Cloning,Expression and Bioinformatics Analysis of Yak lncFAM200B

doi:10.7668/hbnxb.20191071

Abstract

Abstract: The aim of this study was to clone and to identify the yak lncFAM200B, which might lay the foundation for exploring its regulatory role in yak muscle and fat during development. The primers for lncFAM200B gene were designed and used for the full-length cloning with the gluteal cDNA as template. The protein coding potential of lncFAM200B was predicted using the online prediction software CPC and CPAT, and then identified by prokaryotic expression assays. The tissue expression profile was analyzed by Real-time quantitative PCR (RT-qPCR), the target genes of miRNAs, which were interactions with lncFAM200B, were predicted by TargetScan 7.1 and miRanda. GO enrichment and KEGG pathway analysis were conducted with DAVID online software. The results showed that the full-length of yak lncFAM200B was 531 bp, which was 59 bp longer than that in cattle.Bioinformatics predicts results showed that its coding potential was -1.287 4, and prokaryotic expression assay further confirmed that lncFAM200B had no protein coding ability, suggesting that yak lncFAM200B was a real lncRNA. Tissue expression profiling showed that the expression of lncFAM200B had a higher level in yak lung tissue. The lncFAM200B interaction miRNA targets analysis revealed that many genes, such as Sirt1, SCD5, KLF9, PTEN and MYPN, were related to muscle and fat development.Taken together, the present study laid the foundation for further research on the function and regulatory mechanism of yak lncFAM200B in muscle and fat development.

Key words: Yak, lncFAM200B, Cloning, Tissue expression, Muscle development

CLC Number:

S823.85
Q78

ZHAO Liling, WANG Hui, CHAI Zhixin, WANG Jikun, WANG Jiabo, WU Zhijuan, XIN Jinwei, ZHONG Jincheng, JI Qiumei. Cloning,Expression and Bioinformatics Analysis of Yak lncFAM200B[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2020, 35(5): 220-230. doi: 10.7668/hbnxb.20191071.

