The comprehensive detection of miRNA and circRNA in the regulation of intramuscular and subcutaneous adipose tissue of Laiwu pig

  • Zhou, G. et al. Global comparison of gene expression profiles between intramuscular and subcutaneous adipocytes of neonatal landrace pig using microarray. Meat. Sci. 86(2), 440–450 (2010).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Alfaia, C. M. et al. Current feeding strategies to improve pork intramuscular fat content and its nutritional quality. Adv. Food Nutr. Res. 89, 53–94 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Nonneman, D. J. et al. Genome-wide association of meat quality traits and tenderness in swine. J. Anim. Sci. 91(9), 4043–4050 (2013).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Sun, W. X. et al. Global comparison of gene expression between subcutaneous and intramuscular adipose tissue of mature Erhualian pig. Genet. Mol. Res. 12(4), 5085–5101 (2013).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Cristancho, A. G. & Lazar, M. A. Forming functional fat: A growing understanding of adipocyte differentiation. Nat. Rev. Mol. Cell Biol. 12(11), 722–734 (2011).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Du, M. et al. Meat science and muscle biology symposium: Manipulating mesenchymal progenitor cell differentiation to optimize performance and carcass value of beef cattle. J. Anim. Sci. 91(3), 1419–1427 (2013).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Uezumi, A. et al. Identification and characterization of PDGFRalpha+ mesenchymal progenitors in human skeletal muscle. Cell Death Dis. 5, e1186 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Geloen, A., Roy, P. E. & Bukowiecki, L. J. Regression of white adipose tissue in diabetic rats. Am. J. Physiol. 257(4 Pt 1), E547–E553 (1989).

    CAS 
    PubMed 

    Google Scholar
     

  • Sciorati, C. et al. Fat deposition and accumulation in the damaged and inflamed skeletal muscle: Cellular and molecular players. Cell Mol. Life Sci. 72(11), 2135–2156 (2015).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Arner, P. & Ryden, M. The contribution of bone marrow-derived cells to the human adipocyte pool. Adipocyte 6(3), 187–192 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Schubel, R. et al. Key genes of lipid metabolism and WNT-signaling are downregulated in subcutaneous adipose tissue with moderate weight loss. Nutrients 11(3), 639 (2019).

    PubMed Central 
    Article 

    Google Scholar
     

  • Zeng, H. et al. MicroRNA-339 inhibits human hepatocellular carcinoma proliferation and invasion via targeting ZNF689. Drug Des. Dev. Ther. 13, 435–445 (2019).

    ADS 
    CAS 
    Article 

    Google Scholar
     

  • Wang, B. et al. Nutrigenomic regulation of adipose tissue development—Role of retinoic acid: A review. Meat Sci. 120, 100–106 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Jiang, S. et al. Transcriptome comparison between porcine subcutaneous and intramuscular stromal vascular cells during adipogenic differentiation. PLoS ONE 8(10), e77094 (2013).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Poulos, S. P. & Hausman, G. J. A comparison of thiazolidinedione-induced adipogenesis and myogenesis in stromal-vascular cells from subcutaneous adipose tissue or semitendinosus muscle of postnatal pigs. J. Anim. Sci. 84(5), 1076–1082 (2006).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Li, A. et al. Identification and characterization of circRNAs of two pig breeds as a new biomarker in metabolism-related diseases. Cell Physiol. Biochem. 47(6), 2458–2470 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Sanger, H. L. et al. Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proc. Natl. Acad. Sci. USA 73(11), 3852–3856 (1976).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Memczak, S. et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495(7441), 333–338 (2013).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Bozzoni, I. Widespread occurrence of circular RNA in eukaryotes. Nat. Rev. Genet. 22(9), 550–551 (2021).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Li, Y. et al. Accurate identification of circRNA landscape and complexity reveals their pivotal roles in human oligodendroglia differentiation. Genome Biol. 23(1), 48 (2022).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Zhang, S. et al. Characterization of circRNA-associated-ceRNA networks in a senescence-accelerated mouse prone 8 brain. Mol. Ther. 25(9), 2053–2061 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Ashwal-Fluss, R. et al. circRNA biogenesis competes with pre-mRNA splicing. Mol. Cell 56(1), 55–66 (2014).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Dong, R. et al. Increased complexity of circRNA expression during species evolution. RNA Biol. 14(8), 1064–1074 (2017).

