257
Views
5
CrossRef citations to date
0
Altmetric
Molecular, Cellular and Developmental Biology

miRNA-mRNA associations with inosine monophosphate specific deposition in the muscle of Jingyuan chicken

ORCID Icon, , , , , & show all
Pages 821-832 | Received 26 Feb 2022, Accepted 21 Jun 2022, Published online: 31 Aug 2022

References

  • Aigner, A. 2011. “MicroRNAs (Mirnas) in Cancer Invasion and Metastasis: Therapeutic Approaches Based on Metastasis-related miRNAs.” Journal of Molecular Medicine 89 (5): 445–457. doi:10.1007/s00109-010-0716-0.
  • Ballester, M., M. Amills, O. Gonzalez-Rodriguez, T. F. Cardoso, M. Pascual, R. Gonzalez-Prendes, N. Panella-Riera, I. Díaz, J. Tibau, and R. Quintanilla. 2018. “Role of AMPK Signalling Pathway during Compensatory Growth in Pigs.” BMC Genomics 19 (1): 682. doi:10.1186/s12864-018-5071-5.
  • Bao, A. D., C. Q. Liu, S. Liu, H. M. Wu, T. F. Lu, W. J. Guan, and Y. H. Ma. 2008. “Candidate Gene AMPD1, ADSL and ATIC of Meat Quality and Flavor in Chicken.”China Animal Husbandry and Veterinary Medicine 35 (2): 32–35. In Chinese. .
  • Blonde, G. D., and A. C. Spector. 2017. “An Examination of the Role of l-glutamate and Inosine 5’-monophosphate in Hedonic Taste-guided Behavior by Mice Lacking the T1R1 + T1R3 Receptor.” Chemical Senses 42 (5): 393–404. doi:10.1093/chemse/bjx015.
  • Bushati, N., and S. M. Cohen. 2007. “MicroRNA Functions.” Annual Review of Cell and Developmental Biology 23 (1): 175–205. doi:10.1146/annurev.cellbio.23.090506.123406.
  • Cai, Z. W., L. F. Zhang, X. L. Jiang, Y. F. Sheng, and N. Y. Xu. 2015. “Differential miRNA Expression Profiles in the Longissimus Dorsi Muscle between Intact and Castrated Male Pigs.” Research in Veterinary Science 99: 99–104. doi:10.1016/j.rvsc.2014.12.012.
  • Chen, J. L. 2004. “Studies on Inheritance and Candidate Genes of Inosine-5’-monophosphate and Intramuscular Fat Contents in Chicken Meat”. PhD diss., China Agricultural University.
  • Chen, Y. B. 2021. “Study on the Relationship between the Change Rule of IMP Content and Correlation of Related Genes Expression in Muscle of Lueyang black-bone Chicken.” Master’s diss., Shaanxi University of Technology.
  • Chen, J. F., E. M. Mandel, J. M. Thomson, Q. L. Wu, T. E. Callis, S. M. Hammond, F. L. Conlon, and D. Z. Wang. 2006. “The Role of microRNA-1 and microRNA-133 in Skeletal Muscle Proliferation and Differentiation.” Nature Genetics 38 (2): 228–233. doi:10.1038/ng1725.
  • Chen, Y., Y. L. Zhao, W. J. Jin, Y. F. Li, Y. H. Zhang, X. J. Ma, G. R. Sun, et al. 2019. “MicroRNAs and their Regulatory Networks in Chinese Gushi Chicken Abdominal Adipose Tissue during Postnatal Late Development.” BMC Genomics 20 (1): 778. doi:10.1186/s12864-019-6094-2.
  • Cheng, A. M., M. W. Byrom, J. Shelton, and L. P. Ford. 2005. “Antisense Inhibition of Human miRNAs and Indications for an Involvement of miRNA in Cell Growth and Apoptosis.” Nucleic Acids Research 33 (4): 1290–1297. doi:10.1093/nar/gki200.
  • Cho, J., J. S. King, X. Qian, A. J. Harwood, and S. B. Shears. 2008. “Dephosphorylation of 2,3-bisphosphoglycerate by MIPP Expands the Regulatory Capacity of the Rapoport-Luebering Glycolytic Shunt.” Proceedings of the National Academy of Sciences of the United States of America 105 (16): 5998–6003. doi:10.1073/pnas.0710980105.
  • Deyle, D. R., I. F. Khan, G. Ren, P. R. Wang, J. Kho, U. Schwarze, and D. W. Russell. 2012. “Normal Collagen and Bone Production by gene-targeted Human Osteogenesis Imperfecta iPSCs.” Molecular Therapy 20 (1): 204–213. doi:10.1038/mt.2011.209.