/ / Recommend / Download Citations

URL: http://www.hbnxb.net/EN/10.7668/hbnxb.20191071

http://www.hbnxb.net/EN/Y2020/V35/I5/220

References

[1] 秦文. PPARα信号通路基因与牦牛肌内脂肪酸含量的相关性研究[D]. 兰州:甘肃农业大学, 2014.
Qin W.Correlation between PPARα signal pathway genes and fatty acid content in yak muscle[D]. Lanzhou:Gansu Agricultural University, 2014.
[2] 路畅, 黄银花.动物长链非编码RNA研究进展[J]. 遗传, 2017, 39(11):1054-1065.doi:10.16288/j.yczz.17-120.
Lu C, Huang Y H. Progress in long non-coding RNAs in animal[J]. Hereditas, 2017, 39(11):1054-1065.
[3] Kallen A N, Zhou X B, Xu J, Qiao C, Ma J, Yan L, Lu L G, Liu C C, Yi J S, Zhang H F, Min W, Bennett A M, Gregory R I, Ding Y, Huang Y Q. The imprinted H19 lncRNA antagonizes let-7 microRNAs[J]. Mol Cell, 2013, 52(1):101-112. doi:10.1016/j.molcel.2013.08.027.
[4] Tsai M C, Manor O, Wan Y, Mosammaparast N, Wang J K, Lan F, Shi Y, Segal E, Chang H Y. Long noncoding RNA as modular scaffold of histone modification complexes[J]. Science, 2010, 329(5992):689-693. doi:10.1126/science.1192002.
[5] Wang L J, Zhao Y, Bao X C, Zhu X H, Kwok Y K, Sun K, Chen X N, Huang Y H, Jauch R, Esteban M A, Sun H, Wang H T. LncRNA Dum interacts with Dnmts to regulate Dppa2 expression during myogenic differentiation and muscle regeneration[J]. Cell Research, 2015, 25(3):335-350. doi:10.1038/cr.2015.21.
[6] Chen M M, Li X, Zhang X J, Li Y, Zhang J X, Liu M H, Zhang L L, Ding X B, Liu X F, Guo H. A novel long non-coding RNA, lncKBTBD10, involved in bovine skeletal muscle myogenesis[J]. In Vitro Cellular & Developmental Biology-Animal, 2019, 55(1):25-35. doi:10.1007/s11626-018-0306-y.
[7] Kino T, Hurt D E, Ichijo T, Nader N, Chrousos G P. Noncoding RNA Gas5 is a growth arrest-and starvation-associated repressor of the glucocorticoid receptor[J]. Science Signaling, 2010, 3(107):ra8. doi:10.1126/scisignal.2000568.
[8] Wagner S D, Kugel J F, Goodrich J A. TFIIF facilitates dissociation of RNA polymerase Ⅱ from noncoding RNAs that lack a repression domain[J]. Mol Cell Biol, 2010, 30(1):91-97. doi:10.1128/MCB.01115-09.
[9] Tripathi V, Ellis J D, Shen Z, Song D Y, Pan Q, Watt A T, Freier S M, Bennett C F, Sharma A, Bubulya P A, Blencowe B J, Prasanth S G, Prasanth K V. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation[J]. Mol Cell, 2010, 39(6):925-938. doi:10.1016/j.molcel.2010.08.011.
[10] Wu X Y, Brewer G. The regulation of mRNA stability in mammalian cells:2.0[J]. Gene, 2012, 500(1):10-21. doi:10.1016/j.gene.2012.03.021.
[11] Liang R B, Han B, Li Q, Yuan Y W, Li J G, Sun D X. Using RNA sequencing to identify putative competing endogenous RNAs (ceRNAs) potentially regulating fat metabolism in bovine liver[J]. Sci Rep, 2017, 7(1):6396. doi:10.1038/s41598-017-06634-w.
[12] Billerey C, Boussaha M, Esquerré D, Rebours E, Djari A, Meersseman C, Klopp C, Gautheret D, Rocha D. Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing[J]. BMC Genomics, 2014, 15(1):499. doi:10.1186/1471-2164-15-499.
[13] Sun X M, Li M X, Sun Y J, Cai H F, Lan X Y, Huang Y Z, Bai Y Y, Qi X L, Cheng H. The developmental transcriptome sequencing of bovine skeletal muscle reveals a long noncoding RNA, lncMD, promote muscle differentiation by sponging miR-125b[J]. Biochimica et Biophysica Acta, 2016, 1863(11):2835-2845. doi:10.1016/j.bbamcr.2016.08.014.
[14] Li H, Yang J M, Jiang R, Wei X F, Song C C, Huang Y Z, Lan X Y, Lei C Z, Ma Y, Hu L Y, Chen H. Long non-coding RNA profiling reveals an abundant MDNCR that promotes differentiation of myoblasts by sponging miR-133a[J]. Mol Ther Nucleic Acids, 2018, 12:610-625. doi:10.1016/j.omtn.2018.07.003.
[15] 李明勋. 长链非编码RNA ADNCR通过竞争性结合miR-204抑制牛脂肪细胞分化[D]. 杨凌:西北农林科技大学, 2016.
