Genome-wide Analysis of Circular RNAs in Prenatal and Postnatal Muscle of Sheep

Overview

Journal Oncotarget

Specialty Oncology

Date 2017 Dec 13

PMID 29228601

Citations 25

Authors

Cunyuan Li

Xiaoyue Li

Yang Yao

Qiman Ma

Wei Ni

Xiangyu Zhang

Yang Cao

Wureli Hazi

Dawei Wang

Renzhe Quan

Xiaoxu Hou

Zhijin Liu

Qianqian Zhan

Li Liu

Mengdan Zhang

Shuting Yu

Shengwei Hu

Affiliations

Soon will be listed here.

Abstract

Circular RNAs (circRNAs), a type of non-coding RNA with circular structure, were generated by back splicing and widely expressed in animals and plants. Recent studies have shown that circRNAs extensively participate in cell proliferation, cell differentiation, cell autophagy and other biological processes. However, the role and expression of circRNAs in the development and growth of muscle have not been studied in sheep. In our study, we first used RNA-seq to study the circRNAs in prenatal and postnatal longissimus dorsi muscle of sheep. A total of 6113 circRNAs were detected from the RNA-seq data. Several circRNAs were identified using reverse transcription PCR, DNA sequencing and RNase R digestion experiments. The expression levels of several circRNAs in prenatal and postnatal muscle were confirmed by Real-Time RT-PCR. The gene ontology (GO) and KEGG enrichment analysis of the host gene of the circRNAs showed that these circRNAs were mainly involved in the growth and development of muscle related signaling pathways. These circRNAs might sponge microRNAs (miRNAs) in predicted circRNA-miRNA-mRNA networks. The circRNAs expression profiles in muscle provided an important reference for the study of circRNAs in sheep.

Citing Articles

Comprehensive circular RNA profiling in various sheep tissues.

Bakhtiarizade M, Heidari M, Ghanatghestani A Sci Rep. 2024; 14(1):26238.

PMID: 39482374 PMC: 11527890. DOI: 10.1038/s41598-024-76940-7.

Understanding Circular RNAs in Health, Welfare, and Productive Traits of Cattle, Goats, and Sheep.

Kirgiafini D, Kyrgiafini M, Gournaris T, Mamuris Z Animals (Basel). 2024; 14(5).

PMID: 38473119 PMC: 10931498. DOI: 10.3390/ani14050733.

Genome wide identification and characterization of fertility associated novel CircRNAs as ceRNA reveal their regulatory roles in sheep fecundity.

Yousuf S, Malik W, Feng H, Liu T, Xie L, Miao X J Ovarian Res. 2023; 16(1):115.

PMID: 37340323 PMC: 10280924. DOI: 10.1186/s13048-023-01178-2.

Expression Profile Analysis to Identify Circular RNA Expression Signatures in Muscle Development of Wu'an Goat Longissimus Dorsi Tissues.

Zhou Z, Li K, Liu J, Zhang H, Fan Y, Chen Y Front Vet Sci. 2022; 9:833946.

PMID: 35518637 PMC: 9062782. DOI: 10.3389/fvets.2022.833946.

Characterization of the circRNA-miRNA-mRNA Network to Reveal the Potential Functional ceRNAs Associated With Dynamic Changes in the Meat Quality of the Longissimus Thoracis Muscle in Tibetan Sheep at Different Growth Stages.

Bao G, Zhao F, Wang J, Liu X, Hu J, Shi B Front Vet Sci. 2022; 9:803758.

PMID: 35433904 PMC: 9011000. DOI: 10.3389/fvets.2022.803758.

References

Brunelli G, Spano P, Barlati S, Guarneri B, Barbon A, Bresciani R . Glutamatergic reinnervation through peripheral nerve graft dictates assembly of glutamatergic synapses at rat skeletal muscle. Proc Natl Acad Sci U S A. 2005; 102(24):8752-7. PMC: 1142481. DOI: 10.1073/pnas.0500530102. View

Nair K, Schwartz R, Welle S . Leucine as a regulator of whole body and skeletal muscle protein metabolism in humans. Am J Physiol. 1992; 263(5 Pt 1):E928-34. DOI: 10.1152/ajpendo.1992.263.5.E928. View

Jeck W, Sharpless N . Detecting and characterizing circular RNAs. Nat Biotechnol. 2014; 32(5):453-61. PMC: 4121655. DOI: 10.1038/nbt.2890. View