  • Enright, A. J., B. John, U. Gaul, T. Tuschl, C. Sander, and D. Marks. 2003. “MicroRNA Targets in Drosophila.” Genome Biology 5 (1): R1. doi:10.1186/gb-2003-5-1-r1.
  • Friedlander, M. R., S. D. Mackowiak, N. Li, W. Chen, and N. Rajewsky. 2011. “MiRDeep2 Accurately Identifies Known and Hundreds of Novel microRNA Genes in Seven Animal Clades.” Nucleic Acids Research 40 (1): 37–52. doi:10.1093/nar/gkr688.
  • Fu, R. Q., G. P. Zhao, R. R. Liu, M. Q. Zheng, J. L. Chen, and J. Wen. 2013. “Research on Body Fat Distribution and Deposition Pattern of Beijing-You Chickens.” Chinese Journal of Animal Nutrition 25 (7): 1465–1472.In Chinese. doi:10.3969/j.1006-267x.2013.07.010.
  • Ghosh, D. 2019. “Wavelet-based Benjamini-Hochberg Procedures for Multiple Testing under Dependence.” Mathematical Biosciences and Engineering 17 (1): 56–72. doi:10.3934/mbe.2020003.
  • Gupta, V. A., and A. H. Beggs. 2014. “Kelch Proteins: Emerging Roles in Skeletal Muscle Development and Diseases.” Skelet Muscle 4 (1): 11. doi:10.1186/2044-5040-4-11.
  • Hennessy, E. J., F. J. Sheedy, D. Santamaria, M. Barbacid, and L. A. J. O’Neill. 2011. “Toll-like Receptor-4 (TLR4) Down-regulates microRNA-107, Increasing Macrophage Adhesion via cyclin-dependent Kinase 6.” Journal of Biological Chemistry 286 (29): 25531–25539. doi:10.1074/jbc.M111.256206.
  • Hong, J. S., S. H. Noh, J. S. Lee, J. M. Kim, K. C. Hong, and Y. S. Lee. 2012. “Effects of Polymorphisms in the Porcine microRNA miR-1 Locus on Muscle Fiber Type Composition and miR-1 Expression.” Gene 506 (1): 211–216. doi:10.1016/j.gene.2012.06.050.
  • Imamura, K., and T. Tanaka. 1972. “Multimolecular Forms of Pyruvate Kinase from Rat and Other Mammalian Tissues. I. Electrophoretic Studies.” Journal of Biochemistry 71 (6): 1043–1051. doi:10.1093/oxfordjournals.jbchem.a129852.
  • Jayasena, D. D., S. Jung, H. J. Kim, H. I. Yong, K. C. Nam, and C. Jo. 2015. “Taste-active Compound Levels in Korean Native Chicken Meat: The Effects of Bird Age and the Cooking Process.” Poultry Science 94 (8): 1964–1972. doi:10.3382/ps/pev154.
  • Jin, C. L., H. R. Zeng, C. Q. Gao, H. C. Yan, H. Z. Tan, and X. Q. Wang. 2020. “Dietary Supplementation with Pioglitazone Hydrochloride and Chromium Methionine Manipulates Lipid Metabolism with Related Genes to Improve the Intramuscular Fat and Fatty Acid Profile of Yellow-feathered Chickens.” Journal of the Science of Food and Agriculture 100 (3): 1311–1319. doi:10.1002/jsfa.10146.
  • Johnson, C. D., A. Esquela-Kerscher, G. Stefani, M. Byrom, K. Kelnar, D. Ovcharenko, M. Wilson, et al. 2007. “The Let-7 microRNA Represses Cell Proliferation Pathways in Human Cells.” Cancer Research 67 (16): 7713–7722. doi:10.1158/0008-5472.CAN-07-1083.
  • Kanehisa, M., M. Araki, S. Goto, M. Hattori, M. Hirakawa, M. Itoh, T. Katayama, et al. 2008. “KEGG for Linking Genomes to Life and the Environment.” Nucleic Acids Research 36 (Database): D480–484. doi:10.1093/nar/gkm882.
  • Kozomara, A., and S. Griffiths-Jones. 2011. “miRBase: Integrating microRNA Annotation and Deep-sequencing Data.” Nucleic Acids Research 39 (Database): D152–157. doi:10.1093/nar/gkq1027.
