شناسایی همریخت‌ RNA های بیان شده در ماهیچۀ اسکلتی مرغ بومی و تجاری با روش توالی‌یابی

نوع مقاله : مقاله پژوهشی

نویسندگان

1 مربی، مرکز تحقیقات و آموزش کشاورزی خوزستان، اهواز، ایران

2 استادیار، دانشکدۀ کشاورزی و منابع طبیعی دانشگاه تهران، پردیس ابوریحان، ایران

3 استاد، دانشکدۀ کشاورزی دانشگاه فردوسی مشهد، مشهد، ایران

چکیده

این آزمایش به‌منظور بررسی و شناسایی همریخت (ایزوفرم)‌های RNA مرتبط با ساختار پروتئین‌های ماهیچه‌ای بین مرغ بومی اصفهان و جوجۀ تجاری راس با سرعت رشدهای متفاوت، انجام شد. بدین منظور و پس از استخراج کل RNA از نمونه‌های ماهیچۀ سینۀ مرغان یادشده در سن 28 روزگی، توالی‌یابی جفتی با استفاده از پلاتفرم illumine Hiseq 2000 انجام شد. برای همترازی خوانش‌ها به ژنگان (ژنوم) مرجع مرغ اهلی، از نرم‌افزار Hisat2 و برای اسمبلی ترانسکریپت‌ها و شناسایی بیان ژن‌های با تفاوت معنی‌دار از بستۀ Cufflinks استفاده شد. مقایسۀ آماری همریخت‌های توالی‌یابی‌شده بین دو گروه، 259 همریخت (161 همریخت در جوجۀ تجاری و 98 همریخت در مرغ بومی) با تفاوت بیان معنی‌دار را مشخص کرد. در بین همریخت‌های جوجۀ تجاری، 4 ژن ACTC1، ATF3، CYR61 و FABP4 هر یک با دو همریخت مختلف افزایش بیان داشتند. در جوجۀ تجاری فراوانی همریخت‌های مرتبط به ماهیچۀ کالبدی (اسکلتی) با انقباضات آهسته بیشتر از همریخت‌های ماهیچۀ اسکلتی با انقباض سریع بود. بررسی عملکردی نشان داد، همریخت‌ها در جوجۀ تجاری در ارتباط با افزونش و تمایز یاخته‌ای، پررشدی (هایپرتروفی) و ساخت پروتئین‌های ساختمانی ماهیچه‌ای بوده درحالی‌که در مرغ بومی مرتبط به فرآیندهای ایمنی، حاملان یون‌ها و فلزها، نوار (باند) شونده‌های به فلزها، DNA و RNA، و عامل‌های شرکت‌کننده در شکست پروتئین‌های ماهیچه‌ای بودند. نتایج این بررسی نشان داد، چنین تغییرهایی به‌احتمال توانسته با کاهش دادن سطح نیازهای مرغ بومی و افزایش توان ایمنی و سازگاری، امکان تداوم و چیره شدن بر شرایط سخت محیطی و غذایی را در طول دورۀ تکاملی این مرغ تقویت کند.

کلیدواژه‌ها

عنوان مقاله [English]

Identification of RNA isoforms expressed in skeletal muscle of native and commercial chickens by sequencing method

نویسندگان [English]

  • Seyed Nader Albooshoke 1
  • Mohammad Reza Bakhtiarizadeh 2
  • Mojtaba Tahmoorespur 3
1 Instructor, Khuzestan Agricultural and Natural Resources Research and Education Center, AREEO, Ahvaz, Iran
2 Assistant Professor, Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Tehran, Campus of Aburaihan, Iran
3 Professor, Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
چکیده [English]

