牦牛不同年龄肌肉组织microRNA表达谱及生物信息学分析

doi:10.11843/j.issn.0366-6964.2019.05.007

畜牧兽医学报 ›› 2019, Vol. 50 ›› Issue (5): 957-971.doi: 10.11843/j.issn.0366-6964.2019.05.007

牦牛不同年龄肌肉组织microRNA表达谱及生物信息学分析

纪会¹, 王会¹, 柴志欣¹, 王吉坤¹, 王嘉博¹, 罗晓林², 姬秋梅³, 信金伟³, 钟金城^1*

1. 西南民族大学青藏高原动物遗传资源保护与利用教育部重点实验室, 成都 610041;
2. 四川省草原科学研究院, 成都 611731;
3. 西藏自治区农牧科学院省部共建青稞和牦牛种质资源与遗传改良国家重点实验室, 拉萨 850009

收稿日期:2018-11-05 出版日期:2019-05-23 发布日期:2019-05-23
通讯作者: 钟金城,主要从事动物遗传育种与繁殖研究,E-mail:zhongjincheng518@126.com
作者简介:纪会(1995-),女,哈尼族,云南景东人,硕士生,主要从事动物遗传学研究,E-mail:1328051168@qq.com
基金资助:
西南民族大学研究生创新型科研项目（CX2018SZ113）；国家肉牛牦牛产业技术体系项目（CARS-37）

Differential Expression Profile and Bioinformatics Analysis of miRNAs in Yak Muscle Tissue during Development

JI Hui¹, WANG Hui¹, CHAI Zhixin¹, WANG Jikun¹, WANG Jiabo¹, LUO Xiaolin², JI Qiumei³, XIN Jinwei³, ZHONG Jincheng^1*

1. Key Laboratory of the Qinghai-Tibet Plateau Animal Genetic Resources Protection and Utilization of the Ministry of Education, Southwest Minzu University, Chengdu 610041, China;
2. Sichuan Academy of Grassland Sciences, Chengdu 611731, China;
3. State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China

Received:2018-11-05 Online:2019-05-23 Published:2019-05-23

摘要/Abstract

摘要：

旨在挖掘牦牛不同年龄肌肉组织中miRNA表达谱，分析其生物学特征，以探索其在牦牛肌肉发育过程中的调节模式。本研究构建0.5、2.5、4.5和7.5岁肌肉组织的4个小RNA文库，利用Solexa技术进行测序，用生物信息学方法和RT-qPCR技术对测序结果进行分析和验证。结果，获得各miRNAs分别在4个年龄段肌肉组织中的表达量，在7.5岁肌肉组织中发现58个共同与0.5、2.5、4.5岁差异表达的miRNAs，其中53个miRNAs在7.5岁肌肉组织中显著下调，5个显著上调。运用R语言进行GO富集和KEGG信号通路分析，58个miRNAs可能通过PI3K-Akt、MAPK、Ras和肌动蛋白细胞骨架调节通路（regulation of actin cytoskeleton）参与调节牦牛肌肉细胞的增殖与分化，且PI3K-Akt、MAPK、Ras 3个信号通路共同靶向53个靶基因，说明3个信号通路相互关联。随机选择8个miRNAs进行RT-qPCR验证，结果表明其中7个miRNAs的表达趋势与测序结果一致。结果表明，牦牛肌肉发育可能受到多种miRNA的调控并涉及多个信号通路，有助于构建肌肉组织中miRNA的调控网络，为进一步研究miRNA调控哺乳动物肌肉发育奠定了理论基础。

Abstract:

The aim of this study was to explore the the miRNA expression profile in muscle tissues at different ages of yak and analyze their biological characteristics to explore their regulation patterns during yak muscle development. Four small RNA libraries of muscle tissues during 0.5-year-old, 2.5-year-old, 4.5-year-old and 7.5-year-old of yak were constructed and sequenced using Solexa technology. The sequencing results were verified and analyzed by RT-qPCR and bioinformatics methods. The expression profile of each miRNA in 4 age groups were obtained. Fifty eight miRNAs were differentially expressed in muscle tissues during the 7.5-year-old of yak compared with other 3 age groups, of which 53 miRNAs were significantly down-regulated and 5 were significantly up-regulated in 7.5-year-old muscle tissue. GO enrichment and KEGG analysis were performed using R language, 58 miRNAs might be involved in the regulation of proliferation and differentiation of yak muscle cells through PI3K-Akt,MAPK, Ras and the regulation of actin cytoskeleton signaling pathways. PI3K-Akt, MAPK and Ras signaling pathways jointly targeted 53 target genes, which indicated that the 3 signaling pathways were related to each other. Furthermore, the RT-qPCR results showed that the expression tendency of 7 of the 8 randomly selected miRNAs were consistent with the sequencing results. The results indicate that yak muscle development may be regulated by multiple miRNAs and involve in multiple signaling pathways, which may help to construct the regulatory network of miRNAs in muscle tissue, which lays a theoretical foundation for further study the miRNA regulating the mammalian muscle development.

中图分类号:

S823.85

纪会, 王会, 柴志欣, 王吉坤, 王嘉博, 罗晓林, 姬秋梅, 信金伟, 钟金城. 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 Hui, WANG Hui, CHAI Zhixin, WANG Jikun, WANG Jiabo, LUO Xiaolin, JI Qiumei, XIN Jinwei, ZHONG Jincheng. 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.