Li M X. Long non-coding RNA ADNCR inhibits bovine adipocyte differentiation through competitive binding with miR-204[D]. Yangling:Northwest A & F University, 2016.
[16] 阿果约达, 熊显荣, 王艳, 杨显英, 韩杰, 王斌, 李键. 犏牛雄性不育相关lncRNA的鉴定与分析[J]. 畜牧兽医学报, 2019, 50(3):551-561.doi:10.11843/j.issn.0366-6964.2019.03.010.
A GUO Y D, Xiong X R, Wang Y, Yang X Y, Han J, Wang B, Li J. Identification and analysis of long non-coding RNA associated with cattle-yak male infertility[J]. Acta Veterinaria et Zootechnica Sinica, 2019, 50(3):551-561.
[17] 王会, 柴志欣, 朱江江, 钟金城, 张成福, 信金伟. 牦牛Linc24063 的克隆鉴定及其与miRNAs表达水平的相关性分析[J]. 中国农业科学, 2019, 52(14):2538-2547. doi:10.3864/j.issn.0578-1752.2019.14.012.
Wang H, Chai Z X, Zhu J J, Zhong J C, Zhang C F, Xin J W. Cloning and identification of long-chain non-coding RNA Linc24063 and its correlation with the expression level of miRNAs in yak[J]. Scientia Agricultura Sinica, 2019, 52(14):2538-2547.
[18] 张思欢. 牛肌肉与脂肪发育相关lncRNA lncFAM200B的鉴定、启动子活性及遗传变异研究[D]. 杨凌:西北农林科技大学, 2017.
Zhang S H. Identification of lncRNA lncFAM200B, promoter activity and genetic variation of bovine muscle and fat development[D]. Yangling:Northwest A & F University, 2017.
[19] Bionaz M, Loor J J. Identification of reference genes for quantitative Real-time PCR in the bovine mammary gland during the lactation cycle[J]. Physiol Genomics,2007,29(3):312-319. doi:10.1152/physiolgenomics.00223.2006.
[20] Sun M, Huang F, Yu D, Zhang Y, Xu H, Zhang L, Li L, Dong L, Guo L, Wang S. Autoregulatory loop between TGF-β1/miR-411-5p/SPRY4 and MAPK pathway in rhabdomyosarcoma modulates proliferation and differentiation[J]. Cell Death and Disease, 2015, 6(8):e1859. doi:10.1038/cddis.2015.225.
[21] Miao H W, Zeng H H, Gong H. microRNA-212 promotes lipid accumulation and attenuates cholesterol efflux in THP-1 human macrophages by targeting SIRT1[J]. Gene, 2018,643(15):55-60. doi:10.1016/j.gene.2017.11.058.
[22] Xu J, Li L, Yun H F, Han Y S. MiR-138 promotes smooth muscle cells proliferation and migration in db/db mice through down-regulation of SIRT1[J]. Biochemical and Biophysical Research Communications, 2015, 463(4):1159-1164. doi:10.1016/j.bbrc.2015.06.076.
[23] Peng Y, Chen F F, Ge J, Zhu J Y, Shi X E, Li X, Yu T Y, Chu G Y, Yang G S. miR-429 inhibits differentiation and promotes proliferation in porcine preadipocytes[J]. Int J Mol Sci, 2016, 17(12):2047. doi:10.3390/ijms17122047.
[24] Shen L Y, Gan M L, Li Q, Wang J Y, Li X W, Zhang S H, Zhu L. MicroRNA-200b regulates preadipocyte proliferation and differentiation by targeting KLF4[J]. Biomed Pharmacother, 2018, 103:1538-1544. doi:10.1016/j.biopha.2018.04.170.
[25] Poon E N, Hao B X, Guan D G, Jun L M, Lu J, Yang Y, Wu B B, Wu S C M, Webb S E, Liang Y, Miller A L, Yao X Q, Wang J W, Yan B, Boheler K R. Integrated transcriptomic and regulatory network analyses identify microRNA-200c as a novel repressor of human pluripotent stem cell-derived cardiomyocyte differentiation and maturation[J]. Cardiovasc Res, 2018, 114(6):894-906. doi:10.1093/cvr/cvy019.
[26] Tsiloulis T, Pike J, Powell D, Rossello F J, Canny B J, Meex R C, Watt M J. Impact of endurance exercise training on adipocyte microRNA expression in overweight men[J]. FASEB J, 2017, 31(1):161-171. doi:10.1096/fj.201600678R.
[27] Russell A P, Wallace M A, Kalanon M, Zacharewicz E, Della Gatta P A, Garnham A, Lamon S. Striated muscle activator of Rho signalling (STARS) is reduced in ageing human skeletal muscle and targeted by miR-628-5p[J]. Acta Physiol, 2017, 220(2):263-274. doi:10.1111/apha.12819.
[28] Liu T Y, Chen Y C, Jong Y J, Tsai H J, Lee C C, Chang Y S, Chang J G, Chang Y F. Muscle developmental defects in heterogeneous nuclear Ribonucleoprotein A1 knockout mice[J]. Open Biol, 2017, 7(1):160303. doi:10.1098/rsob.160303.
