Abstract：Long non-coding RNA (lncRNA) is known to be involved in adipogenesis, but the exact molecular mechanisms remain largely unknown. In order to further explore the potential role of lncRNAs in fat deposition and provide theoretical basis for beef cattle (Bos taurus) improvement, a total of 3 040 lncRNAs was identified in Nanyang and Pinan cattle back fat using high-throughput RNA sequencing technology, among which 3 008 (98.9%) lncRNAs were co-expressed by the two cattle. Characteristic analysis results showed that most (66.02%) lncRNAs were concentrated in length from 1 000 to 2 500 bp and distributed in all chromosomes. Differential expression analysis showed that there were 67 differentially expressed lncRNAs in Pinan cattle compared with Nanyang cattle, among which 32 were up-regulated and 35 were down-regulated. GO analysis results showed that differentially expressed lncRNAs were mainly enriched in lipids transport process, membrane composition and lipid antigen binding and other related biological processes. KEGG pathway analysis showed that these differentially expressed lncRNAs genes were mainly enriched in glycerophospholipid metabolism, ether lipid metabolism, triglyceride metabolism, carbohydrate digestion and absorption pathways. In order to explore the function mechanism of lncRNA, lncRNA-miRNA-mRNA control network was constructed. It was found that LOC104972839/LOC107131703-miR-27b-phospholipase A2 group IVF (PLA2G4F)/ major facilitator superfamily domain containing 2A (MFSD2A) might play an important role in fatty acid degradation and fat deposition. It can be used as a candidate target to study the mechanism of fat development. To test the reliability of sequencing results, qRT-PCR was used for expression level identification, and online software was used for coding ability prediction. The results showed that the expression level of differentially expressed lncRNAs was consistent with the RNA-sequencing results, and the coding ability was very low. In conclusion, this study provides new insights into the discovery and annotation of lncRNA related to fat deposition, and provides basis for further elucidation of the molecular regulatory mechanism of fat deposition in cattle.
[1] 何春, 张琦悦, 孙浩玮, 等. 2020. miRNA和lncRNA在动物脂肪沉积中的研究进展[J]. 生物工程学报, 36: 1504-1514. (He C, Zhang Q Y, Sun H W, et al.2020. Research progress of miRNA and lncRNA in animal fat deposition[J]. Chinese Journal of Biotechnology, 36: 1504-1514.) [2] 李鹏涛, 范逸婷, 张宁宁, 等. 2021. 影响牛羊肌内脂肪沉积因素的研究进展[J]. 黑龙江畜牧兽医, (05):48-52. (Li P T, Fan Y T, Zhang N N, et al. 2021. Research progress on factors affecting fat deposition in cattle and sheep[J]. Heilongjiang Animal Science and Veterinary Medicine, (05): 48-52.) [3] 邵静, 张珈溯, 尹宝珍, 等. 2020. miR-17-3p靶向KCTD15调控延边黄牛前体脂肪细胞分化[J]. 畜牧兽医学报, 51: 2689-2698. (Shao J, Zhang J S, Yin B Z, et al.2020. miR-17-3p targets KCTD15 to regulate the differentiation of Yanbian yellow cattle precursor adipocytes[J]. Chinese Journal of Animal and Veterinary Sciences, 51: 2689-2698.) [4] 王建钦, 王玉海, 谭书江, 等. 2019. 皮南牛生长繁殖屠宰肉质等性能研究[J]. 