藏鸡不同发育阶段腿部肌肉组织转录组及microRNA联合分析

doi:10.11843/j.issn.0366-6964.2019.12.004

Abstract

Abstract: The objectives of this study were to investigate the regulation mechanism and particularity of muscle development in Tibetan chicken by RNA-sequencing and miRNA-sequencing. mRNA and small RNA in muscle tissues of Tibetan chicken on 120-and 150-day-old were sequenced. The differentially expressed genes (DEGs) and miRNAs were screened between two stages. The sequencing results were verified by qRT-PCR. A total of 1 691 DEGs were screened, of which 330 genes were up-regulated and 1 361 genes were down-regulated. Twenty two differentially expressed miRNAs were screened, of which 9 miRNAs were up-regulated and 13 miRNAs were down-regulated. qPCR verification results of 5 randomly selected genes and miRNAs showed that the expression trend was consistent with the sequencing results. GO enrichment analysis showed that the terms related to immunization accounted for a large proportion in the top 10 enrichment terms. The KEGG analysis showed that the immune-related pathways accounted for a large proportion in the 19 significant enriched pathways, and 83 miRNA target genes were in the significant enriched pathways. The integrated analysis of transcriptome and small RNA sequencing data indicated that 343 pairs of miRNA-mRNA were in the negatively correlated regulation pattern. This study provides a theoretical basis for further understanding the muscle development of Tibetan chicken from the multi-omics.

Key words: Tibetan chicken, muscle development, transcriptome, miRNA

CLC Number:

S831.2

YUAN Mao, JIANG Mingfeng, XU Ya'ou, LIN Yaqiu, JIANG Xiaosong, YANG Chaowu, YU Chunlin, LI Zhixiong. Analysis of Transcriptome and microRNA in Leg Muscle of Tibetan Chicken at Different Developmental Stages[J]. Acta Veterinaria et Zootechnica Sinica, 2019, 50(12): 2400-2412.