Zou M, Huang C, Li X, He X, Chen Y, Liao W . Circular RNA expression profile and potential function of hsa_circRNA_101238 in human thoracic aortic dissection. Oncotarget. 2017; 8(47):81825-81837. PMC: 5669851. DOI: 10.18632/oncotarget.18998. View

LeBrasseur N, Cote G, Miller T, Fielding R, Sawyer D . Regulation of neuregulin/ErbB signaling by contractile activity in skeletal muscle. Am J Physiol Cell Physiol. 2003; 284(5):C1149-55. DOI: 10.1152/ajpcell.00487.2002. View

Braun S, Domdey H, Wiebauer K . Inverse splicing of a discontinuous pre-mRNA intron generates a circular exon in a HeLa cell nuclear extract. Nucleic Acids Res. 1996; 24(21):4152-7. PMC: 146224. DOI: 10.1093/nar/24.21.4152. View

Li Y, Xu Z, Li H, Xiong Y, Zuo B . Differential transcriptional analysis between red and white skeletal muscle of Chinese Meishan pigs. Int J Biol Sci. 2010; 6(4):350-60. PMC: 2899453. DOI: 10.7150/ijbs.6.350. View

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

Llovera M, Agell N, Lopez-Soriano F, Argiles J . Muscle wasting associated with cancer cachexia is linked to an important activation of the ATP-dependent ubiquitin-mediated proteolysis. Int J Cancer. 1995; 61(1):138-41. DOI: 10.1002/ijc.2910610123. View

10.

Shan L, Wu Q, Li Y, Shang H, Guo K, Wu J . Transcriptome profiling identifies differentially expressed genes in postnatal developing pituitary gland of miniature pig. DNA Res. 2013; 21(2):207-16. PMC: 3989491. DOI: 10.1093/dnares/dst051. View

11.

Kartha R, Subramanian S . Competing endogenous RNAs (ceRNAs): new entrants to the intricacies of gene regulation. Front Genet. 2014; 5:8. PMC: 3906566. DOI: 10.3389/fgene.2014.00008. View

12.

Salzman J, Gawad C, Wang P, Lacayo N, Brown P . Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One. 2012; 7(2):e30733. PMC: 3270023. DOI: 10.1371/journal.pone.0030733. View

13.

Li L, Guo J, Chen Y, Chang C, Xu C . Comprehensive CircRNA expression profile and selection of key CircRNAs during priming phase of rat liver regeneration. BMC Genomics. 2017; 18(1):80. PMC: 5237265. DOI: 10.1186/s12864-016-3476-6. View

14.

Stern H, Brown A, Hauschka S . Myogenesis in paraxial mesoderm: preferential induction by dorsal neural tube and by cells expressing Wnt-1. Development. 1995; 121(11):3675-86. DOI: 10.1242/dev.121.11.3675. View

15.

Li Y, Zheng Q, Bao C, Li S, Guo W, Zhao J . Circular RNA is enriched and stable in exosomes: a promising biomarker for cancer diagnosis. Cell Res. 2015; 25(8):981-4. PMC: 4528056. DOI: 10.1038/cr.2015.82. View

16.

Sun J, Xie M, Huang Z, Li H, Chen T, Sun R . Integrated analysis of non-coding RNA and mRNA expression profiles of 2 pig breeds differing in muscle traits. J Anim Sci. 2017; 95(3):1092-1103. DOI: 10.2527/jas.2016.0867. View

17.

Huang D, Sherman B, Lempicki R . Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009; 4(1):44-57. DOI: 10.1038/nprot.2008.211. View

18.

Yang X, Xia D, Chen J, Wegner J, Jiang Z, Zhao R . Sterol regulatory element binding transcription factor 1 expression and genetic polymorphism significantly affect intramuscular fat deposition in the longissimus muscle of Erhualian and Sutai pigs. J Anim Sci. 2007; 86(1):57-63. DOI: 10.2527/jas.2007-0066. View

19.

Molkentin J, Olson E . Defining the regulatory networks for muscle development. Curr Opin Genet Dev. 1996; 6(4):445-53. DOI: 10.1016/s0959-437x(96)80066-9. View

20.

Liu J, Damon M, Guitton N, Guisle I, Ecolan P, Vincent A . Differentially-expressed genes in pig Longissimus muscles with contrasting levels of fat, as identified by combined transcriptomic, reverse transcription PCR, and proteomic analyses. J Agric Food Chem. 2009; 57(9):3808-17. DOI: 10.1021/jf8033144. View