湖羊卵巢不同发育阶段的miRNA鉴定与分析

doi:10.11843/j.issn.0366-6964.2019.07.008

Abstract

Abstract: The aim of this study was to analyze the expression level of miRNAs in Hu sheep ovaries at different developmental stages and to understand the expression of miRNAs and their regulatory mechanism. In this study, RNA-seq was used to identify miRNAs in ovarian tissues of 1 month and 8 months old Hu sheep. Bioinformatics methods were used to predict target genes of differentially expressed miRNAs. GO and KEGG functional annotations were performed on target genes to screen miRNAs and biological processes involved in ovarian development. The results showed that the numbers of known miRNAs expressed in the 6 samples were 2 186, 2 091, 2 217, 2 136, 2 176 and 2 088, respectively. The number of novel miRNAs was 613, 567, 668, 640, 662 and 450, respectively. 701 novel differentially expressed miRNAs and 38 known differentially expressed miRNAs were identified. GO and KEGG analysis of genes targeting to differentially expressed miRNAs revealed that they mainly were enriched in vascular endothelial growth factor pathway and ovarian steroidogenesis. The qRT-PCR verification result of 3 differential miRNAs was consistent with the sequencing results. Target genes of oar-let-7b, oar-miR-29a, oar-miR-134-3p, oar-miR-541-3p were enriched in the biological processes associated with ovarian development such as TGF-beta signaling pathway and ovarian follicular growth. The target genes of oar-miR-148a and oar-miR-136 regulate granulosa cell proliferation and steroidogenesis. It's inferred that they are involved in the regulation of ovarian development in sheep.

CLC Number:

S826.3

XIE Lingli, LI Ai, HUANG Wanlong, ZHANG Xiuxiu, MIAO Xiangyang. Identification and Analysis of miRNAs at Different Developmental Stages in Hu Sheep Ovaries[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(7): 1396-1404.

