling F, Yang W , et al. Induction of tumor apoptosis through a circular RNA enhancing Foxo3 activity[J]. Cell Death & Differentiation, 2016,24(2):357. doi: 10.1038/cdd.2016.133 URL pmid: 27886165
[33]	Du W W, Yang W, Liu E , et al. Foxo3 circular RNA retards cell cycle progression via forming ternary complexes with p21 and CDK2[J]. Nucleic Acids Research, 2016,44(6):2846. doi: 10.1093/nar/gkw027 URL pmid: 26861625
[34]	Wang F, Nazarali A J, Ji S . Circular RNAs as potential biomarkers for cancer diagnosis and therapy[J]. Am J Cancer Res., 2016,6(6):1167-1176. URL pmid: 27429839
[35]	Shao Y, Chen Y . Roles of Circular RNAs in Neurologic Disease[J]. Frontiers in Molecular Neuroscience, 2016,9(307):25. doi: 10.3389/fnmol.2016.00025 URL pmid: 27147959
[36]	Sun J, Xie M, Huang Z , et al. Integrated analysis of non-coding RNA and mRNA expression profiles of 2 pig breeds differing in muscle traits[J]. Journal of Animal Science, 2017,95(3):1092. doi: 10.2527/jas.2016.0867 URL pmid: 28380516
[37]	Chen J, Zou Q, Lv D , et al. Comprehensive transcriptional landscape of porcine cardiac and skeletal muscles reveals differences of aging[J]. Oncotarget, 2018,9(2):1524. doi: 10.18632/oncotarget.23290 URL pmid: 29416711
[38]	Wei X, Li H, Yang J , et al. Circular RNA profiling reveals an abundant circLMO7 that regulates myoblasts differentiation and survival by sponging miR-378a-3p.[J]. Cell Death & Disease, 2017,8(10):e3153. doi: 10.1038/cddis.2017.541 URL pmid: 29072698
[39]	Li H, Yang J, Wei X , et al. CircFUT10 reduces proliferation and facilitates differentiation of myoblasts by sponging miR-133a[J]. Journal of Cellular Physiology, 2017,233(11). doi: 10.1002/jcp.26230 URL pmid: 29044517
[40]	Cao Y, You S, Yao Y , et al. Expression profiles of circular RNAs in sheep skeletal muscle[J]. Asian-Australasian journal of animal sciences, 2018. doi: 10.5713/ajas.17.0563 URL pmid: 29642686
[41]	Huang M, Shen Y, Mao H , et al. Circular RNA expression profiles in the porcine liver of two distinct phenotype pig breeds[J]. Asian-Australasian journal of animal sciences, 2017. doi: 10.5713/ajas.17.0651 URL pmid: 29268579
[42]	Li C, Li X, Ma Q , et al. Genome-wide analysis of circular RNAs in prenatal and postnatal pituitary glands of sheep[J]. Sci Rep., 2017,8(57):97165-97177. doi: 10.1038/s41598-017-16344-y URL pmid: 29170496
[43]	Tao H, Xiong Q, Zhang F , et al. Circular RNA profiling reveals chi_circ_0008219 function as microRNA sponges in pre-ovulatory ovarian follicles of goats (Capra hircus)[J]. Genomics, 2017. doi: 10.1016/j.ygeno.2017.10.005 URL pmid: 29107014
[44]	Zhang X, Yan Y, Lei X , et al. Circular RNA alterations are involved in resistance to avian leukosis virus subgroup-J-induced tumor formation in chickens[J]. Oncotarget, 2017,8(21):34961-34970. doi: 10.18632/oncotarget.16442 URL pmid: 28415618