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参考文献

[1] XIE Z X,KASSCHAU K D,CARRINGTON J C.Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation[J].Curr Biol,2003,13(9):784-789.
[2] THERMANN R,HENTZE M W.Drosophila miR2 induces pseudo-polysomes and inhibits translation initiation[J].Nature,2012,447(7146):875-878.
[3] LEE R C,FEINBAUM R L,AMBROS V.The C.elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14[J].Cell,1993,75(5):843-854.
[4] 徐盛玉,王定越,吴德.microRNA及其对哺乳动物繁殖的影响[J].畜牧兽医学报,2011,42(6):747-753.
XU S Y,WANG D Y,WU D.Effects of microRNA on the mammalian reproduction[J].Acta Veterinaria et Zootechnica Sinica,2011,42(6):747-753.(in Chinese)
[5] 杨雪梅,顾以韧,梁艳,等.miR-1、miR-27a、miR-369和miR-378在7个地方猪种背最长肌中的表达与肉质性状的关系研究[J].中国畜牧杂志,2018,54(2):30-34.
YANG X M,GU Y R,LIANG Y,et al.Relationship between expression of miR-1,miR-27a,miR-369,miR-378 and meat quality traits in the longissimus dorsi muscle of 7 local pig breeds[J].Chinese Journal of Animal Science,2018,54(2):30-34.(in Chinese)
[6] MA T H,CHENG L,WANG B,et al.miR-378 induces apoptsis of granulosa cells during follicle development in cattle[J].J Anim Plant Sci,2017,27(5):1738-1742.
[7] 李新云,付亮亮,程会军,等.microRNA调控哺乳动物骨骼肌发育[J].遗传,2017,39(11):1046-1053.
LI X Y,FU L L,CHENG H J,et al.Advances on microRNA in regulating mammalian skeletal muscle development[J].Hereditas,2017,39(11):1046-1053.(in Chinese)
[8] 赵谦.miR-192在绵羊骨骼肌卫星细胞增殖和成肌分化中的功能研究[D].北京:中国农业科学院,2016.
ZHAO Q.The role of miR-192 in proliferation and myogenic differentiation of sheep skeletal muscle satellite cells[D].Beijing:Chinese Academy of Agricultural Sciences,2016.(in Chinese)
[9] 侯欣华.猪骨骼肌相关miRNA的鉴定及miR-378对肌肉发育调控的研究[D].南京:南京农业大学,2011.
HOU X H.Identification of porcine skeletal muscle related miRNA and regulation role of miR-378 in myogenesis[D].Nanjing:Nanjing Agricultural University,2011.(in Chinese)
[10] 孙加节.秦川牛肌肉与脂肪组织发育相关miRNA鉴定及miR-10020调控机制解析[D].杨凌:西北农林科技大学,2015.
SUN J J.Identification of microRNAs from Chinese Qinchuan bovine muscle and adipose tissues and functional analysis of miR-10020 during myogenesis[D].Yangling:Northwest A&F University,2015.(in Chinese)
[11] WANG Q,QI R L,WANG J,et al.Differential expression profile of miRNAs in porcine muscle and adipose tissue during development[J].Gene,2017,618:49-56.
[12] 褚敏.营养胁迫条件下牦牛皮下脂肪和背肌差异microRNAs的筛选与鉴定[D].兰州:中国农业科学院,2015.
CHU M.Identification and analysis of differential expressed microRNAs in subcutaneous and longissimus muscle of yak under nutrition pressure[D].Lanzhou:Chinese Academy of Agricultural Sciences,2015.(in Chinese)
[13] TONG H L,JIANG R Y,LIU T T,et al.bta-miR-378 promote the differentiation of bovine skeletal muscle-derived satellite cells[J].Gene,2018,668:246-251.
[14] 张阳阳.miR-378在牛前体脂肪细胞分化的作用与机制[D].长春:吉林大学,2014.
ZHANG Y Y.Effect and mechanism of bovine miR-378 in preadipocyte differentiation[D].Changchun:Jilin University,2014.(in Chinese)
[15] DEO A,CARLSSON J,LINDLÖF A.How to choose a normalization strategy for miRNA quantitative real-time (qPCR) arrays[J].J Bioinform Comput Biol,2011,9(6):795-812.
[16] 习欠云,周莲莲,李虹仪,等.不同品种猪肌肉组织miR-1和miR-133基因的表达分析[J].畜牧兽医学报,2012,43(6):843-848.
XI Q Y,ZHOU L L,LI H Y,et al.The expression analysis of miR-1 and miR-133 in Longissimus dorsi muscle from different pig breeds[J].Acta Veterinaria et Zootechnica Sinica,2012,43(6):843-848.(in Chinese)
[17] 徐瑛,文鹏程,梁琪,等.不同岁龄牦牛肉肉用品质的变化规律[J].食品工业科技,2014,35(20):121-124.
XU Y,WEN P C,LIANG Q,et al.Changing cule of meat quality of yak in different ages[J].Science and Technology of Food Industry,2014,35(20):121-124.(in Chinese)
[18] 熊显荣,兰道亮,李键,等.牦牛卵巢小RNA高通量测序及生物信息学分析[J].畜牧兽医学报,2016,47(1):55-63.
XIONG X R,LAN D L,LI J,et al.Solexa sequencing of small RNAs in yak (Bos grunniens) ovaries and bioinformatics analysis[J].Acta Veterinaria et Zootechnica Sinica,2016,47(1):55-63.(in Chinese)
[19] ZHOU Y,TANG X,SONG Q,et al.Identification and characterization of pig embryo microRNAs by Solexa sequencing[J].Reprod Domest Anim,2013,48(1):112-120.
[20] 凌英会,张晓东,王丽娟,等.山羊肌肉组织microRNA Solexa测序与生物信息学分析[J].畜牧兽医学报,2013,44(3):481-487.