中国牛业科学, 45: 52-54. (Wang J Q, Wang Y H, Tan S J, et al.2019. Research on growth, reproduction and slaughter meat quality and other properties of Pinan cattle[J]. China Cattle Science, 45: 52-54.) [5] 王琪, 田晨映, 张细权, 等. 2019. 高低脂肉鸡中与腹脂沉积相关基因的差异表达[J]. 中国家禽, 41: 6-10. (Wang Q, Tian C Y, Zhang X Q, et al.2019. Differential expression of genes related to abdominal fat deposition in high- and low-fat broilers[J]. China Poultry, 41: 6-10.) [6] 魏成斌, 张彬, 施巧婷, 等. 2013. 南阳牛种质资源个性描述[J]. 河南农业科学, 42: 124-127. (Wei C B, Zhang B, Shi Q T, et al.2013. Characterization of Nanyang cattle germplasm resources[J]. Journal of Henan Agricultural Sciences, 42: 124-127.) [7] 于德浩, 李巧珍, 卢天佑, 等. 2009. 皮南牛与南阳牛育肥屠宰对比试验研究[C]//2009中国牛业进展论文集. 中国畜牧业协会, 179-181. (Yu D H, Li Q Z, Lu T Y, et al.2009. Comparative study on fattening and slaughter of Pinan and Nanyang cattle[C]//2009 China Cattle Industry Progress Papers. China Animal Husbandry Association, 179-181.) [8] 于树龙, 张昊, 李岑岑. 2020. 长链非编码RNA调控脂肪发育与代谢研究进展[J]. 生物技术进展, 10: 333-338. (Yu S L, Zhang H, Li C C.2020. Research progress in the regulation of fat development and metabolism by long non-coding RNA[J]. Current Biotechnology, 10: 333-338.) [9] 余梅, 毛华明, 黄必志. 2007. 牛肉品质的评定指标及影响牛肉品质的因素[J]. 中国畜牧兽医, (02):33-35. (Yu M, Mao H M, Huang B Z. 2007. Evaluation indexes of beef quality and factors affecting beef quality[J]. China Animal Husbandry and Veterinary Medicine, (02): 33-35.) [10] 张进威, 罗毅, 王宇豪, 等. 2015. MicroRNA调控动物脂肪细胞分化研究进展[J]. 遗传, 37: 1175-1184. (Zhang J W, Luo Y, Wang Y H, et al.2015. Research progress in microRNA regulation of animal adipocyte differentiation[J]. Hereditas, 37: 1175-1184. [11] 宗楷淇, 马增春, 高月. 2008. 腺苷A1受体的作用研究进展[J]. 中国药理学通报, 24: 573-576. (Zong K Q, Ma Z C, Gao Y.2008. Research progress on the role of adenosine A1 receptor[J]. Chinese Pharmacological Bulletin, 24: 573-576.) [12] Arner P, Kulyté A.2015. MicroRNA regulatory networks in human adipose tissue and obesity[J]. Nature Reviews Endocrinology, 11: 276-288. [13] Babak T, Blencowe B J, Hughes T R.2005. A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription[J]. BMC Genomics, 6(1): 1-12. [14] Baik M, Kang H J, Park S J, et al.2017. Triennial growth and development symposium: molecular mechanisms related to bovine intramuscular fat deposition in the longissimus muscle[J]. Journal of Animal Science, 95(5): 2284-2303. [15] Batista P J, Chang H Y.2013. Long noncoding RNAs: Cellular address codes in development and disease[J]. Cell, 152: 1298-1307. [16] Burnstock G.2014. Purinergic signalling in endocrine organs[J]. Purinergic Signalling, 10(1): 189-231. [17] Chen X, Tan X R, Li S J, et al.2019. LncRNA NEAT1 promotes hepatic lipid accumulation via regulating miR-146a-5p/ROCK1 in nonalcoholic fatty liver disease[J]. Life Sciences, 235: 116829. [18] Chen X, Xu Y, Zhao D, et al.2018. LncRNA-AK012226 is involved in fat accumulation in db/db mice fatty liver and non-alcoholic fatty liver disease cell model[J]. Frontiers in Pharmacology, 9: 888. [19] Choe S S, Huh J Y, Hwang I J, et al.2016. Adipose tissue remodeling: Its role in energy metabolism and metabolic disorders[J]. Frontiers in Endocrinology, 7: 30. [20] Ding Y, Qian L, Wang L, et al.2020. Relationship among porcine lncRNA TCONS_00010987, miR-323, and leptin receptor