Differentially Expressed Genes and Related Pathways in the Ovine Muscle Transcriptome pre and postnatal Using the Integration of Microarray and RNA-seq Data

Journal of Cell and Molecular Research

مقاله 2، دوره 16، شماره 1 - شماره پیاپی 31، دی 2024، صفحه 13-24   

نوع مقاله: Research Articles

شناسه دیجیتال (DOI): 10.22067/jcmr.2024.86067.1085

نویسندگان

Fahime Mohammadi¹؛ Mojtaba Tahmoorespour¹؛ Ali Javadmanesh^{* 1، 2}

¹Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran

²Industrial Biotechnology Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran

چکیده

The formation of muscle myofibrils as well as the growth and hypertrophy of the muscle are controlled by various genes. Bioinformatics tools could also be used to integrate and analyze heterogeneous data sets. In this study, the DEGs, gene network, GO and biological pathways have been investigated by incorporating the data obtained by expression array and RNA-Seq, related to the muscle tissue transcriptome of Texel sheep respectively before and after birth. The microarray expression profile was extracted from the GEO database, and the RNA-Seq expression profile was extracted from the ArrayExpress database. DEGs were identified with limma and sva software packages in R environment and a gene network was drawn with STRING, an application in Cytoscape software. The clustering and gene ontology were done with CytoCluster and ClueGO applications. The results showed a significant difference between the juvenile and 70-day embryonic stages the expression of 103 genes, between the adult and juvenile stages the expression of 28 genes and between the adult and 70-day embryonic stages the expression of 62 genes. By constructing the gene network between these DEGs, a total of 37 selected genes were identified. The results revealed the function of these genes in cell proliferation, protein synthesis, formation and organization of myofibrils, muscle contraction, and lipid metabolism. By integrating the expression data, this study provided a general view of the differences in transcriptomes in the muscle tissue of sheep. Also, the selected genes such as BUB1, RFC2, KIAA0101, RAD51, CKS2, and UQCRB were identified for the first time being reported as effective genes for myogenesis.

کلیدواژه‌ها

DEGs؛ Gen Ontology؛ Physiological pathway؛ Muscle tissue؛ Sheep

مراجع

Almenar-Queralt A., Lee A., Conley C. A., de Pouplana L. s. R. and Fowler V. M. (1999) Identification of a novel tropomodulin isoform, skeletal tropomodulin, that caps actin filament pointed ends in fast skeletal muscle. Journal of Biological Chemistry 274:28466-28475.

Bakhshalizadeh S., Zerehdaran S. and Javadmanesh A. (2021) Meta-analysis of genome-wide association studies for somatic cells score trait in dairy cows. Journal of Ruminant Research 9:39-58.

Bakhshalizadeh S., Zerehdaran S., Hasanpur K. and Javadmanesh A. (2024) Identification of potential candidate genes associated with milk protein differences in Holstein cows: a meta-analysis integrating GWAS and RNA-Seq transcriptome. Canadian Journal of Animal Science. e-First  https://doi.org/10.1139/cjas-2023-0108

Bassel-Duby R. and Olson E. N. (2006) Signaling pathways in skeletal muscle remodeling. Annual Review of Biochemistry 75:19-37.

Beggs A. H., Byers T., Knoll J., Boyce F., Bruns G. and Kunkel L. (1992) Cloning and characterization of two human skeletal muscle alpha-actinin genes located on chromosomes 1 and 11. Journal of Biological Chemistry 267:9281-9288.

Betti S. B., Tahmoorespur M. and Javadmanesh A. (2022a) Alternative Splicing Novel lncRNAs and Their Target Genes in Ovine Skeletal Muscles. Journal of Cell and Molecular Research 13:129-136.

Betti S. B., Tahmoorespur M. and Javadmanesh A. (2022b) Identification of lncRNAs expression and their regulatory networks associated with development and growth of skeletal muscle in sheep using RNA-Seq. Agriculture and Natural Resources 56:373–386-373–386.

Boss O., Giacobino J.-P. and Muzzin P. (1998) Genomic Structure of Uncoupling. Genomics 47:425-426.

Castillo D., Gálvez J. M., Herrera L. J., Román B. S., Rojas F. and Rojas I. (2017) Integration of RNA-Seq data with heterogeneous microarray data for breast cancer profiling. BMC Bioinformatics 18:1-15.