    PubMed 
    Article 

    Google Scholar
     

  • Ozdemir, S. & Arslan, H. circRNA-based biomarker candidates for acute cypermethrin and chlorpyrifos toxication in the brain of zebrafish (Danio rerio). Chemosphere 298, 134330 (2022).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Sharma, P. et al. Generation of transgenic rice expressing circRNA and its functional characterization. Methods Mol. Biol. 2362, 35–68 (2021).

    PubMed 
    Article 

    Google Scholar
     

  • Glazar, P., Papavasileiou, P. & Rajewsky, N. circBase: A database for circular RNAs. RNA 20(11), 1666–1670 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Hansen, T. B. et al. Natural RNA circles function as efficient microRNA sponges. Nature 495(7441), 384–388 (2013).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Du, W. W. et al. Identifying and characterizing circRNA-protein interaction. Theranostics 7(17), 4183–4191 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Dube, U. et al. An atlas of cortical circular RNA expression in Alzheimer disease brains demonstrates clinical and pathological associations. Nat. Neurosci. 22(11), 1903–1912 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Tang, Q. & Hann, S. S. Biological roles and mechanisms of circular RNA in human cancers. Onco Targets Ther. 13, 2067–2092 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Zhang, S. et al. Circular RNA circ_0003204 inhibits proliferation, migration and tube formation of endothelial cell in atherosclerosis via miR-370-3p/TGFbetaR2/phosph-SMAD3 axis. J. Biomed. Sci. 27(1), 11 (2020).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Zhou, Z. B. et al. Silencing of circ.RNA2837 plays a protective role in sciatic nerve injury by sponging the miR-34 family via regulating neuronal autophagy. Mol. Ther. Nucleic Acids 12, 718–729 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Dong, W. et al. The RNA-binding protein RBM3 promotes cell proliferation in hepatocellular carcinoma by regulating circular RNA SCD-circRNA 2 production. EBioMedicine 45, 155–167 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Ragusa, M. et al. CircNAPEPLD is expressed in human and murine spermatozoa and physically interacts with oocyte miRNAs. RNA Biol. 16(9), 1237–1248 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Liu, K. S. et al. Biological functions of circular RNAs and their roles in occurrence of reproduction and gynecological diseases. Am. J. Transl. Res. 11(1), 1–15 (2019).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gao, Y., Wang, J. & Zhao, F. CIRI: An efficient and unbiased algorithm for de novo circular RNA identification. Genome Biol. 16, 4 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11(10), R106 (2010).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Quan, L. et al. Identification of target genes regulated by KSHV miRNAs in KSHV-infected lymphoma cells. Pathol. Oncol. Res. 21(4), 875–880 (2015).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Ebbesen, K. K., Hansen, T. B. & Kjems, J. Insights into circular RNA biology. RNA Biol. 14(8), 1035–1045 (2017).

    PubMed 
    Article 

    Google Scholar
     

  • John, B. et al. Human microRNA targets. PLoS Biol. 2(11), e363 (2004).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Yu, G. et al. clusterProfiler: An R package for comparing biological themes among gene clusters. OMICS 16(5), 284–287 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Livak, K.J. & Schmittgen, T.D. Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2(−Delta Delta C(T)) Method. (2013).

  • Prats, A. C. et al. Circular RNA, the key for translation. Int. J. Mol. Sci. 21(22), 8591 (2020).