0
/ / Recommend

Add to citation manager EndNote|Reference Manager|ProCite|BibTeX|RefWorks

URL: https://www.xmsyxb.com/EN/10.11843/j.issn.0366-6964.2019.07.008

https://www.xmsyxb.com/EN/Y2019/V50/I7/1396

References

[1] 丁存振,肖海峰.我国羊肉供需现状及趋势分析[J].农业经济与管理,2016(3):86-96.
DING C Z,XIAO H F.Analysis on current situation and trend of mutton supply and demand in China[J].Agricultural Economics and Management,2016(3):86-96.(in Chinese)
[2] 王贝贝,肖海峰.中国羊肉供需状况及展望[J].农业展望,2012,8(10):19-22.
WANG B B,XIAO H F.Supply and demand of mutton in China and its prospect[J].Agricultural Outlook,2012,8(10):19-22.(in Chinese)
[3] 邓蓉,张存根,郭爱云.中国肉羊生产与贸易的现状及其发展对策[J].北京农学院学报,2006,21(3):69-73.
DENG R,ZHANG C G,GUO A Y.Study on the production and trade of meet sheep and goats in China[J].Journal of Beijing Agricultural College,2006,21(3):69-73.(in Chinese)
[4] ADUR M K,HALE B J,ROSS J W.Detection of miRNA in mammalian oocytes and embryos[M]//LEE K.Zygotic genome activation:Methods and protocols.New York,NY:Humana Press,2017:63-81.
[5] VOGLOVA K,BEZAKOVA J,HERICHOVA I.Progress in microRNA focused research in endocrinology[J].Endocr Regul,2016,50(2):83-105.
[6] LEE R C,FEINBAUM R L,AMBROS V.The C.elegans heterochronic gene lin-4encodes small RNAs with antisense complementarity to lin-14[J].Cell,1993,75(5):843-854.
[7] REINHART B J,SLACK F J,BASSON M,et al.The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans[J].Nature,2000,403(6772):901-906.
[8] MA L,TERUYA-FELDSTEIN J,WEINBERG R A.Tumour invasion and metastasis initiated by microRNA-10b in breast cancer[J].Nature,2007,449(7163):682-688.
[9] 程海霞,张静,贾增增,等.miRNA-10a在消化系统疾病分子机制中的研究进展[J].中外医疗,2017,36(26):193-195.
CHENG H X,ZHANG J,JIA Z Z,et al.Research progress of miRNA-10a in the molecular mechanism of digestive disease[J].China Foreign Medical Treatment,2017,36(26):193-195.(in Chinese)
[10] ZHOU X,HUANG Z B,XU L,et al.A panel of 13-miRNA signature as a potential biomarker for predicting survival in pancreatic cancer[J].Oncotarget,2016,7(43):69616-69624.
[11] GUO Y T,ZHANG X X,HUANG W L,et al.Identification and characterization of differentially expressed miRNAs in subcutaneous adipose between Wagyu and Holstein cattle[J].Sci Rep,2017,7:44026.
[12] ZHANG Y,ZHAO B,ROY S,et al.microRNA-309 targets the Homeobox gene SIX4 and controls ovarian development in the mosquito Aedes aegypti[J].Proc Natl Acad Sci U S A,2016,113(33):E4828-E4836.
[13] SMIRNOVA L,GRÄFE A,SEILER A,et al.Regulation of miRNA expression during neural cell specification[J].Eur J Neurosci, 2005,21(6):1469-1477.
[14] LANGMEAD B,SALZBERG S L.Fast gapped-read alignment with Bowtie 2[J].Nat Methods,2012,9(4):357-359.
[15] GRIFFITHS-JONES S,BATEMAN A,MARSHALL M,et al.Rfam:an RNA family database[J].Nucleic Acids Res,2003,31(1):439-441.
[16] GRIFFITHS-JONES S,GROCOCK R J,VON DONGEN S,et al.miRBase:microRNA sequences,targets and gene nomenclature[J].Nucleic Acids Res,2006,34(S1):D140-D144.
[17] GRIFFITHS-JONES S,SAINI H K,VAN DONGEN S.miRBase:tools for microRNA genomics[J].Nucleic Acids Res,2008,36(S1):D154-D158.
[18] FRIEDLÄNDER M R,MACKOWIAK S D,LI N,et al.miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades[J].Nucleic Acids Res,2012,40(1):37-52.
[19] WANG L K,FENG Z X,WANG X,et al.DEGseq:an R package for identifying differentially expressed genes from RNA-seq data[J].Bioinformatics,2010,26(1):136-138.
[20] ENRIGHT A J,JOHN B,GAUL U,et al.microRNA targets in Drosophila[J].Genome Biol,2004,5(1):R1.
[21] BINDEA G,MLECNIK B,HACKL H,et al.ClueGO:a cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks[J].Bioinformatics,2009,25(8):1091-1093.
[22] KANEHISA M,ARAKI M,GOTO S,et al.KEGG for linking genomes to life and the environment[J].Nucleic Acids Res,2007,36(D1):D480-D484.
[23] SMOOT M E,ONO K,RUSCHEINSKI J,et al.Cytoscape 2.8:new features for data integration and network visualization[J].Bioinformatics,2011,27(3):431-432.
[24] SHIN C,NAM J W,FARH K K H,et al.Expanding the microRNA targeting code:functional sites with centered pairing[J].Mol Cell,2010, 38(6):789-802.
[25] BRODERSEN P,VOINNET O.Revisiting the principles of microRNA target recognition and mode of action[J].Nat Rev Mol Cell Biol,2009, 10(2):141-148.
[26] STARK A,BRENNECKE J,BUSHATI N,et al.Animal microRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution[J].Cell,2005,123(6):1133-1146.
[27] MIAO X Y,LUO Q M,ZHAO H J,et al.Genome-wide analysis of miRNAs in the ovaries of Jining Grey and Laiwu Black goats to explore the regulation of fecundity[J].Sci Rep,2016,6:37983.
[28] MIAO X Y,LUO Q M,ZHAO H J,et al.An integrated analysis of miRNAs and methylated genes encoding mRNAs and lncRNAs in sheep breeds with different fecundity[J].Front Physiol,2017,8:1049.
[29] LI Y,KOWDLEY K V.microRNAs in common human diseases[J].Genomics Proteomics Bioinformatics,2012,10(5):246-253.
[30] DI LEVA G,GAROFALO M,CROCE C M.microRNAs in cancer[J].Annu Rev Pathol,2014,9:287-314.
[31] SHI B X,MA C,LIU G L,et al.miR-106a directly targets LIMK1 to inhibit proliferation and EMT of oral carcinoma cells[J].Cell Mol Biol Lett,2019,24:1.
[32] TAO H,XIONG Q,JI Z Y,et al.NFAT5 is regulated by p53/miR-27a signal axis and promotes mouse ovarian granulosa cells proliferation[J].Int J Biol Sci,2019,15(2):287-297.
[33] KIM Y Y,KANG B C,YUN J W,et al.Expression of transcripts in marmoset oocytes retrieved during follicle isolation without gonadotropin induction[J].Int J Mol Sci,2019,20(5):1133.
[34] MCBRIDE D,CARRÉ W,SONTAKKE S D,et al.Identification of miRNAs associated with the follicular-luteal transition in the ruminant ovary[J].Reproduction,2012,144(2):221-233.
[35] OTSUKA M,ZHENG M,HAYASHI M,et al.Impaired microRNA processing causes corpus luteum insufficiency and infertility in mice[J].J Clin Invest,2008,118(5):1944-1954.
[36] HOSSAIN M M,GHANEM N,HOELKER M,et al.Identification and characterization of miRNAs expressed in the bovine ovary[J].BMC Genomics,2009,10:443.
[37] CHANG C,LIU T,HUANG Y Y,et al.microRNA-134-3p is a novel potential inhibitor of human ovarian cancer stem cells by targeting RAB27A[J].Gene,2017,605:99-107.
[38] MADAN P,BRIDGES P J,KOMAR C M,et al.Expression of messenger RNA for ADAMTS subtypes changes in the periovulatory follicle after the gonadotropin surge and during luteal development and regression in cattle[J].Biol Reprod,2003,69(5):1506-1514.
[39] SPICER L J,SUDO S,AAD P Y,et al.The hedgehog-patched signaling pathway and function in the mammalian ovary:a novel role for hedgehog proteins in stimulating proliferation and steroidogenesis of theca cells[J].Reproduction,2009,138(2):329-339.
[40] LIU C,PENG J,MATZUK M M,et al.Lineage specification of ovarian theca cells requires multicellular interactions via oocyte and granulosa cells[J].Nat Commun,2015,6:6934.
[41] KWOK S C,CHAKRABORTY D,SOARES M J,et al.Relative expression of proprotein convertases in rat ovaries during pregnancy[J].J Ovarian Res,2013,6:91.
[42] SHIMIZU T,JAYAWARDANA B C,NISHIMOTO H,et al.Hormonal regulation and differential expression of neuropilin (NRP)-1and NRP-2 genes in bovine granulosa cells[J].Reproduction,2006,131(3):555-559.
[43] NIVET A L,VIGNEAULT C,BLONDIN P,et al.Changes in granulosa cells' gene expression associated with increased oocyte competence in bovine[J].Reproduction,2013,145(6):555-565.
[44] TUJ J,YANG Y Z,HOI-HUNG A C,et al.Conserved miR-10 family represses proliferation and induces apoptosis in ovarian granulosa cells[J].Sci Rep,2017,7:41304.
[45] FERANIL J B,ISOBE N,NAKAO T.Immunolocalization of von willebrand factor and vascular endothelial growth factor during follicular atresia in the swamp buffalo ovary[J].J Reprod Dev,2005,51(4):419-426.