This experiment was conducted to investigate and identify the isoforms related to the structure of muscular proteins between Isfahani native and Ross commercial chickens with different growth rates. We extracted total RNA from breast muscle samples of two groups at end of 4 weeks of age. After paired-end sequencing of samples using the Illumina Hiseq 2000 platform, Hisat2 was applied to align clean reads to chicken reference genome. Then, Cufflinks package was used to assemble transcripts and identify significantly differentially expressed genes. The statistical comparison of the isoforms between two groups revealed 259 isoforms with significant difference in expression, of which 161 isoforms were up-regulated and 98 isoforms were downregulated in commercial chickens. Among the commercial chicken isoforms, four genes (ACTC1, ATF3, CYR61 and FABP4) were upregulated with two different isoforms. In addition, in commercial chicks, the frequency of isoforms associated with slow contraction fibers was greater than that of rapid contraction fibers. Functional study showed that the isoforms in commercial chickens were more related to cell proliferation and differentiation, hypertrophy growth and biosynthesis of muscle proteins, whereas in native chickens, mainly they were associated to immune processes, carriers of ions and metals, binding to metals, DNA and RNA, and factors contributing to degradation of muscle proteins. The results of this study showed that such changes may have been able to strengthen the ability to maintain and overcome the severe environmental and nutritional conditions during the developmental period of the chicken by reducing the level of requirements and enhancing immunity and adaptability in native chicken.

کلیدواژه‌ها [English]