    CAS 
    PubMed Central 
    Article 

    Google Scholar
     

  • Guo, J. U. et al. Expanded identification and characterization of mammalian circular RNAs. Genome Biol. 15(7), 409 (2014).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Chandrasinghe, P. et al. Role of SMAD proteins in colitis-associated cancer: From known to the unknown. Oncogene 37(1), 1–7 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Lee, M. J. Transforming growth factor beta superfamily regulation of adipose tissue biology in obesity. Biochim. Biophys. Acta Mol. Basis Dis. 1864(4 Pt A), 1160–1171 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Budi, E. H., Duan, D. & Derynck, R. Transforming growth factor-beta receptors and smads: Regulatory complexity and functional versatility. Trends Cell Biol. 27(9), 658–672 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Matsubara, T. et al. TGF-beta-SMAD3 signaling mediates hepatic bile acid and phospholipid metabolism following lithocholic acid-induced liver injury. J. Lipid Res. 53(12), 2698–2707 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Xiao, J. et al. miR-212 downregulation contributes to the protective effect of exercise against non-alcoholic fatty liver via targeting FGF-21. J. Cell Mol. Med. 20(2), 204–216 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Xiao, J. et al. miR-149 controls non-alcoholic fatty liver by targeting FGF-21. J. Cell Mol. Med. 20(8), 1603–1608 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Chen, T. et al. The effect of microRNA-331-3p on preadipocytes proliferation and differentiation and fatty acid accumulation in Laiwu pigs. Biomed. Res. Int. 2019, 9287804 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Salama, I. I. et al. Plasma microRNAs biomarkers in mild cognitive impairment among patients with type 2 diabetes mellitus. PLoS ONE 15(7), e0236453 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Pan, S. et al. MicroRNA-128 is involved in dexamethasone-induced lipid accumulation via repressing SIRT1 expression in cultured pig preadipocytes. J. Steroid Biochem. Mol. Biol. 186, 185–195 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Wang, J. et al. Comprehensive analysis of differentially expressed mRNA, lncRNA and circRNA and their ceRNA networks in the longissimus dorsi muscle of two different pig breeds. Int. J. Mol. Sci. 20(5), 1107 (2019).

    CAS 
    PubMed Central 
    Article 

    Google Scholar
     

  • Petan, T., Jarc, E. & Jusovic, M. Lipid droplets in cancer: Guardians of fat in a stressful world. Molecules 23(8), 1941 (2018).

    PubMed Central 
    Article 

    Google Scholar
     

  • Santasusagna, S. et al. miR-328 mediates a metabolic shift in colon cancer cells by targeting SLC2A1/GLUT1. Clin. Transl. Oncol. 20(9), 1161–1167 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Saberi, A. et al. MiR-328 may be considered as an oncogene in human invasive breast carcinoma. Iran Red Crescent. Med. J. 18(11), e42360 (2016).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Qin, X. & Guo, J. MicroRNA-328-3p protects vascular endothelial cells against oxidized low-density lipoprotein induced injury via targeting forkhead box protein O4 (FOXO4) in atherosclerosis. Med. Sci. Monit. 26, e921877 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Wu, C. Y. et al. MicroRNA-328 ameliorates oxidized low-density lipoprotein-induced endothelial cells injury through targeting HMGB1 in atherosclerosis. J. Cell Biochem. 120, 1643–1650 (2018).