References 44

[1]	徐珑洋,梅寒,王志敏,等.藏鸡、泸宁鸡POU1F1基因外显子2多态性与生长性能的关联研究[J].黑龙江畜牧兽医,2018(16):67-71.XU L Y,MEI H,WANG Z M,et al.Polymorphism analysis of POU1F1 gene exon 2 and its correlation study on growth performance in Tibetan chicken and Luning chicken[J].Heilongjiang Animal Science and Veterinary Medicine, 2018(16):67-71.(in Chinese)
[2]	王英明,徐亚欧,王志敏,等.藏鸡KLF15基因克隆、组织表达谱及其表达与肌内脂肪含量相关性的研究[J].畜牧兽医学报,2019,50(2):261-270.WANG Y M,XU Y O,WANG Z M,et al.Studies on the cloning of KLF15 gene,tissue expression profile and the association between its expression and intramuscular fat content in Tibetan chicken[J].Acta Veterinaria et Zootechnica Sinica,2019, 50(2):261-270.(in Chinese)
[3]	张燕,吴锦波,何世明,等.阿坝州藏鸡生长曲线拟合与分析[J].中国家禽,2017,39(19):56-59.ZHANG Y,WU J B,HE S M,et al.Fitting and analysis of growth curve of Tibetan chicken in Aba prefecture[J].China Poultry, 2017,39(19):56-59.(in Chinese)
[4]	刘光伟,赵燕英,王海,等.泸宁鸡不同饲养期屠宰性能与肉品质特性测定与分析[J].黑龙江畜牧兽医,2015(5):87-90.LIU G W,ZHAO Y Y,WANG H,et al.Determination and analysis of slaughter performance and meat quality characteristics of Luning chicken in different rearing periods[J].Heilongjiang Animal Science and Veterinary Medicine,2015(5):87-90.(in Chinese)
[5]	KAMBADUR R,SHARMA M,SMITH T P L,et al.Mutations in myostatin (GDF8) in double-muscled belgian blue and piedmontese cattle[J].Genome Res,1997,7(9):910-915.
[6]	字向东,罗斌,夏威,等.基于RNA-Seq技术的牦牛体外受精胚胎发育转录组分析[J].中国农业科学, 2018, 51(8):1577-1589.ZI X D,LUO B,XIA W,et al.Transcriptomic analysis of IVF embryonic development in the Yak (Bos grunniens) via RNA-Seq[J]. Scientia Agricultura Sinica,2018,51(8):1577-1589.(in Chinese)
[7]	MOTAMENY S,WOLTERS S,NÜRNBERG P,et al.Next generation sequencing of miRNAs-strategies,resources and methods[J]. Genes,2010,1(1):70-84.
[8]	LEPPER C,PARTRIDGE T A,FAN C M.An absolute requirement for Pax7-positive satellite cells in acute injury-induced skeletal muscle regeneration[J].Development,2011,138(17):3639-3646.
[9]	CHEN J F,TAO Y Z,LI J,et al.microRNA-1 and microRNA-206 regulate skeletal muscle satellite cell proliferation and differentiation by repressing Pax7[J].J Cell Biol,2010,190(5):867-879.
[10]	吴宁昭.miRNA-1和miRNA-133在鸭骨骼肌发育中的表达及功能初步研究[D].扬州:扬州大学,2017.WU N Z.The expression of miRNA-1 and miRNA-133 and its function on duck skeletal cell proliferation and differentiation[D]. Yangzhou:Yangzhou University,2017.(in Chinese)
[11]	MIAO X Y,LUO Q M.Genome-wide transcriptome analysis between small-tail Han sheep and the Surabaya fur sheep using high-throughput RNA sequencing[J].Reproduction,2013,145(6):587-596.
[12]	纪会,王会,柴志欣,等.牦牛不同年龄肌肉组织microRNA表达谱及生物信息学分析[J].畜牧兽医学报, 2019, 50(5):957-971.JI H,WANG H,CHAI Z X,et al.Differential expression profile and bioinformatics analysis of miRNAs in Yak muscle tissue during development[J].Acta Veterinaria et Zootechnica Sinica,2019,50(5):957-971.(in Chinese)
[13]	成志敏,张宁芳,王媛媛,等.基于RNA-Seq技术筛选影响猪肌纤维性状的候选基因[J].畜牧兽医学报,2019,50(5):918-929.CHENG Z M,ZHANG N F,WANG Y Y,et al.Screening of candidate genes for muscle fiber characteristics in pig using RNA-Seq[J].Acta Veterinaria et Zootechnica Sinica,2019,50(5):918-929.(in Chinese)
[14]	张敏,王杰,孙艳发,等.肉鸡肌肉与脂肪组织基因组差异剪接基因分析[J].畜牧兽医学报,2018,49(10):2124-2132.ZHANG M,WANG J,SUN Y F,et al.Differential splicing gene analysis between muscle and fat tissues in broilers[J].Acta Veterinaria et Zootechnica Sinica,2018,49(10):2124-2132.(in Chinese)
[15]	RIFFO-CAMPOS Á L,RIQUELME I,BREBI-MIEVILLE P.Tools for sequence-based miRNA target prediction:what to choose?[J]. Int J Mol Sci,2016,17(12):1987.
[16]	WRIGHT W E,SASSOON D A,LIN V K.Myogenin,a factor regulating myogenesis,has a domain homologous to MyoD[J]. Cell,1989,56(4):607-617.
[17]	COMAI G,TAJBAKHSH S.Molecular and cellular regulation of skeletal myogenesis[J].Curr Top Dev Biol,2014,110:1-73.
[18]	VENUTI J M,MORRIS J H,VIVIAN J L,et al.Myogenin is required for late but not early aspects of myogenesis during mouse development[J].J Cell Biol,1995,128(4):563-576.
[19]	LIU C,GERSCH R P,HAWKE T J,et al.Silencing of Mustn1 inhibits myogenic fusion and differentiation[J].Am J Physiol Cell Physiol,2010,298(5):C1100-C1108.
[20]	XU T S,GU L H,SUN Y,et al.Characterization of MUSTN1 gene and its relationship with skeletal muscle development at postnatal stages in Pekin ducks[J].Genet Mol Res,2015,14(2):4448-4460.
[21]	李娟.鸡生长发育和肌纤维生长的影响因素与相关基因表达研究[D].成都:四川农业大学,2013.LI J.Study on the influence factors about growth and muscle fiber related gene expression of chickens[D].Chengdu:Sichuan Agricultural University,2013.(in Chinese)