  • gene expression
  • Isfahan native chicken
  • Ross broiler chickens

مراجع

Babic, A. M., Kireeva, M. L., Kolesnikova, T. V. & Lau, L. F. (1998).  CYR61, a product of a growth factor-inducible immediate early gene, promotes angiogenesis and tumor growth. Proceedings of the National Academy of Sciences of the United States of America, 95(11),  6355-6360.
2.   Baeuerle, P. A. & Henkel, T. (1994).  Function and activation of NF-kappaB in the immune system. Annual review of immunology, 12(1),  141-179.
3.   Barber, G. (2001).  Host defense, viruses and apoptosis. Cell death and differentiation, 8(2),  113-126.
4.   Bello, N. F., Lamsoul, I., Heuzé, M. L., Métais, A., Moreaux, G., Calderwood, D. A., Duprez, D., Moog-Lutz, C. & Lutz, P. G. (2009).  The E3 ubiquitin ligase specificity subunit ASB2β is a novel regulator of muscle differentiation that targets filamin B to proteasomal degradation. Cell Death & Differentiation, 16(6),  921-932.
5.   Benjamini, Y. & Hochberg, Y. (1995).  Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the royal statistical society. Series B (Methodological),  289-300.
6.   Bottje, W., Kong, B.-W., Reverter, A., Waardenberg, A. J., Lassiter, K. & Hudson, N. J. (2017).  Progesterone signalling in broiler skeletal muscle is associated with divergent feed efficiency. BMC systems biology, 11(1), 29.
7.   Brink, M., Wellen, J. & Delafontaine, P. (1996).  Angiotensin II causes weight loss and decreases circulating insulin-like growth factor I in rats through a pressor-independent mechanism. Journal of Clinical Investigation, 97(11), 2509.
8.   Cadenas, E. & Davies, K. J. (2000). Mitochondrial free radical generation, oxidative stress, and aging. Free Radical Biology and Medicine, 29(3), 222-230.
9.   Cavanaugh, B. L. & Lonstein, J. S. (2010).  Social novelty increases tyrosine hydroxylase immunoreactivity in the extended olfactory amygdala of female prairie voles. Physiology & Behavior, 100(4), 381-386.
10. Choi, Y. & Kim, B. (2009). Muscle fiber characteristics, myofibrillar protein isoforms, and meat quality. Livestock Science, 122(2), 105-118.
11. Conley, C. A. (2001). Leiomodin and tropomodulin in smooth muscle. American Journal of Physiology-Cell Physiology, 280(6), C1645-C1656.
12. David, C. J., Chen, M., Assanah, M., Canoll, P. & Manley, J. L. (2010).  HnRNP proteins controlled by c-Myc deregulate pyruvate kinase mRNA splicing in cancer. Nature, 463(7279), 364-368.
13. Davis, A. J. & Austic, R. E. (1997). Dietary protein and amino acid levels alter threonine dehydrogenase activity in hepatic mitochondria of Gallus domesticus. The Journal of Nutrition, 127(5), 738-744.
14. Dennis, G., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C. & Lempicki, R. A. (2003).  DAVID: database for annotation, visualization, and integrated discovery. Genome Biology, 4(9), 1.
15. Dong, J.-Q., Zhang, H., Jiang, X.-F., Wang, S.-Z., Du, Z.-Q., Wang, Z.-P., Leng, L., Cao, Z.-P., Li, Y.-M. & Luan, P. (2015). Comparison of serum biochemical parameters between two broiler chicken lines divergently selected for abdominal fat content. Journal of animal science, 93(7), 3278-3286.
16. Donkor, J., Sariahmetoglu, M., Dewald, J., Brindley, D. N. & Reue, K. (2007). Three mammalian lipins act as phosphatidate phosphatases with distinct tissue expression patterns. Journal of Biological Chemistry, 282(6), 3450-3457.
17. Furuyama, T., Kitayama, K., Yamashita, H. & Nozomu, M. (2003).  Forkhead transcription factor FOXO1 (FKHR)-dependent induction of PDK4 gene expression in skeletal muscle during energy deprivation. Biochemical Journal, 375(2), 365-371.
18. Griffin, H. & Goddard, C. (1994).  Rapidly growing broiler (meat-type) chickens. Their origin and use for comparative studies of the regulation of growth. International Journal of Biochemistry, 26(1), 19-28.
19. Hishiya, A., Iemura, S. I., Natsume, T., Takayama, S., Ikeda, K. & Watanabe, K. (2006).  A novel ubiquitin‐binding protein ZNF216 functioning in muscle atrophy. The EMBO Journal, 25(3), 554-564.