  • Krüger, J., and M. Rehmsmeier. 2006. “RNAhybrid: MicroRNA Target Prediction Easy, Fast and Flexible.” Nucleic Acids Research 34 (Web Server): W451–454. doi:10.1093/nar/gkl243.
  • Lang, Y. M. 2016. “Mechanism and Effects of Muscle Fiber Types on Beef Tenderness.” PhD diss., Chinese Academy of Agricultural Sciences.
  • Langmead, B., C. Trapnell, M. Pop, and S. L. Salzberg. 2009. “Ultrafast and memory-efficient Alignment of Short DNA Sequences to the Human Genome.” Genome Biology 10 (3): R25. doi:10.1186/gb-2009-10-3-r25.
  • Lee, K. H., C. Lotterman, C. Karikari, N. Omura, G. Feldmann, N. Habbe, M. G. Goggins, J. T. Mendell, and A. Maitra. 2009. “Epigenetic Silencing of microRNA miR-107 Regulates cyclin-dependent Kinase 6 Expression in Pancreatic Cancer.” Pancreatology 9 (3): 293–301. doi:10.1159/000186051.
  • Li, L., S. Q. Jiang, C. T. Zheng, Z. Y. Gou, F. Chen, Q. L. Fan, and Q. Luo. 2015b. “Comparisons of Meat Quality Characteristics of Different Yellow-feathered Broilers.” China Poultry 37 (21): 6–11.In Chinese. doi:10.16372/j.1004-6364.2015.21.002.
  • Li, X. Y., X. S. Wang, L. L. Wang, Y. J. Zhang, R. Su, R. J. Wang, and J. Q. Li. 2015a. “Application Research Progress on Transcriptome Sequencing Technology in Wool Sheep and Cashmere Goat.” China Animal Husbandry and Veterinary Medicine 42 (7): 1692–1698.In Chinese. doi:10.16431/j.cnki.1671-7236.2015.07.011.
  • Liu, W. Y., L. F. Zhu, Z. F. Wen, and H. M. Shen. 1980. “A Comparative Study of Inosinic Acid Contents in Chicken Muscle.” Scientia Agricultura Sinica 4: 79–83. In Chinese. .
  • Livak, K. J., and T. D. Schmittgen. 2001. “Analysis of Relative Gene Expression Data Using Real-time Quantitative PCR and the 2(-Delta Delta C(T)) Method.” Methods 25 (4): 402–408. doi:10.1006/meth.2001.1262.
  • Love, M. I., W. Huber, and S. Anders. 2014. “Moderated Estimation of Fold Change and Dispersion for RNA-seq Data with DESeq2.” Genome Biology 15 (12): 550. doi:10.1186/s13059-014-0550-8.
  • Ma, J. D., H. M. Wang, R. Liu, L. Jin, Q. Z. Tang, X. Wang, and A. A. Jiang. 2015a. “The miRNA Transcriptome Directly Reflects the Physiological and Biochemical Differences between Red, White, and Intermediate Muscle Fiber Types.” International Journal of Molecular Sciences 16 (5): 9635–9653. doi:10.3390/ijms16059635.
  • Ma, M., Z. R. Zhang, H. R. Du, W. X. Wang, Q. Li, C. W. Yang, W. Li, Z. Y. Chen, and X. H. Chen. 2015b. “Quality Broilers of Different Breeds under free-range Conditions Comparative Analysis of Meat Quality.” China Poultry 37 (21): 53–54. In Chinese. doi:10.16372/j.1004-6364.2015.21.011.
  • Mishima, Y., A. J. Giraldez, Y. Takeda, T. Fujiwara, H. Sakamoto, A. F. Schier, and K. Inoue. 2006. “Differential Regulation of Germline mRNAs in Soma and Germ Cells by Zebrafish miR-430.” Current Biology 16 (21): 2135–2142. doi:10.1016/j.cub.2006.08.086.
  • Mourelatos, Z., J. Dostie, S. Paushkin, A. Sharma, B. Charroux, L. Abel, J. Rappsilber, M. Mann, and G. Dreyfuss. 2002. “miRNPs: A Novel Class of Ribonucleoproteins Containing Numerous microRNAs.” Genes & Development 16 (6): 720–728. doi:10.1101/gad.974702.
  • Nakashima, K., S. Miwa, S. Oda, T. Tanaka, K. Imamura, and T. Nishina. 1974. “Electrophoretic and Kinetic Studies of Mutant Erythrocyte Pyruvate Kinases.” Blood 43 (4): 537–548. doi:10.1182/blood.V43.4.537.537.