    Article 

    Google Scholar
     

  • Xie, W. et al. Beneficial role of microRNA-328-3p in fracture healing by enhancing osteoblastic viability through the PTEN/PI3K/AKT pathway. Exp. Ther. Med. 20(6), 271 (2020).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Oliverio, M. et al. Dicer1-miR-328-Bace1 signalling controls brown adipose tissue differentiation and function. Nat. Cell Biol. 18(3), 328–336 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Cazanave, S. C. et al. A role for miR-296 in the regulation of lipoapoptosis by targeting PUMA. J. Lipid Res. 52(8), 1517–1525 (2011).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Belarbi, Y. et al. MicroRNAs-361-5p and miR-574-5p associate with human adipose morphology and regulate EBF1 expression in white adipose tissue. Mol. Cell Endocrinol. 472, 50–56 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Lefterova, M. I. & Lazar, M. A. New developments in adipogenesis. Trends Endocrinol. Metab. 20(3), 107–114 (2009).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Katoh, M. & Katoh, M. WNT signaling pathway and stem cell signaling network. Clin. Cancer Res. 13(14), 4042–4045 (2007).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Otto, T. C. & Lane, M. D. Adipose development: from stem cell to adipocyte. Crit. Rev. Biochem. Mol. Biol. 40(4), 229–242 (2005).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Takada, I. et al. A histone lysine methyltransferase activated by non-canonical Wnt signalling suppresses PPAR-gamma transactivation. Nat. Cell Biol. 9(11), 1273–1285 (2007).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Kanazawa, A. et al. Wnt5b partially inhibits canonical Wnt/beta-catenin signaling pathway and promotes adipogenesis in 3T3-L1 preadipocytes. Biochem. Biophys. Res. Commun. 330(2), 505–510 (2005).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Wang, Y. X. et al. Peroxisome-proliferator-activated receptor delta activates fat metabolism to prevent obesity. Cell 113(2), 159–170 (2003).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Tanaka, T. et al. Activation of peroxisome proliferator-activated receptor delta induces fatty acid beta-oxidation in skeletal muscle and attenuates metabolic syndrome. Proc. Natl. Acad. Sci. U S A 100(26), 15924–15929 (2003).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Luquet, S. et al. Roles of PPAR delta in lipid absorption and metabolism: A new target for the treatment of type 2 diabetes. Biochim. Biophys. Acta 1740(2), 313–317 (2005).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Yu, Y. H. et al. Ectopic expression of porcine peroxisome proliferator-activated receptor delta regulates adipogenesis in mouse myoblasts. J. Anim. Sci. 86(1), 64–72 (2008).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Odegaard, J. I. et al. Alternative M2 activation of Kupffer cells by PPARdelta ameliorates obesity-induced insulin resistance. Cell Metab. 7(6), 496–507 (2008).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Brestoff, J. R. et al. Intercellular mitochondria transfer to macrophages regulates white adipose tissue homeostasis and is impaired in obesity. Cell Metab. 33(2), 270–2828 (2021).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Han, J. K. et al. Peroxisome proliferator-activated receptor-delta activates endothelial progenitor cells to induce angio-myogenesis through matrix metallo-proteinase-9-mediated insulin-like growth factor-1 paracrine networks. Eur. Heart J. 34(23), 1755–1765 (2013).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Wang, L. & Shan, T. Factors inducing transdifferentiation of myoblasts into adipocytes. J. Cell Physiol. 236(4), 2276–2289 (2021).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Kotlinowski, J. & Jozkowicz, A. PPAR gamma and angiogenesis: Endothelial cells perspective. J. Diabetes Res. 2016, 8492353 (2016).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Hurt, B. et al. Cancer-promoting mechanisms of tumor-associated neutrophils. Am. J. Surg. 214(5), 938–944 (2017).

    PubMed 
    Article 

    Google Scholar
     

  • Mazzotti, D. R. et al. Association of APOE, GCPII and MMP9 polymorphisms with common diseases and lipid levels in an older adult/elderly cohort. Gene 535(2), 370–375 (2014).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Stephens, D. C. et al. Imaging the rapid yet transient accumulation of regulatory lipids, lipid kinases, and protein kinases during membrane fusion, at sites of exocytosis of MMP-9 in MCF-7 cells. Lipids Health Dis. 19(1), 195 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Allott, E. H. et al. MMP9 expression in oesophageal adenocarcinoma is upregulated with visceral obesity and is associated with poor tumour differentiation. Mol. Carcinog. 52(2), 144–154 (2013).

    PubMed 
    Article 

    Google Scholar
     

  • Ii, H. et al. Group IVA phospholipase A2-associated production of MMP-9 in macrophages and formation of atherosclerotic lesions. Biol. Pharm. Bull. 31(3), 363–368 (2008).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Zhang, N. et al. Ketogenic diet elicits antitumor properties through inducing oxidative stress, inhibiting MMP-9 expression, and rebalancing M1/M2 tumor-associated macrophage phenotype in a mouse model of colon cancer. J. Agric. Food Chem. 68(40), 11182–11196 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Thamer, C. et al. Variations in PPARD determine the change in body composition during lifestyle intervention: A whole-body magnetic resonance study. J. Clin. Endocrinol. Metab. 93(4), 1497–1500 (2008).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Scott, L. J. et al. A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science 316(5829), 1341–1345 (2007).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Lu, L. et al. Associations of type 2 diabetes with common variants in PPARD and the modifying effect of vitamin D among middle-aged and elderly Chinese. PLoS ONE 7(4), e34895 (2012).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Zhang, Y. et al. The functional SNPs in the 5’ regulatory region of the porcine PPARD gene have significant association with fat deposition traits. PLoS ONE 10(11), e0143734 (2015).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

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