德州驴与泌阳驴睾丸组织mRNA与microRNA表达鉴定与分析

doi:10.16431/j.cnki.1671-7236.2019.08.022

摘要/Abstract

摘要：

试验旨在探究驴睾丸组织中mRNA和microRNA的表达模式，为中国地方驴的转录组研究提供遗传数据。利用RNA-Seq和生物信息学方法分析了中国地方驴睾丸组织表达基因和microRNA，并分析了泌阳驴和德州驴品种间差异表达基因及microRNA。结果表明，mRNA平均clean reads为57837506条，Small RNA平均clean reads为9952015条，分别占原始数据的96.34%和88.86%。在驴睾丸组织中共发现24751个表达基因及1074个表达microRNAs，其中，睾丸组织表达量较高的基因为LOC106836782、XLOC_066401、HSP90AA1、TNP1和COF2，表达量最高的microRNAs为eca-miR-143、eca-miR-21、eca-miR-99a、eca-miR-148a和eca-miR-26a。对泌阳驴与德州驴睾丸组织进行差异表达分析共发现102个差异表达基因及2个差异表达microRNAs，但未富集到功能条目，说明泌阳驴和德州驴品种间差异不明显。本研究提供了驴睾丸组织mRNA及microRNA表达模式和转录组学数据，并鉴定了泌阳驴与德州驴睾丸组织的差异表达mRNA和microRNA，对驴的遗传资源研究具有一定的科学意义。

关键词: 驴; 睾丸; 转录组; 差异表达基因; microRNA

Abstract:

This study was aimed to explore the expression patterns of mRNA and microRNA in donkey testis, and provide genetic data for transcriptome studies of Chinese local donkeys.The mRNA and microRNA expressed in testis of Chinese domestic donkeys were analyzed by RNA-Seq and bioinformatics methods, and the differentially expressed genes and microRNA between Biyang and Dezhou donkeys were identified.The results showed that 57 837 506 (accounted for 96.34%) and 9 952 015 (accounted for 88.86%) clean reads of mRNA and Small RNA were obtained.A total of 24 751 genes and 1 074 microRNAs expressed in testis were identified.The top five expressed genes were LOC106836782, XLOC_066401, HSP90AA1, TNP1 and COF2, the top five expressed microRNAs were eca-miR-143, eca-miR-21, eca-miR-99a, eca-miR-148a and eca-miR-26a.The results revealed 102 differentially expressed genes and 2 microRNAs between Biyang and Dezhou donkeys.However, no significant function term was annotated, which suggested that there was no obvious difference of genetic expression pattern between Biyang and Dezhou donkeys.This study provided gene expression pattern and transcriptome data for donkey testis tissue and identified differentially expressed mRNA and microRNA between Biyang and Dezhou donkeys, which had scientific significance for studying genetic sources of donkeys in the future.

Key words: donkey; testis; transcriptome; differentially expressed genes; microRNA

中图分类号:

S822

韩浩园, 李婉涛, 雷初朝. 德州驴与泌阳驴睾丸组织mRNA与microRNA表达鉴定与分析[J]. 《中国畜牧兽医》, 2019, 46(8): 2371-2380.

HAN Haoyuan, LI Wantao, LEI Chuzhao. Identification and Analysis of mRNA and microRNA Expression of Testis Tissue in Dezhou and Biyang Donkeys[J]. , 2019, 46(8): 2371-2380.