20. Karni, R., de Stanchina, E., Lowe, S. W., Sinha, R., Mu, D. & Krainer, A. R. (2007).  The gene encoding the splicing factor SF2/ASF is a proto-oncogene. Nature Structural & Molecular Biology, 14(3), 185-193.
21. Kim, D., Langmead, B. & Salzberg, S. L. (2015).  HISAT: a fast spliced aligner with low memory requirements. Nature Methods, 12(4), 357-360.
22. Kim, N. K., Joh, J. H., Park, H. R., Kim, O. H., Park, B. Y. & Lee, C. S. (2004). Differential expression profiling of the proteomes and their mRNAs in porcine white and red skeletal muscles. Proteomics, 4(11), 3422-3428.
23. Klont, R., Brocks, L. & Eikelenboom, G. (1998). Muscle fibre type and meat quality. Meat Science, 49, S219-S229.
24. Kong, B.-W., Hudson, N., Seo, D., Lee, S., Khatri, B., Lassiter, K., Cook, D., Piekarski, A., Dridi, S. & Anthony, N. (2017).  RNA sequencing for global gene expression associated with muscle growth in a single male modern broiler line compared to a foundational Barred Plymouth Rock chicken line. BMC genomics, 18(1), 82.
25. Lau, L. F. (2011). CCN1/CYR61: The Very Model of a Modern Matricellular Protein. Cellular and Molecular Life Sciences: CMLS, 68(19), 3149-3163.
26. Lee, A., Suh, Y., Wick, M. & Lee, K. (2012). Temporal myosin heavy chain isoform expression transitions faster in broiler chickens compared with Single Comb White Leghorns. Poultry Science, 91(11), 2872-2876.
27. Lee, J. H., Budanov, A. V. & Karin, M. (2013).  Sestrins orchestrate cellular metabolism to attenuate aging. Cell Metabolism, 18(6), 792-801.
28. Li, S., Chen, W., Kang, X., Han, R., Sun, G. & Huang, Y. (2013).  Distinct tissue expression profiles of chicken Lpin1-α/β isoforms and the effect of the variation on muscle fiber traits. Gene, 515(2), 281-290.
29. Lin, J., Wu, H., Tarr, P.T., Zhang, C.-Y., Wu, Z., Boss, O., Michael, L. F., Puigserver, P., Isotani, E. & Olson, E.N. (2002).  Transcriptional co-activator PGC-1α drives the formation of slow-twitch muscle fibres. Nature, 418(6899), 797-801.
30. Liu, C.-C., Lin, Y.-C., Chen, Y.-H., Chen, C.-M., Pang, L.-Y., Chen, H.-A., Wu, P.-R., Lin, M.-Y., Jiang, S.-T. & Tsai, T.-F. (2016). Cul3-KLHL20 ubiquitin ligase governs the turnover of ULK1 and VPS34 complexes to control autophagy termination. Molecular Cell, 61(1), 84-97.
31. Lohse, M., Bolger, A. M., Nagel, A., Fernie, A. R., Lunn, J. E., Stitt, M. & Usadel, B. (2012).  R obi NA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Research, 40(W1), W622-W627.
32. Matsakas, A. & Patel, K. (2009). Skeletal muscle fibre plasticity in response to selected environmental and physiological stimuli. Histology and Histopathology, 24(5), 611-629.
33. Mendoza, K., Sporer, K., Strasburg, G., Tempelman, R. & Velleman, S. (2011).  Differential Cardiac Gene Expression in Turkeys Genetically Selected for Increased Body Weight. J Veterinar Sci Technol S, 7, 2.
34. Merino, R., Rodriguez-Leon, J., Macias, D., Ganan, Y., Economides, A. & Hurle, J. (1999). The BMP antagonist Gremlin regulates outgrowth, chondrogenesis and programmed cell death in the developing limb. Development, 126(23), 5515-5522.
35. Mutryn, M. F., Brannick, E. M., Fu, W., Lee, W. R. & Abasht, B. (2015). Characterization of a novel chicken muscle disorder through differential gene expression and pathway analysis using RNA-sequencing. BMC Genomics, 16(1), 399.
36. Okamoto, A., Iwamoto, Y. & Maru, Y. (2006). Oxidative stress-responsive transcription factor ATF3 potentially mediates diabetic angiopathy. Molecular and Cellular Biology, 26(3), 1087-1097.
37. Parmigiani, A., Nourbakhsh, A., Ding, B., Wang, W., Kim, Y. C., Akopiants, K., Guan, K.-L., Karin, M. & Budanov, A. V. (2014). Sestrins inhibit mTORC1 kinase activation through the GATOR complex. Cell Reports, 9(4), 1281-1291.
38. Phan, J. & Reue, K. (2005). Lipin, a lipodystrophy and obesity gene. Cell Metabolism, 1(1), 73-83.
39. Polge, C., Attaix, D. & Taillandier, D. (2015). Role of E2-Ub-conjugating enzymes during skeletal muscle atrophy. Frontiers in Physiology, 6.
40. Pompella, A., Visvikis, A., Paolicchi, A., De Tata, V. & Casini, A. F. (2003). The changing faces of glutathione, a cellular protagonist. Biochemical pharmacology, 66(8), 1499-1503.