CHEUNG P. C., SALT I. P., DAVIES S. P., HARDIE D. G. and CARLING D. (2000) Characterization of AMP-activated protein kinase γ-subunit isoforms and their role in AMP binding. Biochemical Journal 346:659-669.

Ewen M. E., Sluss H. K., Sherr C. J., Matsushime H., Kato J.-y. and Livingston D. M. (1993) Functional interactions of the retinoblastoma protein with mammalian D-type cyclins. Cell 73:487-497.

Filadi R., Pendin D. and Pizzo P. (2018) Mitofusin 2: from functions to disease. Cell Death & Disease 9:1-13.

Flintoft L. (2008) Digging deep with RNA-Seq. Nature Reviews Genetics 9:568-568.

Gaeini A. (2013) Changes in ACTN3 gene expression and fiber type composition in flexor hallucis longus muscle after eight weeks progressive resistance training in Sprague-Dawley rats. Tehran University Medical Journal TUMS Publications 71:37-45.

Geiman T. M., Sankpal U. T., Robertson A. K., Chen Y., Mazumdar M., Heale J. T., Schmiesing J. A., Kim W., Yokomori K. and Zhao Y. (2004) Isolation and characterization of a novel DNA methyltransferase complex linking DNMT3B with components of the mitotic chromosome condensation machinery. Nucleic Acids Research 32:2716-2729.

Horisberger M. A. (1992) Interferon-induced human protein MxA is a GTPase which binds transiently to cellular proteins. Journal of Virology 66:4705-4709.

Huang C.-Y. F., Yuan C.-J., Livanova N. B. and Graves D. J. 1993. Expression, purification, characterization, and deletion mutations of phosphorylase kinase γ subunit: identification of an inhibitory domain in the γ subunit. In Reversible Protein Phosphorylation in Cell Regulation. Springer. 7-18.

Hüttemann M., Kadenbach B. and Grossman L. I. (2001) Mammalian subunit IV isoforms of cytochrome c oxidase. Gene 267:111-123.

Javadmanesh A. 2020. Genes and Genomes in Farm Animals: A Perpective. In Javadmanesh A. 2020. Proceedings of the 4th International and 16th Iranian Genetics Congress. , Tehran, Iran.

Jung H. J., Kim K. H., Kim N. D., Han G. and Kwon H. J. (2011) Identification of a novel small molecule targeting UQCRB of mitochondrial complex III and its anti-angiogenic activity. Bioorganic & Medicinal Chemistry Letters 21:1052-1056.

Lefrançois-Martinez A.-M., Bertherat J., Val P., Tournaire C., Gallo-Payet N., Hyndman D., Veyssière G., Bertagna X., Jean C. and Martinez A. (2004) Decreased expression of cyclic adenosine monophosphate-regulated aldose reductase (AKR1B1) is associated with malignancy in human sporadic adrenocortical tumors. The Journal of Clinical Endocrinology & Metabolism 89:3010-3019.

Liu N., He J., Yu W., Liu K., Cheng M., Liu J., He Y., Zhao J. and Qu X. (2015) Transcriptome analysis of skeletal muscle at prenatal stages in Polled Dorset versus Small-tailed Han sheep. Genetics and Molecular Research 14:1085-1095.

Ma T., Liang F., Oesterreich S. and Tseng G. C. (2017) A joint Bayesian model for integrating microarray and RNA sequencing transcriptomic data. Journal of Computational Biology 24:647-662.

Mohammadi F., Tahmoorespur M. and Javadmanesh A. (2019) Study of differentially expressed genes, related pathways and gene networks in sheep fetal muscle tissue in thin-and fat-tailed breeds. Animal Sciences Journal 32:301-312.

Ohta S., Ohsawa I., Kamino K., Ando F. and Shimokata H. 2004. Mitochondrial ALDH2 deficiency as an oxidative stress. In Mitochondrial Pathogenesis. Springer. 36-44.

Rakus D., Maciaszczyk E., Wawrzycka D., Ułaszewski S., Eschrich K. and Dzugaj A. (2005) The origin of the high sensitivity of muscle fructose 1, 6-bisphosphatase towards AMP. FEBS Letters 579:5577-5581.

Ribeiro J. E. A., Pinotsis N., Ghisleni A., Salmazo A., Konarev P. V., Kostan J., Sjöblom B., Schreiner C., Polyansky A. A. and Gkougkoulia E. A. (2014) The structure and regulation of human muscle α-actinin. Cell 159:1447-1460.

