鸡miR-10b-5p生物信息学及组织表达分析

doi:10.16431/j.cnki.1671-7236.2022.04.007

Abstract

Abstract: 【Objective】 The target gene prediction,bioinformatics analysis and tissue expression of miR-10b-5p in Suqin No.3 chickens at different growth stages were carried out to explore its role in chicken muscle growth and development.【Method】 The miR-10b-5p sequence of vertebrates were obtained through scientific research and miRBase database,the position of miR-10b-5p was determined using the Ensembl database,the phylogenetic tree was constructed based on the miRNA precursor sequence.The target genes of miR-10b-5p were predicted by using miRDB,microT and TargetScan websites,then GO function and KEGG pathway analysis were performed to reveal the function of miR-10b-5p gene.The expression changes of miR-10b-5p were detected by Real-time quantitative PCR in brain,cerebellum,pituitary gland,chest muscle,leg muscle,ovary,heart,liver,spleen,lung and kidney of chickens at different growth stages.【Result】 A total of 59 miR-10b-5p sequences from 59 species of animals were retrieved by miRBase.Each animal had only one miR-10b-5p form.Gene mapping analysis revealed that chicken miR-10b-5p was located in HOX gene family cluster on chromosome 2.Alignment analysis of the mature sequence of miR-10b-5p in common species showed that the mature sequence of miR-10b-5p had high homology and was relatively conserved among species.The phylogenetic tree analysis showed that miR-10b in primates,rodents,birds,and fishes in mammals were clustered first,and then clustered together into one group,which indicated that miR-10b was conservative in the process of evolution.Target genes prediction revealed that miR-10b-5p had 300 target genes.GO function analysis showed that target genes were mainly enriched mainly to chromatin assembly and post-transcriptional regulation of gene expression,histone methyltransferase complexes,transcription factor complexes and other functions.KEGG pathway analysis showed that target genes were mainly enriched in Wnt and p53 signaling pathways.Tissue expression analysis showed that miR-10b-5p was detective in all tissues tested, the expression of miR-10b-5p in brain, cerebellum, pituitary, chest and leg muscles at 3-day-old were significantly higher than those in heart, hypothalamus, kidney and lung (P<0.05). The expression of miR-10b-5p in pituitary, chest muscle, leg muscle and brain were significantly higher than that in other tissues at 90-day-old (P<0.05).Compared with 3-day-old chicks,the expression of miR-10b-5p in pituitary,chest and leg muscles of chickens at 90-day-old was significantly increased (P<0.05).【Conclusion】 Chicken miR-10b-5p was a miRNA that was widely expressed in tissues,and miR-10b was conserved in the evolutionary process,it might regulate muscle growth and cell proliferation and differentiation through Wnt and p53 signaling pathways.

Key words: chickens; miR-10b-5p; target gene; expression analysis; bioinformatics

CLC Number:

S831

HUANG Zhengyang, ZHAO Zhenhua, HUANG Huayun, LI Chunmiao, WANG Qianbao, MU Chunyu, LI Shoufeng. Bioinformatics and Gene Expression Analysis of miR-10b-5p in Different Tissues of Chickens[J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(4): 1262-1270.

