MicroRNA Transcriptome Profiles During Swine Skeletal Muscle Development

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2009 Feb 12

PMID 19208255

Citations 56

Authors

Tara G McDaneld

Timothy P L Smith

Matthew E Doumit

Jeremy R Miles

Luiz L Coutinho

Tad S Sonstegard

Lakshmi K Matukumalli

Dan J Nonneman

Ralph T Wiedmann

Affiliations

Soon will be listed here.

Abstract

Background: MicroRNA (miR) are a class of small RNAs that regulate gene expression by inhibiting translation of protein encoding transcripts. To evaluate the role of miR in skeletal muscle of swine, global microRNA abundance was measured at specific developmental stages including proliferating satellite cells, three stages of fetal growth, day-old neonate, and the adult.

Results: Twelve potential novel miR were detected that did not match previously reported sequences. In addition, a number of miR previously reported to be expressed in mammalian muscle were detected, having a variety of abundance patterns through muscle development. Muscle-specific miR-206 was nearly absent in proliferating satellite cells in culture, but was the highest abundant miR at other time points evaluated. In addition, miR-1 was moderately abundant throughout developmental stages with highest abundance in the adult. In contrast, miR-133 was moderately abundant in adult muscle and either not detectable or lowly abundant throughout fetal and neonate development. Changes in abundance of ubiquitously expressed miR were also observed. MiR-432 abundance was highest at the earliest stage of fetal development tested (60 day-old fetus) and decreased throughout development to the adult. Conversely, miR-24 and miR-27 exhibited greatest abundance in proliferating satellite cells and the adult, while abundance of miR-368, miR-376, and miR-423-5p was greatest in the neonate.

Conclusion: These data present a complete set of transcriptome profiles to evaluate miR abundance at specific stages of skeletal muscle growth in swine. Identification of these miR provides an initial group of miR that may play a vital role in muscle development and growth.

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References

Takada S, Mano H . Profiling of microRNA expression by mRAP. Nat Protoc. 2007; 2(12):3136-45. DOI: 10.1038/nprot.2007.457. View

Ueda H, Ohno S, Kobayashi T . Myotonic dystrophy and myotonic dystrophy protein kinase. Prog Histochem Cytochem. 2000; 35(3):187-251. DOI: 10.1016/s0079-6336(00)80002-9. View

Lai E . miRNAs: whys and wherefores of miRNA-mediated regulation. Curr Biol. 2005; 15(12):R458-60. DOI: 10.1016/j.cub.2005.06.015. View

Sweetman D, Rathjen T, Jefferson M, Wheeler G, Smith T, Wheeler G . FGF-4 signaling is involved in mir-206 expression in developing somites of chicken embryos. Dev Dyn. 2006; 235(8):2185-91. DOI: 10.1002/dvdy.20881. View

Mott J, Kobayashi S, Bronk S, Gores G . mir-29 regulates Mcl-1 protein expression and apoptosis. Oncogene. 2007; 26(42):6133-40. PMC: 2432524. DOI: 10.1038/sj.onc.1210436. View

Rao P, Kumar R, Farkhondeh M, Baskerville S, Lodish H . Myogenic factors that regulate expression of muscle-specific microRNAs. Proc Natl Acad Sci U S A. 2006; 103(23):8721-6. PMC: 1482645. DOI: 10.1073/pnas.0602831103. View

Cimmino A, Calin G, Fabbri M, Iorio M, Ferracin M, Shimizu M . miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc Natl Acad Sci U S A. 2005; 102(39):13944-9. PMC: 1236577. DOI: 10.1073/pnas.0506654102. View

Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R . Fast and effective prediction of microRNA/target duplexes. RNA. 2004; 10(10):1507-17. PMC: 1370637. DOI: 10.1261/rna.5248604. View

Xu H, Wang X, Du Z, Li N . Identification of microRNAs from different tissues of chicken embryo and adult chicken. FEBS Lett. 2006; 580(15):3610-6. DOI: 10.1016/j.febslet.2006.05.044. View

10.

Hafner M, Landgraf P, Ludwig J, Rice A, Ojo T, Lin C . Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods. 2007; 44(1):3-12. PMC: 2847350. DOI: 10.1016/j.ymeth.2007.09.009. View

11.

Anderson C, Catoe H, Werner R . MIR-206 regulates connexin43 expression during skeletal muscle development. Nucleic Acids Res. 2006; 34(20):5863-71. PMC: 1635318. DOI: 10.1093/nar/gkl743. View

12.

Hutvagner G . Small RNA asymmetry in RNAi: function in RISC assembly and gene regulation. FEBS Lett. 2005; 579(26):5850-7. DOI: 10.1016/j.febslet.2005.08.071. View

13.

Coutinho L, Matukumalli L, Sonstegard T, Van Tassell C, Gasbarre L, Capuco A . Discovery and profiling of bovine microRNAs from immune-related and embryonic tissues. Physiol Genomics. 2006; 29(1):35-43. DOI: 10.1152/physiolgenomics.00081.2006. View

14.

Lu C, Tej S, Luo S, Haudenschild C, Meyers B, Green P . Elucidation of the small RNA component of the transcriptome. Science. 2005; 309(5740):1567-9. DOI: 10.1126/science.1114112. View

15.

Carthew R . Gene regulation by microRNAs. Curr Opin Genet Dev. 2006; 16(2):203-8. DOI: 10.1016/j.gde.2006.02.012. View

16.

Lee R, Ambros V . An extensive class of small RNAs in Caenorhabditis elegans. Science. 2001; 294(5543):862-4. DOI: 10.1126/science.1065329. View

17.

Hamelin M, Sayd T, Chambon C, Bouix J, Bibe B, Milenkovic D . Differential expression of sarcoplasmic proteins in four heterogeneous ovine skeletal muscles. Proteomics. 2007; 7(2):271-80. DOI: 10.1002/pmic.200600309. View

18.

Gunawan A, Richert B, Schinckel A, Grant A, Gerrard D . Ractopamine induces differential gene expression in porcine skeletal muscles. J Anim Sci. 2007; 85(9):2115-24. DOI: 10.2527/jas.2006-540. View

19.

Pette D, Staron R . Mammalian skeletal muscle fiber type transitions. Int Rev Cytol. 1997; 170:143-223. DOI: 10.1016/s0074-7696(08)61622-8. View

20.

Neufer P, Carey J, Dohm G . Transcriptional regulation of the gene for glucose transporter GLUT4 in skeletal muscle. Effects of diabetes and fasting. J Biol Chem. 1993; 268(19):13824-9. View