Rother K., Dengl M., Lorenz J., Tschöp K., Kirschner R., Mössner J. and Engeland K. (2007) Gene expression of cyclin-dependent kinase subunit Cks2 is repressed by the tumor suppressor p53 but not by the related proteins p63 or p73. FEBS letters 581:1166-1172.

Saedi N., Aminafshar M., Chamani M., Honarvar M. and Javadmanesh A. (2022) Expression pattern and network visualization of genes involved in milk persistency in bovine mammary tissue. Agriculture and Natural Resources 56(1): 23–34.

Salmikangas P., Mykkänen O.-M., Grönholm M., Heiska L., Kere J. and Carpén O. (1999) Myotilin, a novel sarcomeric protein with two Ig-like domains, is encoded by a candidate gene for limb-girdle muscular dystrophy. Human Molecular Genetics 8:1329-1336.

Sartor H., Ehlert F., Grzeschik K.-H., Müller R. and Adolph S. (1992) Assignment of two human cell cycle genes, CDC25C and CCNB1, to 5q31 and 5q12, respectively. Genomics (San Diego, Calif.) 13:911-912.

Sigruener A., Buechler C., Orso E., Hartmann A., Wild P., Terracciano L., Roncalli M., Bornstein S. and Schmitz G. (2007) Human aldehyde oxidase 1 interacts with ATP-binding cassette transporter-1 and modulates its activity in hepatocytes. Hormone and Metabolic Research 39:781-789.

Simpson F., van Bueren K. L., Butterfield N., Bennetts J. S., Bowles J., Adolphe C., Simms L. A., Young J., Walsh M. D. and Leggett B. (2006) The PCNA-associated factor KIAA0101/p15PAF binds the potential tumor suppressor product p33ING1b. Experimental Cell Research 312:73-85.

Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., ... & Ideker, T. (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research, 13(11), 2498-2504.

Sun L., Bai M., Xiang L., Zhang G., Ma W. and Jiang H. (2016a) Comparative transcriptome profiling of longissimus muscle tissues from Qianhua Mutton Merino and Small Tail Han sheep. Scientific Reports 6:33586.

Sun L., Bai M., Xiang L., Zhang G., Ma W. and Jiang H. (2016b) Comparative transcriptome profiling of longissimus muscle tissues from Qianhua Mutton Merino and Small Tail Han sheep. Scientific Reports 6:1-13.

Taheri S., Saedi N., Zerehdaran S. and Javadmanesh A. (2023) Identification of selection signatures in Capra hircus and Capra aegagrus in Iran. Animal Science Journal. 94(1): e13864.

Terentyev D., Viatchenko-Karpinski S., Györke I., Volpe P., Williams S. C. and Györke S. (2003) Calsequestrin determines the functional size and stability of cardiac intracellular calcium stores: mechanism for hereditary arrhythmia. Proceedings of the National Academy of Sciences 100:11759-11764.

Vikenes K., Andersen K. S., Melberg T., Farstad M. and Nordrehaug J. E. (2009) Long-term prognostic value of creatine kinase-myocardial band mass after cardiac surgery in low-risk patients with stable angina. Cardiology 113:122-131.

Zelko I. N., Mariani T. J. and Folz R. J. (2002) Superoxide dismutase multigene family: a comparison of the CuZn-SOD (SOD1), Mn-SOD (SOD2), and EC-SOD (SOD3) gene structures, evolution, and expression. Free Radical Biology and Medicine 33:337-349.

Zeraatpisheh, Y., Zerehdaran, S., & Javadmanesh, A. (2023). Investigation of metabolic pathways related to the QTLs of parasite resistance trait in sheep genome using gene network and gene ontology. Veterinary Research & Biological Products, 36(1), 83-90. doi: 10.22092/vj.2022.357660.1941

Zhan S., Zhao W., Song T., Dong Y., Guo J., Cao J., Zhong T., Wang L., Li L. and Zhang H. (2018) Dynamic transcriptomic analysis in hircine longissimus dorsi muscle from fetal to neonatal development stages. Functional & Integrative Genomics 18:43-54.

 Zhang C., Wang G., Wang J., Ji Z., Liu Z., Pi X. and Chen C. (2013) Characterization and comparative analyses of muscle transcriptomes in Dorper and small-tailed Han sheep using RNA-Seq technique. PloS one 8:e72686.