References

[1] MACCHIAROLI N,CUCHER M,KAMENETZKY L,et al.Identification and expression profiling of microRNAs in Hymenolepis[J].International Journal for Parasitology,2019,49(3-4):211-223.
[2] VALENZUELA-MUOZ V,NOVOA B,FIGUERAS A,et al.Modulation of Atlantic salmon miRNome response to sea louse infestation[J].Developmental and Comparative Immunology,2017,76:380-391.
[3] HENSLEY A P,MCALINDEN A.The role of microRNAs in bone development[J].Bone,2021,143:115760.
[4] ZEALY R W,WRENN S P,DAVILA S,et al.microRNA-binding proteins:Specificity and function[J].Wiley Interdisciplinary Reviews:RNA,2017,8(5):e1414.
[5] 沈建.miR-10a在小鼠精子发生过程中的调控作用[D].杨凌:西北农林科技大学,2016. SHEN J.The regulation of microRNA-10a in spermatogenesis of mouse[D].Yangling:Northwest A&F University,2016.(in Chinese)
[6] 方芳.miR-10b和BDNF对山羊卵巢颗粒细胞活性的影响[D].杨凌:西北农林科技大学,2014. FANG F.Effect of miR-10b and BDNF on activity of ovarian granulosa cells in goats[D].Yangling:Northwest A&F University,2014.(in Chinese)
[7] 邱小宇.山羊排卵卵泡与从属卵泡中差异表达miRNAs的筛选及其功能研究[D].重庆:西南大学,2017. QIU X Y.Screening and function of differentially expressed miRNAs between ovulatory and subordinate follicles in goats (Capra hircus)[D].Chongqing:Southwest University,2017.(in Chinese)
[8] 魏金销,张月,方芳,等.miR-10b和BDNF对山羊卵巢颗粒细胞活性的影响[J].家畜生态学报,2018,39(12):44-50. WEI J X,ZHANG Y,FANG F,et al.Effect of miR-10b and BDNF on activity of ovarian granulosa cells in goats[J].Journal of Domestic Animal Ecology,2018,39(12):44-50.(in Chinese)
[9] 刘鸿艳,郑仰清,徐晶,等.猪E2F3基因3'UTR双荧光素酶报告基因质粒构建及其与miR-10a-5p的靶向验证[J].黑龙江畜牧兽医,2020,15:28-32. LIU H Y,ZHENG Y Q,XU J,et al.Construction of porcine E2F3 gene 3'UTR dual luciferase reporter plasmid and its targeting verification with miR-10a-5p[J].Heilongjiang Animal Science and Veterinary Medicine,2020,15:28-32.(in Chinese)
[10] LIU X,LIAO S,XU Z,et al.Identification and analysis of the porcine microRNA in porcine cytomegalovirus-infected macrophages using deep sequencing[J].PLoS One,2016,11(3):e0150971.
[11] 冉茂良.猪睾丸组织发育过程中差异表达基因和microRNA的鉴定及功能研究[D].长沙:湖南农业大学,2017. RAN M L.Identification and functional studies of differentially expressed genes and microRNAs during development of porcine testicular tissue[D].Changsha:Hunan Agricultural University,2017.(in Chinese)
[12] 张惠子,刘然,陈阳,等.miRNA-10基因家族序列分析及其在鹅卵巢组织表达分析[J].中国家禽,2016,38(6):6-9. ZHANG H Z,LIU R,CHEN Y,et al.Sequence analysis of miRNA-10 gene family and its expression in ovarian tissue of goose[J].China Poultry,2016,38(6):6-9.(in Chinese)
[13] KOZOMARA A,BIRGAOANU M,GRIFFITHS-JONES S.miRBase:From microRNA sequences to function[J].Nucleic Acids Research,2019,47(D1):D155-D162.
[14] TAMURA K,STECHER G,KUMAR S.MEGA11:Molecular evolutionary genetics analysis version 11[J].Molecular Biology and Evolution,2021,38(7):3022-3027.
[15] PARASKEVOPOULOU M D,GEORGIOS G,NIKOS K,et al.DIANA-microT web server v5.0:Service integration into miRNA functional analysis workflows[J].Nucleic Acids Research,2013,41(W1):W169-W173.
[16] CHEN Y H,WANG X W.MiRDB:An online database for prediction of functional microRNA targets[J].Nucleic Acids Research,2019,48(D1):D127-D131.
[17] AGARWAL V,BELL G W,NAM J W,et al.Predicting effective microRNA target sites in mammalian mRNAs[J].eLife,2015,4:e05005.
[18] JIAO X L,SHERMAN B T,HUANG D W.DAVID-WS:A stateful web service to facilitate gene/protein list analysis[J].Bioinformatics (Oxford,England),2012,28(13):1805-1806.
[19] 郭乐薇,赵静,刘红羽,等.miR-10b对牛卵巢颗粒细胞凋亡的影响[J].中国畜牧杂志,2020,56(7):115-119. GUO L W,ZHAO J,LIU H Y,et al.Effects of miR-10b on apoptosis of bovine ovarian granulosa cells[J].Chinese Journal of Animal Science,2020,56(7):115-119.(in Chinese)
[20] 刘丽莉.白藜芦醇对乌骨鸡热应激损伤的修复机制研究[D].长沙:湖南农业大学,2014. LIU L L.Research on the repair mechanisms of resveratrol to heat stress-induced damages in black-boned chicken[D].Changsha:Hunan Agricultural University,2014.(in Chinese)
[21] 王雪,王卫军,骆启豪,等.长牡蛎性腺中调控型非编码RNA的生物信息学[J].水产学报,2020,44(5):723-734. WANG X,WANG W J,LUO Q H,et al.Bioinformatics analysis of regulatory non-coding RNA in gonad of Crassostrea gigas[J].Journal of Fisheries of China,2020,44(5):723-734.(in Chinese)
[22] 吴志胜,陈慧芳,刘俊杰,等.长白猪精浆外泌体miRNAs的鉴定与功能分析[J].农业生物技术学报,2021,29(2):279-287. WU Z S,CHEN H F,LIU J J,et al.Identification and functional analysis of miRNAs in seminal plasma exosomes of Landrace Boar (Sus scrofa domestica)[J].Journal of Agricultural Biotechnology,2021,29(2):279-287.(in Chinese)
[23] WENG B,RAN M L,CAO R,et al.miR-10b promotes porcine immature Sertoli cell proliferation by targeting the DAZAP1 gene[J].Journal of Integrative Agriculture,2019,18(8):1924-1935.
[24] LI Q Q,DU X,PAN Z X,et al.The transcription factor SMAD4 and miR-10b contribute to E2 release and cell apoptosis in ovarian granulosa cells by targeting CYP19A1[J].Molecular and Cellular Endocrinology,2018,476:84-95.
[25] 张家庆,武松霞,任巧玲,等.猪miR-149靶基因预测及生物信息学分析[J].河南农业科学,2019,48(3):123-131. ZHANG J Q,WU S X,REN Q L,et al.Prediction and bioinformatics analysis of ssc-miR-149 target genes[J].Journal of Henan Agricultural Sciences,2019,48(3):123-131.(in Chinese)
[26] 张名媛,郭晓萍,孙晴超,等.广西巴马小型猪miR-148b慢病毒制备及靶基因通路预测分析[J].南方农业学报,2019,50(7):1596-1604. ZHANG M Y,GUO X P,SUN Q C,et al.Construction of miR-148b lentivirus vector and prediction of target gene pathways in Guangxi Bama mini-pig[J].Journal of Southern Agriculture,2019,50(7):1596-1604.(in Chinese)

Bioinformatics and Gene Expression Analysis of miR-10b-5p in Different Tissues of Chickens

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