based on dual luciferase reporter gene assays and expression patterns[J]. Asian-Australasian Journal of Animal Sciences, 33(2): 219. [21] Du J, Xu Y, Zhang P, et al.2018. MicroRNA-125a-5p affects adipocytes proliferation, differentiation and fatty acid composition of porcine intramuscular fat[J]. International Journal of Molecular Sciences, 19(2): 501. [22] Duttaroy A K, Basak S.2020. Maternal dietary fatty acids and their roles in human placental development[J]. Prostaglandins, Leukotrienes and Essential Fatty Acids, 155: 102080. [23] Fan Y, Gan M, Tan Y, et al.2019. Mir-152 regulates 3T3-L1 preadipocyte proliferation and differentiation[J]. Molecules, 24(18): 3379. [24] Gan C C, Ni T W, Yu Y, et al.2017. Flavonoid derivative (Fla-CN) inhibited adipocyte differentiation via activating AMPK and up-regulating microRNA-27 in 3T3-L1 cells[J]. European Journal of Pharmacology, 797: 45-52. [25] Ge K, Chen X, Kuang J, et al.2019. Comparison of liver transcriptome from high-and low-intramuscular fat Chaohu ducks provided additional candidate genes for lipid selection[J]. 3 Biotech, 9: 1-11. [26] Gondelaud F, Ricard‐Blum S.2019. Structures and interactions of syndecans[J]. The FEBS Journal, 286: 2994-3007. [27] Götting C, Kuhn J, Zahn R, et al.2000. Molecular cloning and expression of human UDP-D-xylose: Proteoglycan core protein β-D-xylosyltransferase and its first isoform XT-II[J]. Journal of Molecular Biology, 304: 517-528. [28] Hardwick J P.2008. Cytochrome P450 omega hydroxylase (CYP4) function in fatty acid metabolism and metabolic diseases[J]. Biochemical Pharmacology, 75: 2263-2275. [29] Huang J, Liu X, Feng X, et al.2020. Characterization of different adipose depots in fattened buffalo: Histological features and expression profiling of adipocyte markers[J]. Archives Animal Breeding, 63(1): 61-67. [30] Huang J, Zheng Q, Wang S, et al.2019. High-throughput RNA sequencing reveals NDUFC2-AS lncRNA promotes adipogenic differentiation in chinese buffalo (Bubalus bubalis L.)[J]. Genes, 10(9): 689. [31] Huang W, Zhang X, Li A, et al.2018. Genome-wide analysis of mRNAs and lncRNAs of intramuscular fat related to lipid metabolism in two pig breeds[J]. Cellular Physiology and Biochemistry, 50: 2406-2422. [32] Hudson N J, Reverter A, Greenwood P L, et al.2015. Longitudinal muscle gene expression patterns associated with differential intramuscular fat in cattle[J]. Animal, 9: 650-659. [33] Jiang R, Li H, Yang J, et al.2020. CircRNA profiling reveals an abundant circFUT10 that promotes adipocyte proliferation and inhibits adipocyte differentiation via sponging let-7[J]. Molecular Therapy-Nucleic Acids, 20: 491-501. [34] Jiang S, Wei H, Song T, et al.2015. KLF13 promotes porcine adipocyte differentiation through PPARγ activation[J]. Cell & Bioscience, 5: 1-14. [35] Li M, Sun X, Cai H, et al.2016. Long non-coding RNA ADNCR suppresses adipogenic differentiation by targeting miR-204[J]. Biochimica et Biophysica Acta, 1859(7): 871-882. [36] Ling C, Svensson L, OdéN B, et al.2003. Identification of functional prolactin (PRL) receptor gene expression: PRL inhibits lipoprotein lipase activity in human white adipose tissue[J]. The