[29] Tyzack G E, Luisier R, Taha D M, Neeves J, Modic M, Mitchell J S, Meyer I, Greensmith L, Newcombe J, Ule J, Luscombe N M, Patani R. Widespread FUS mislocalization is a molecular hallmark of amyotrophic lateral sclerosis[J]. Brain, 2019, 142(9):2572-2580. doi:10.1093/brain/awz217.
[30] Shigunov P, Sotelo-Silveira J, Kuligovski C, de Aguiar A M, Rebelatto C K, Moutinho J A, Brofman P S, Krieger M A, Goldenberg S, Munroe D, Correa A, Dallagiovanna B. PUMILIO-2 is involved in the positive regulation of cellular proliferation in human adipose-derived stem cells[J]. Stem Cells Dev, 2012, 21(2):217-227. doi:10.1089/scd.2011.0143.
[31] Zhang B W, Cai H F, Wei X F, Sun J J, Lan X Y, Lei C Z, Lin F P, Qi X L, Plath M, Chen H. miR-30-5p regulates muscle differentiation and alternative splicing of muscle-related genes by targeting MBNL[J]. Int J Mol Sci, 2016, 17(2):182-197. doi:10.3390/ijms17020182.
[32] 侯丽. 青海牦牛肉与秦川牛肉品质比较研究[D]. 西宁:青海大学, 2012.
Hou L. Comparative study on quality of Qinghai beef and Qinchuan beef[D]. Xining:Qinghai University, 2012.
[33] 何俊峰, 余四九, 崔燕. 不同年龄高原牦牛肺脏的组织结构特征[J]. 畜牧兽医学报, 2009, 40(5):748-755. doi:10.3321/j.issn:0366-6964.2009.05.023.
He J F, Yu S J, Cui Y. Characteristics of lung structure in different age plateau Yak[J]. Acta Veterinaria et Zootechnica Sinica, 2009, 40(5):748-755.
[34] Glazov E A, McWilliam S, Barris W C, Dalrymple B P. Origin, evolution, and biological role of miRNA cluster in DLK-DIO3 genomic region in placental mammals[J]. Mol Biol Evol, 2008, 25(5):939-948. doi:10.1093/molbev/msn045.
[35] Harafuji N, Schneiderat P, Walter M C, Chen Y W. miR-411 is up-regulated in FSHD myoblasts and suppresses myogenic factors[J]. Orphanet Journal of Rare Diseases, 2013, 8(1):55. doi:10.1186/1750-1172-8-55.
[36] Guo Y J, Yu J J, Wang C X, Li K, Liu B, Du Y, Xiao F, Chen S H, Guo F F. miR-212-5p suppresses lipid accumulation by targeting FAS and SCD1[J]. J Mol Endocrinol, 2017, 59(3):205-217. doi:10.1530/JME-16-0179.
[37] Liu Y, Yang K Z, Sun X Z, Fang P, Shi H Y, Xu J, Xie M, Li M X. MiR-138 suppresses airway smooth muscle cell proliferation through the PI3K/AKT signaling pathway by targeting PDK1[J]. Experimental Lung Research, 2015, 41(7):363-369. doi:10.3109/01902148.2015.1041581.
[38] 白亮, 庞卫军, 杨公社. Sirt1:一种新的脂肪细胞和肌细胞调控因子[J]. 遗传, 2006, 28(11):1462-1466. doi:10.3321/j.issn:0253-9772.2006.11.022.
Bai L, Pang W J, Yang G S. Sirt1:a novel adipocyte and myocyte regulatory factor[J]. Hereditas, 2006, 28(11):1462-1466.
[39] 杜东升, 翟丽维, 徐丹丹, 王楚端. 猪EPOR 和MYPN 基因SNPs检测及其与肉质、胴体性状关联分析[J]. 中国畜牧兽医, 2009, 36(10):80-83.
Du D S, Zhai L W, Xu D D, Wang C D. SNPs detection of EPOR & MYPN gene and association with meat quality traits in porcine[J]. China Animal Husbandry & Veterinary Medicine, 2009, 36(10):80-83.
[40] Pei H, Yao Y, Yang Y, Liao K, Wu J R. Krüppel-like factor KLF9 regulates PPARγ transactivation at the middle stage of adipogenesis[J]. Cell Death & Differentiation, 2010, 18(2):315-327. doi:10.1038/cdd.2010.100.
[41] 陶璇, 张健, 魏学良. 牛SCD基因研究进展[J]. 中国草食动物, 2009, 29(4):62-64. doi:10.3969/j.issn.2095-3887.2009.04.026.
Tao X, Zhang J, Wei X L. Advances in bovine stearoyl-coenzyme a desaturase (SCD)gene[J]. China Herbivores, 2009, 29(4):62-64.
[42] 韩天苍, 柳海星, 耿春银, 戢爽. PTEN 基因干扰对牛脂肪细胞凋亡的影响[J]. 中国畜牧杂志, 2018, 54(9):109-113.doi:10.19556/j.0258-7033.2018-09-104.
Han T C, Liu H X, Geng C Y, Ji S. Effect of PTEN gene interference on apoptosis in adipocytes of cattle[J]. Chinese Journal of Animal Science, 2018, 54(9):109-113.

Please choose a citation manager

Content to export