参考文献 40

[1]	DE KRETSER D M,LOVELAND K L,MEINHARDT A,et al. Spermatogenesis[J]. Human Reproduction,1998,13(Suppl 1):1-8.
[2]	KLEENE K C.A possible meiotic function of the peculiar patterns of gene expression in mammalian spermatogenic cells[J]. Mechanisms of Development,2001,106(1-2):3-23.
[3]	SONG H,ZHU L,LI Y,et al.Exploiting RNA-sequencing data from the porcine testes to identify the key genes involved in spermatogenesis in Large White pigs[J]. Gene,2015,573(2):303-309.
[4]	YU Z,GUO R,GE Y,et al.Gene expression profiles in different stages of mouse spermatogenic cells during spermatogenesis[J]. Biology of Reproduction,2003,69(1):37-47.
[5]	MOROZOVA O,MARRA M A.Applications of next-generation sequencing technologies in functional genomics[J]. Genomics,2013,92(5):255-264.
[6]	ROBINSON M D,OSHLACK A.A scaling normalization method for differential expression analysis of RNA-seq data[J]. Genome Biology,2010,11(3):R25.
[7]	GAN X,STEGLE O,BEHR J,et al.Multiple reference genomes and transcriptomes for Arabidopsis thaliana[J]. Nature,2011,477(7365):419-423.
[8]	LIU Z,LIU W,MA Y,et al.Transcriptome comparison between the pubertal and adult testis in goat[A].World Congress on Genetics Applied to Livestock Production[C].2014.
[9]	BAI M,SUN L,ZHAO J,et al.Histological analysis and identification of spermatogenesis-related genes in 2-,6-,and 12-month-old sheep testes[J]. The Science of Nature,2017,104(9-10):84.
[10]	PAPAIOANNOU M,SERGE N.microRNAs in the testis:Building up male fertility[J]. Journal of Andrology,2010,31(1):26-33.
[11]	KRAWETZ S A,KRUGER A,LALANCETTE C,et al.A survey of small RNAs in human sperm[J]. Human Reproduction,2011,26(12):3401-3412.
[12]	KAWANO M,KAWAJI H,GRANDJEAN V,et al.Novel small noncoding RNAs in mouse spermatozoa,zygotes and early embryos[J]. PLoS One,2012,7(9):e44542.
[13]	LUO Z Y,DAI X L,RAN X Q,et al.Identification and profile of microRNAs in Xiang pig testes in four different ages detected by Solexa sequencing[J]. Theriogenology,2017,6(23):1-11.
[14]	ROTA A,PUDDU B,SABATINI C,et al.Reproductive parameters of donkey jacks undergoing puberty[J]. Animal Reproduction Science,2018,192:119-125.
[15]	STEGER K,KLONISCH T,GAVENIS K,et al.Round spermatids show normal testis-specific H1t but reduced cAMP-responsive element modulator and transition protein 1 expression in men with round-spermatid maturation arrest[J]. Journal of Andrology,1999,20(6):747-754.
[16]	HEIDARI M M,KHATAMI M,TALEBI A R,et al.Mutation analysis of TNP1 gene in infertile men with varicocele[J]. International Journal of Reproductive Biomedicine,2014,12(4):257-262.
[17]	MIYAGAWA Y,NISHIMURA H,TSUJIMURA A,et al.Single-nucleotide polymorphisms and mutation analyses of the TNP1 and TNP2 genes of fertile and infertile human male populations[J]. Journal of Andrology,2005,26(6):779-786.
[18]	PANIGRAHI S K,YADAV B R.Polymorphism in TNP-1 gene of Murrah buffalo bulls[J]. African Journal of Biotechnology,2010,9(43):7224-7229.
[19]	ULLRICH S J,MOORE S K,APPELLA E.Transcriptional and translational analysis of the murine 84-and 86-kDa heat shock proteins[J]. The Journal of Biological Chemistry,1989,264(12):6810-6816.
[20]	TIAN W L,HE F,FU X,et al.High expression of heat shock protein 90 alpha and its significance in human acute leukemia cells[J]. Gene,2014,542(2):122-128.
[21]	HACKER S,LAMBERS C,HOETZENCKER K,et al.Elevated Hsp27,Hsp70 and Hsp90 alpha in chronic obstructive pulmonary disease:Markers for immune activation and tissue destruction[J]. Clinical Laboratory,2009,55(1-2):31-40.
[22]	LEE Y,JUNG H,YOON M.Undifferentiated embryonic cell transcription factor 1(UTF1) and deleted in azoospermia-like (DAZL) expression in the testes of donkeys[J]. Reproduction in Domestic Animals,2017,52(2):264-269.