Journal of Clinical Endocrinology & Metabolism, 88(4): 1804-1808. [37] Liu W, Ma C, Yang B, et al.2017. LncRNA Gm15290 sponges miR-27b to promote PPARγ-induced fat deposition and contribute to body weight gain in mice[J]. Biochemical and Biophysical Research Communications, 493(3): 1168-1175. [38] Lowe C E, O'rahilly S, Rochford J J.2011. Adipogenesis at a glance[J]. Journal of Cell Science, 124: 2681-2686. [39] Oliveira G, Cesar A, Felício A, et al.2016. Gene network regulated by microRNAs suggests modulation of fat deposition in cattle[J]. Journal of Animal Science, 94(suppl_5): 163-163. [40] Reeves J, Xuan J, Arfanis K, et al.2005. Identification, purification and characterization of a novel human blood protein with binding affinity for prostate secretory protein of 94 amino acids[J]. Biochemical Journal, 385: 105-114. [41] Ren L, Li Q, Hu X, et al.2020. A novel mechanism of bta-miR-210 in bovine early intramuscular adipogenesis[J]. Genes, 11(6): 601. [42] Salmena L, Poliseno L, Tay Y, et al.2011. A ceRNA hypothesis: The rosetta stone of a hidden RNA language?[J]. Cell, 146: 353-358. [43] Vahmani P, Ponnampalam E N, Kraft J, et al.2020. Bioactivity and health effects of ruminant meat lipids. Invited review[J]. Meat Science, 165: 108114. [44] Viladomiu M, Hontecillas R, Bassaganya-Riera J.2016. Modulation of inflammation and immunity by dietary conjugated linoleic acid[J]. European Journal of Pharmacology, 785: 87-95. [45] Wang K C, Chang H Y.2011. Molecular mechanisms of long noncoding RNAs[J]. Molecular Cell, 43(6): 904-914. [46] Wang Y, Zhu K, Yu W, et al.2017. MiR-181b regulates steatosis in nonalcoholic fatty liver disease via targeting SIRT1[J]. Biochemical and Biophysical Research Communications, 493(1): 227-232. [47] Wong B H, Chan J P, Cazenave-Gassiot A, et al.2016. Mfsd2a is a transporter for the essential ω-3 fatty acid docosahexaenoic acid (DHA) in eye and is important for photoreceptor cell development[J]. Journal of Biological Chemistry, 291: 10501-10514. [48] Xie X, Li S, Zhu Y, et al.2017. MicroRNA-27a/b mediates endothelin-1-induced PPARγ reduction and proliferation of pulmonary artery smooth muscle cells[J]. Cell & Tissue Research, 369: 1-13. [49] Xu Y, Qi X, Hu M, et al.2018. Transcriptome analysis of adipose tissue indicates that the cAMP signaling pathway affects the feed efficiency of pigs[J]. Genes, 9(7): 336. [50] Yang B, Chen H, Stanton C, et al.2015. Review of the roles of conjugated linoleic acid in health and disease[J]. Journal of Functional Foods, 15: 314-325. [51] Yang Z, Bian C, Zhou H, et al.2011. MicroRNA hsa-miR-138 inhibits adipogenic differentiation of human adipose tissue-derived mesenchymal stem cells through adenovirus EID-1[J]. Stem Cells & Development, 20(2): 259-267. [52] Yu Y, Chen Y, Zhang X, et al.2018. Knockdown of lncRNA KCNQ1OT1 suppresses the adipogenic and osteogenic differentiation of tendon stem cell via downregulating miR-138 target genes PPARγ and RUNX2[J]. Cell Cycle, 17: 2374-2385. [53] Zhang Y, Wang Y, Wang H, et al.2019. MicroRNA-224 impairs adipogenic differentiation of bovine preadipocytes by targeting LPL[J]. Molecular And Cellular Probes, 44: 29-36.