  • Neuhaus, P., B. Jaschinsky, S. Schneider, H. Neuhaus, A. Wolter, H. Ebelt, and T. Braun. 2006. “Overexpression of Kelch Domain Containing-2 (mKlhdc2) Inhibits Differentiation and Directed Migration of C2C12 Myoblasts.” Experimental Cell Research 312 (16): 3049–3059. doi:10.1016/j.yexcr.2006.06.006.
  • Ninomiya, K. 1998. “Natural Occurrence.” Food Reviews International 14 (2–3): 177–211. doi:10.1080/87559129809541157.
  • Panasyuk, G., C. Espeillac, C. Chauvin, L. A. Pradelli, Y. Horie, A. Suzuki, J. S. Annicotte, et al. 2012. “PPARγ Contributes to PKM2 and HK2 Expression in Fatty Liver.” Nature Communications 3 (1): 672. doi:10.1038/ncomms1667.
  • Pertea, M., D. Kim, G. M. Pertea, J. T. Leek, and S. L. Salzberg. 2016. “Transcript-level Expression Analysis of RNA-seq Experiments with HISAT, StringTie and Ballgown.” Nature Protocols 11 (9): 1650–1667. doi:10.1038/nprot.2016.095.
  • Ponsuksili, S., Y. Du, F. Hadlich, P. Siengdee, E. Murani, M. Schwerin, and K. Wimmers. 2013. “Correlated mRNAs and miRNAs from co-expression and Regulatory Networks Affect Porcine Muscle and Finally Meat Properties.” BMC Genomics 14 (1): 533. doi:10.1186/1471-2164-14-533.
  • Presek, P., M. Reinacher, and E. Eigenbrodt. 1988. “Pyruvate Kinase Type M2 Is Phosphorylated at Tyrosine Residues in Cells Transformed by Rous Sarcoma Virus.” FEBS Letters 242 (1): 194–198. doi:10.1016/0014-5793(88)81014-7.
  • Putri, G. H., S. Anders, P. T. Pyl, J. E. Pimanda, and F. Zanini. 2022. “Analysing high-throughput Sequencing Data in Python with HTSeq 2.0.” Bioinformatics btac166. doi:10.1093/bioinformatics/btac166.
  • Rock, C. O., R. B. Calder, M. A. Karim, and S. Jackowski. 2000. “Pantothenate Kinase Regulation of the Intracellular Concentration of Coenzyme A.” Journal of Biological Chemistry 275 (2): 1377–1383. doi:10.1074/jbc.275.2.1377.
  • Senft, A. W., D. G. Senft, and R. P. Miech. 1973. “Pathways of Nucleotide Metabolism in Schistosoma Mansoni. II. Disposition of Adenosine by Whole Worms.” Biochem Pharmacol 22 (4): 437–447. doi:10.1016/0006-2952(73)90285-2.
  • Shannon, P., A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker. 2003. “Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks.” Genome Research 13 (11): 2498–2504. doi:10.1101/gr.1239303.
  • Shen, L. Y., L. Chen, S. H. Zhang, Y. Zhang, J. Y. Wang, and L. Zhu. 2016b. “MicroRNA-23a Reduces Slow Myosin Heavy Chain Isoforms Composition through Myocyte Enhancer Factor 2C (MEF2C) and Potentially Influences Meat Quality.” Meat Science 116: 201–206. doi:10.1016/j.meatsci.2016.02.023.
  • Shen, L. Y., J. J. Du, Y. D. Xia, Z. D. Tan, Y. H. Fu, Q. Yang, and X. W. Li. 2016a. “Genome-wide Landscape of DNA Methylomes and Their Relationship with mRNA and miRNA Transcriptomes in Oxidative and Glycolytic Skeletal Muscles.” Scientific Reports 6 (1): 32186. doi:10.1038/srep32186.
  • Suzuki, H. I., K. Yamagata, K. Sugimoto, T. Iwamoto, S. Kato, and K. Miyazono. 2009. “Modulation of microRNA Processing by p53.” Nature 460 (7254): 529–533. doi:10.1038/nature08199.
  • Takenaka, M., T. Noguchi, S. Sadahiro, H. Hirai, K. Yamada, T. Matsuda, E. Imai, and T. Tanaka. 1991. “Isolation and Characterization of the Human Pyruvate Kinase M Gene.” European Journal of Biochemistry 198 (1): 101–106. doi:10.1111/j.1432-1033.1991.tb15991.x.