[22]	OHTSUBO H,SATO Y,SUZUKI T,et al.APOBEC2 negatively regulates myoblast differentiation in muscle regeneration[J].Int J Biochem Cell Biol,2017,85:91-101.
[23]	SATO Y,OHTSUBO H,NIHEI N,et al.Apobec2 deficiency causes mitochondrial defects and mitophagy in skeletal muscle[J]. FASEB J,2018,32(3):1428-1439.
[24]	TAN X G,ROTLLANT J,LI H Q,et al.SmyD1,a histone methyltransferase,is required for myofibril organization and muscle contraction in zebrafish embryos[J].Proc Natl Acad Sci U S A,2006,103(8):2713-2718.
[25]	LI H Q,ZHONG Y W,WANG Z F,et al.Smyd1b is required for skeletal and cardiac muscle function in zebrafish[J].Mol Biol Cell,2013,24(22):3511-3521.
[26]	LI D L,NIU Z,YU W S,et al.SMYD1,the myogenic activator,is a direct target of serum response factor and myogenin[J].Nucleic Acids Res,2009,37(21):7059-7071.
[27]	NAKAJIMA T,FUKIAGE C,AZUMA M,et al.Different expression patterns for ubiquitous calpains and Capn3 splice variants in monkey ocular tissues[J].Biochim Biophys Acta,2001,1519(1-2):55-64.
[28]	朱文奇,徐文娟,束婧婷,等.鸭骨骼肌早期发育过程中钙蛋白酶3(CAPN3)基因的表达及其与肌纤维性状的关联[J].畜牧兽医学报,2014,45(3):385-390.ZHU W Q,XU W J,SHU J T,et al.Expression of CAPN3 gene in skeletal muscles and its association with myofiber traits during embryonic and early post-hatching development in ducks[J].Acta Veterinaria et Zootechnica Sinica,2014,45(3):385-390.(in Chinese)
[29]	陶璇,顾以韧,梁艳,等.藏猪和杜洛克猪CAPN3基因表达差异及其与肉质性状相关性分析[J].养猪,2016(4):76-78.TAO X,GU Y R,LIANG Y,et al.Expression differences of CAPN3 gene and its correlation analysis with meat quality traits in Tibet and Duroc pigs[J].Swine Production,2016(4):76-78.(in Chinese)
[30]	LI Z X,XU Y O,LIN Y Q.Transcriptome analyses reveal genes of alternative splicing associated with muscle development in chickens[J].Gene,2018,676:146-155.
[31]	DOU T F,ZHAO S M,RONG H,et al.Biological mechanisms discriminating growth rate and adult body weight phenotypes in two Chinese indigenous chicken breeds[J].BMC Genomics,2017,18(1):469.
[32]	ARNSTEN A F T.Stress signalling pathways that impair prefrontal cortex structure and function[J].Nat Rev Neurosci,2009, 10(6):410-422.
[33]	SAWCHENKO P E,LI H Y,ERICSSON A.Circuits and mechanisms governing hypothalamic responses to stress:a tale of two paradigms[J].Prog Brain Res,2000,122:61-78.
[34]	MADDEN K S,SANDERS V M,FELTEN D L.Catecholamine influences and sympathetic neural modulation of immune responsiveness[J]. Annu Rev Pharmacol Toxicol,1995,35:417-448.
[35]	孙茹.骨骼肌损伤与修复过程中炎症反应与肌卫星细胞再生关系的研究[D].长春:东北师范大学,2009.SUN R.Studies on the relationship between inflammatory response and satellite cell regeneration in skeletal muscle injury and repair process[D].Changchun:Northeast Normal University,2009.(in Chinese)
[36]	KRIPPENDORF B B,RILEY D A.Distinguishing unloading-versus reloading-induced changes in rat soleus muscle[J].Muscle Nerve,1993,16(1):99-108.
[37]	TIDBALL J G.Regulation of muscle growth and regeneration by the immune system[J].Nat Rev Immunol,2017,17(3):165-178.
[38]	NACHTIGALL P G,DIAS M C,CARVALHO R F,et al.microRNA-499 expression distinctively correlates to target genes sox6 and rod1 profiles to resolve the skeletal muscle phenotype in Nile tilapia[J].PLoS One,2015,10(3):e0119804.
[39]	WU J Y,YUE B L,LAN X Y,et al.miR-499 regulates myoblast proliferation and differentiation by targeting transforming growth factor β receptor 1[J].J Cell Physiol,2019,234(3):2523-2536.
[40]	WANG Z J,OUYANG H J,CHEN X L,et al.gga-miR-205a affecting myoblast proliferation and differentiation by targeting CDH11[J].Front Genet,2018,9:414.
[41]	DI BENEDETTO A,WATKINS M,GRIMSTON S,et al.N-cadherin and cadherin 11 modulate postnatal bone growth and osteoblast differentiation by distinct mechanisms[J].J Cell Sci,2010,123(15):2640-2648.
[42]	CHEN W,FANG G F,WANG S D,et al.Characterization and differential expression of microRNA in skeletal muscle of Laiwu and Yorkshire pig breeds[J].Genes Genomics,2017,39(2):173-182.
[43]	SIENGDEE P,TRAKOOLJUL N,MURANI E,et al.MicroRNAs regulate cellular ATP levels by targeting mitochondrial energy metabolism genes during C2C12 myoblast differentiation[J].PLoS One,2015,10(5):e0127850.
[44]	WANG Y H,LI M L,WANG Y H,et al.A Zfp609 circular RNA regulates myoblast differentiation by sponging miR-194-5p[J].Int J Biol Macromol,2019,121:1308-1313.

Analysis of Transcriptome and microRNA in Leg Muscle of Tibetan Chicken at Different Developmental Stages

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