41. Reddish, J., Wick, M., St-Pierre, N. & Lilburn, M. (2005).  Analysis of myosin isoform transitions during growth and development in diverse chicken genotypes. Poultry science, 84(11), 1729-1734.
42. Reue, K. & Dwyer, J. R. (2009). Lipin proteins and metabolic homeostasis. Journal of Lipid Research, 50(Supplement), S109-S114.
43. Reyer, H., Hawken, R., Murani, E., Ponsuksili, S. & Wimmers, K. (2015). The genetics of feed conversion efficiency traits in a commercial broiler line. Scientific Reports, 5, 16387.
44. Robbiani, D. F., Finch, R. A., Jäger, D., Muller, W. A., Sartorelli, A. C. & Randolph, G. J. (2000).  The Leukotriene C4 Transporter MRP1 Regulates CCL19 (MIP-3β, ELC)–Dependent Mobilization of Dendritic Cells to Lymph Nodes. Cell, 103(5), 757-768.
45. Sihvo, H.-K., Immonen, K. & Puolanne, E. (2014). Myodegeneration with fibrosis and regeneration in the pectoralis major muscle of broilers. Veterinary Pathology, 51(3), 619-623.
46. Tawa Jr, N. E., Odessey, R. & Goldberg, A. L. (1997). Inhibitors of the proteasome reduce the accelerated proteolysis in atrophying rat skeletal muscles. Journal of Clinical Investigation, 100(1), 197.
47. Thomas, K., Engler, A. J. & Meyer, G. A. (2015). Extracellular matrix regulation in the muscle satellite cell niche. Connective Tissue Research, 56(1), 1-8.
48. Townsend, K. L., Suzuki, R., Huang, T. L., Jing, E., Schulz, T. J., Lee, K., Taniguchi, C. M., Espinoza, D. O., McDougall, L. E. & Zhang, H. (2012). Bone morphogenetic protein 7 (BMP7) reverses obesity and regulates appetite through a central mTOR pathway. The FASEB Journal, 26(5), 2187-2196.
49. Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D. R., Pimentel, H., Salzberg, S. L., Rinn, J. L. & Pachter, L. (2012).  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature protocols, 7(3), 562-578.
50. Tyra, M., Ropka-Molik, K., Eckert, R., Piórkowska, K. & Oczkowicz, M. (2011). H-FABP and LEPR gene expression profile in skeletal muscles and liver during ontogenesis in various breeds of pigs. Domestic animal endocrinology, 40(3), 147-154.
51. Velleman, S. G., Clark, D. L. & Tonniges, J. R. (2017). Fibrillar Collagen Organization Associated with the Broiler Wooden Breast Fibrotic Myopathy. Avian Diseases, 61(4), 481-490.
52. Weir, E., Chen, Q., DeFrances, M. C., Bell, A., Taub, R. & Zarnegar, R. (1994).  Rapid induction of mRNAs for liver regeneration factor and insulin-like growth factor binding protein-1 in primary cultures of rat hepatocytes by hepatocyte growth factor and epidermal growth factor. Hepatology, 20(4 Pt 1), 955-60.
53. Wu, T., Zhang, Z., Yuan, Z., Lo, L. J., Chen, J., Wang, Y. & Peng, J. (2013). Distinctive genes determine different intramuscular fat and muscle fiber ratios of the longissimus dorsi muscles in Jinhua and landrace pigs. PloS one, 8(1), e53181.
54. Yeung, K. Y. & Ruzzo, W. L. (2001). Principal component analysis for clustering gene expression data. Bioinformatics, 17(9), 763-74.
55. Yoshida, T., Semprun-Prieto, L., Sukhanov, S. & Delafontaine, P. (2010). IGF-1 prevents ANG II-induced skeletal muscle atrophy via Akt-and Foxo-dependent inhibition of the ubiquitin ligase atrogin-1 expression. American Journal of Physiology-Heart and Circulatory Physiology, 298(5), H1565-H1570.
56. Yousefi Zonuz, A., Alijani, S., Mohammadi, H., Rafat, A. & Daghigh Kia, H. (2013). Estimation of genetic parameters for productive and reproductive traits in Esfahan native chickens. Journal of Livestock Science and Technologies, 1(2), 34-38.
57. Yuan, Y., Liu, Y.-G., Shi, X. & Yang, G.-S. (2010). Signaling pathways in skeletal muscle fiber-type transition. Chinese Journal Biochemistry Molecular Biology, 26, 796-801.
58. Zamani, N. & Brown, C. W. (2010). Emerging roles for the transforming growth factor-β superfamily in regulating adiposity and energy expenditure. Endocrine reviews, 32(3), 387-403.

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  • تاریخ دریافت: 17 دی 1396
  • تاریخ بازنگری: 08 اردیبهشت 1397
  • تاریخ پذیرش: 05 خرداد 1397

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