[23]	STATON P C,HATCHER J P,WALKER D J,et al.The putative cannabinoid receptor GPR55 plays a role in mechanical hyperalgesia associated with inflammatory and neuropathic pain[J]. Pain,2008,139(1):225-236.
[24]	KULIKOV A V,KOROSTINA V S,KULIKOVA E A,et al.Knockout Zbtb33,gene results in an increased locomotion,exploration and pre-pulse inhibition in mice[J]. Behavioural Brain Research,2016,297:76-83.
[25]	POZNER A,TEROOATEA T W,BUCKKOEHNTOP B A.Cell specific Kaiso (ZBTB33) regulation of cell cycle through cyclin D1 and cyclin E1[J]. Journal of Biological Chemistry,2017,291(47):24538-24550.
[26]	QIN Z,REN F,XU X,et al.ZNF536,a novel zinc finger protein specifically expressed in the brain,negatively regulates neuron differentiation by repressing retinoic acid-induced gene transcription[J]. Molecular & Cellular Biology,2009,29(13):3633-3643.
[27]	DOBOLYI A,BAGO G,GOL A,et al.Localization of SUCLA2 and SUCLG2 subunits of succinyl CoA ligase within the cerebral cortex suggests the absence of matrix substrate-level phosphorylation in glial cells of the human brain[J]. Journal of Bioenergetics and Biomembranes,2015,47(1-2):33-41.
[28]	RAMIREZ A,WM V D F,HEROLD C,et al.SUCLG2 identified as both a determinator of CSF AÎ21-42 levels and an attenuator of cognitive decline in Alzheimer's disease[J]. Human Molecular Genetics,2014,23(24):6644-6658.
[29]	JULIO C,CRISTINA M,SESE BORJA,et al.SETD7 regulates the differentiation of human embryonic stem cells[J]. PLoS One,2016,11(2):e0149502.
[30]	LAI C Q,PARNELL L D,TROEN A M,et al.MAT1A variants are associated with hypertension,stroke,and markers of DNA damage and are modulated by plasma vitamin B-6 and folate[J]. American Journal of Clinical Nutrition,2010,91(5):1377-1386.
[31]	PARK G H,KIM K Y,CHEONG J Y,et al.Association of GNLY genetic polymorphisms with chronic liver disease in a Korean population[J]. DNA & Cell Biology,2012,31(9):1492-1498.
[32]	XIN M,SMALL E M,SUTHERLAND L B,et al.microRNAs miR-143 and miR-145 modulate cytoskeletal dynamics and responsiveness of smooth muscle cells to injury[J]. Genes & Development,2009,23(18):2166-2178.
[33]	SHEEDY F J,PALSSONMCDERMOTT E,HENNESSY E J,et al.Negative regulation of TLR4 via targeting of the proinflammatory tumor suppressor PDCD4 by the microRNA miR-21[J]. Nature Immunology,2010,11(2):141-147.
[34]	WANG L,CHANG L,LI Z,et al.miR-99a and -99b inhibit cervical cancer cell proliferation and invasion by targeting mTOR signaling pathway[J]. Medical Oncology,2014,31(5):934.
[35]	PANGANIBAN R P L,PINKERTON M H,MARU S Y,et al.Differential microRNA expression in asthma and the role of miR-1248 in regulation of IL-5[J]. American Journal of Clinical & Experimental Immunology,2011,1(2):154.
[36]	MASSARI P U,HSU C H,BARNES R V,et al. Familial hyperuricemia and renal disease[J]. Archives of Internal Medicine,1980,140(5):680-684.
[37]	BACHMANN S,MUFG K,BATES J,et al.Renal effects of Tamm-Horsfall protein (uromodulin) defciency in mice[J]. American Journal of Physiology,2005,288(3):F559-F567.
[38]	HART T C,GORRY M C,HART P S,et al.Mutations of the UMOD gene are responsible for medullary cystic kidney disease 2 and familial juvenile hyperuricaemic nephropathy[J]. Journal of Medical Genetics,2002,39(12):882-892.
[39]	TURNER J J,STACEY J M,HARDING B,et al.UROMODULIN mutations cause familial juvenile hyperuricemic nephropathy[J]. The Journal of Clinical Endocrinology and Metabolism,2003,88(3):1398-1401.
[40]	GRAHAM L A,PADMANABHAN S,FRASER N J,et al.Validation of uromodulin as a candidate gene for human essential hypertension[J]. Hypertension,2014,63(3):551-558.