LING Y H,ZHANG X D,WANG L J,et al.Solexa sequencing and bioinformatics analysis on microRNA from the goat muscle[J].Acta Veterinaria et Zootechnica Sinica,2013,44(3):481-487.(in Chinese)
[21] 张翔宇,邝良德,李丛艳,等.家兔肌肉组织miRNA Solexa测序与生物信息学分析[J].湖北农业科学,2018,57(16):97-101.
ZHANG X Y,KUANG L D,LI C Y,et al.Solexa sequencing and bioinformatics analysis on miRNA from rabbit muscle[J].Hubei Agricultural Sciences,2018,57(16):97-101.(in Chinese)
[22] HOU X H,YANG Y L,ZHU S Y,et al.Comparison of skeletal muscle miRNA and mRNA profiles among three pig breeds[J].Mol Genet Genomics,2016,291(2):559-573.
[23] 陈晨,柴进,蒋思文.Solexa测序鉴定大白猪和梅山猪背部脂肪组织中的microRNAs[C]//第十六次全国动物遗传育种学术讨论会暨纪念吴仲贤先生诞辰100周年大会论文集.扬州:中国畜牧兽医学会,2011.
CHEN C,CHAI J,JIANG S W.Identification of microRNAs in the adipose tissue of the Large White and Meishan pigs by Solexa sequencing[C]//The 16th National Symposium on Animal Genetics and Breeding and the 100th Anniversary of the Birth of Mr.Wu Zhongxian.Yangzhou:Chinese Association of Animal Science and Veterinary Medicine,2011.(in Chinese)
[24] 张方,胡子乔,景炅婕,等.绵羊不同部位脂肪组织microRNA高通量测序及生物信息学分析[J].畜牧兽医学报,2016,47(6):1093-1101.
ZHANG F,HU Z Q,JING J J,et al.High-throughput sequencing and bioinformatics analysis on microRNAs expressed in adipose tissues of sheep[J].Acta Veterinaria et Zootechnica Sinica,2016,47(6):1093-1101.(in Chinese)
[25] MI S J,CAI T,HU Y G,et al.Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide[J].Cell,2008,133(1):116-127.
[26] CHEN X.Molecular mechanism of muscle growth of broiler chicken:a role of miR-199-5p in regulating differentiation of skeletal myoblasts[D].Nanjing:Nanjing University,2015.
[27] YUAN R Q,ZHANG X M,FANG Y,et al.mir-127-3p inhibits the proliferation of myocytes by targeting KMT5a[J].Biochem Biophys Res Commun,2018,503(2):970-976.
[28] AKSAMITIENE E,KIYATKIN A,KHOLODENKO B N.Cross-talk between mitogenic Ras/MAPK and survival PI3K/Akt pathways:a fine balance[J].Biochem Soc Trans,2012,40(1):139-146.
[29] 袁向飞,陆敏.Ras/MAPK与PI3K/Akt信号转导通路及其相互作用[J].国际检验医学杂志,2006,27(3):261-263.
YUAN X F,LU M.Ras/MAPK and PI3K/Akt signaling pathway and their interaction[J].International Journal of Laboratory Medicine,2006,27(3):261-263.(in Chinese)
[30] HU X P,WANG Z W,WU H B,et al.Ras ssDNA aptamer inhibits vascular smooth muscle cell proliferation and migration through MAPK and PI3K pathways[J].Int J Mol Med,2015,35(5):1355-1361.
[31] 邢义珅,胡鑫,任玲,等.牛胎儿骨骼肌来源成肌细胞分化相关microRNA的筛查与鉴定[J].畜牧兽医学报,2018,49(6):1134-1144.
XING Y S,HU X,REN L,et al.Identification of micrornas involved in myogenic differentiation of bovine fetal skeletal muscle derived myoblasts[J].Acta Veterinaria et Zootechnica Sinica,2018,49(6):1134-1144.(in Chinese)
[32] KEREN A,TAMIR Y,BENGAL E.The p38 MAPK signaling pathway:a major regulator of skeletal muscle development[J].Mol Cell Endocrinol,2006,252(1-2):224-230.
[33] LAI K M V,GONZALEZ M,POUEYMIROU W T,et al.Conditional activation of akt in adult skeletal muscle induces rapid hypertrophy[J].Mol Cell Biol,2004,24(21):9295-9304.
[34] MA M L,WANG X M,CHEN X C,et al.microRNA-432 targeting E2F3 and P55PIK inhibits myogenesis through PI3K/AKT/mTOR signaling pathway[J].RNA Biol,2017,14(3):347-360.
[35] LIU Y,YANG K Z,SUN X Z,et al.miR-138 suppresses airway smooth muscle cell proliferation through the PI3K/AKT signaling pathway by targeting PDK1[J].Exp Lung Res,2015,41(7):363-369.
[36] 冯阳.MiR-133b,miR-214和miR-495通过MAPK信号通路调节成肌细胞增殖和分化的研究[D].武汉:华中农业大学,2011.
FENG Y.Regulation of myoblasts proliferation and differentiation by miR-133b,miR-214 and miR-495 through MAPK signaling[D].Wuhan:Huazhong Agricultural University,2011.(in Chinese)
[37] PALLADINO C,MATÀ R,NICOLOSI M L,et al.Abstract 4612:In breast cancer cells IGF-I induces upregulation of DDR1 by suppressing miR-199a-5p via the PI3K/Akt pathway[J].Cancer Res,2016,76(S14):4612.

牦牛不同年龄肌肉组织microRNA表达谱及生物信息学分析

Differential Expression Profile and Bioinformatics Analysis of miRNAs in Yak Muscle Tissue during Development

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