  • Tanaka, T., Y. Harano, F. Sue, and H. Morimura. 1967. “Crystallization, Characterization and Metabolic Regulation of Two Types of Pyruvate Kinase Isolated from Rat Tissues.” Journal of Biochemistry 62 (1): 71–91. doi:10.1093/oxfordjournals.jbchem.a128639.
  • Wan, L. 2021. “Measurement and Analysis Od Meat Performance of Nigdu Yellow Chicken.” Master’s diss., Jiangxi Agricultural University.
  • Wang, S. B. 2004. “Studies on the Deposition of 5’-IMP in Chicken Meat and Its Modification by Nutrition.” PhD diss., Chinese Academy of Agricultural Sciences.
  • Wang, Q., R. L. Qi, J. Wang, W. M. Huang, Y. J. Wu, X. F. Huang, F. Y. Yang, and J. X. Huang. 2017. “Differential Expression Profile of miRNAs in Porcine Muscle and Adipose Tissue during Development.” Gene 618: 49–56. doi:10.1016/j.gene.2017.04.013.
  • Wawrzyniak, J. A., A. Bianchi-Smiraglia, W. Bshara, S. Mannava, J. Ackroyd, A. Bagati, A. R. Omilian, et al. 2013. “A Purine Nucleotide Biosynthesis Enzyme Guanosine Monophosphate Reductase Is A Suppressor of Melanoma Invasion.” Cell Report 5 (2): 493–507. doi:10.1016/j.celrep.2013.09.015.
  • Wei, X. F. 2017. “Mechanism Study on miR-378a-3p, miR-107 and Related circRNA Regulating Bovine Myoblasts Development.” PhD diss., Northwest A&F University.
  • Wen, M., Y. Shen, S. H. Shi, and T. Tang. 2012. “miREvo: An Integrative microRNA Evolutionary Analysis Platform for Next-generation Sequencing Experiments.” BMC Bioinformatics 13 (1): 140. doi:10.1186/1471-2105-13-140.
  • Wilfred, B. R., W. X. Wang, and P. T. Nelson. 2007. “Energizing miRNA Research: A Review of the Role of miRNAs in Lipid Metabolism, with a Prediction that miR-103/107 Regulates Human Metabolic Pathways.” Molecular Genetics and Metabolism 91 (3): 209–217. doi:10.1016/j.ymgme.2007.03.011.
  • Young, M. D., M. J. Wakefield, G. K. Smyth, and A. Oshlack. 2010. “Gene Ontology Analysis for RNA-seq: Accounting for Selection Bias.” Genome Biology 11 (2): 14. doi:10.1186/gb-2010-11-2-r14.
  • Yu, B. J., Z. Z. Den, G. S. Xin, Z. Y. Cai, Y. L. Gu, and J. Zhang. 2021. “Correlation Analysis of Inosine Monophosphate Specific Deposition Related LNC_003828-gga-miR-107-3P-MINPP1 in Jingyuan Chicken Muscle Tissue.” Scientia Agricultura Sinica 54 (19): 4229–4242.In Chinese. doi:10.3864/j.0578-1752.2021.19.017.
  • Yu, G. C., L. G. Wang, Y. Y. Han, and Q. Y. He. 2012. “ClusterProfiler: An R Package for Comparing Biological Themes among Gene Clusters.” OMICS 16 (5): 284–287. doi:10.1089/omi.2011.0118.
  • Zhang, A. R., Z. K. Wu, Z. M. Chen, W. H. Chang, H. Y. Cai, G. H. Liu, and A. J. Zheng. 2021. “Unraveling Molecular Mechanism of Acute Immunological Stress Affecting Meat Quality of Broiler Chickens by Proteomics Analysis.”Acta Veterinaria et Zootechnica Sinica 52 (8): 2138–2150. In Chinese. .
  • Zhang, J., H. H. Hu, T. Mu, W. Z. Wang, B. J. Yu, J. Guo, Y. Wang,et al. 2020. “Correlation Analysis between AK1 mRNA Expression and Inosine Monophosphate Deposition in Jingyuan Chickens.” Animals (Basel) 10 (3): 439. doi:10.3390/ani10030439.
  • Zhou, L., J. H. Chen, Z. Z. Li, X. X. Li, X. D. Hu, Y. Huang, X. K. Zhao, et al. 2010. “Integrated Profiling of microRNAs and mRNAs: MicroRNAs Located on Xq27.3 Associate with Clear Cell Renal Cell Carcinoma.” PLoS One 5 (12): e15224. doi:10.1371/journal.pone.0015224.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.