Identification and Analysis of miRNAs at Different Developmental Stages in Hu Sheep Ovaries

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	DUAN Xiangru, KANG Jia, YANG Ruochen, SHAN Xinyu, LI Taichun, ZHAO Wen, ZHANG Yingjie, LIU Yueqin. Effect of L-cysteine on Proliferation, Apoptosis and the Secretion of Steroid Hormone in Ovine Ovarian Granulosa Cells [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(1): 179-191.
[2]	SONG Pengyan, WANG Siwei, YUE Qiaoxian, ZHANG Yinliang, CHEN Xiaoyong, ZHOU Rongyan. Identification of oar-miR-200b Promoter and Effects on Mitochondrial Function in Follicular Granulosa Cells [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(12): 5066-5076.
[3]	HE Mingyang, MA Yujing, WANG Yong, YANG Ruochen, LIU Yueqin, ZHANG Yingjie, DUAN Chunhui. Effects of Melatonin on Proliferation, Apoptosis of Ovarian Granulosa Cells, and Its Secretion of Steroid Hormones of Sheep [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(8): 3313-3324.
[4]	SONG Meijun, HAO Kexing, HAI Siyu, CHEN Yan, WANG Jing, HU Guangdong. Effects of SRIF-14 on Proliferation and Apoptosis of Endometrial Epithelial Cells in Sheep [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(8): 3325-3334.
[5]	LI Yuexin, LIU Aiju, MA Xiaofei, ZHENG Zhong, HU Boxin, ZHI Yunxia, TIAN Shujun. Effect of TGFβR1 on the Function of Sheep Granulosa Cells Mediated by TGF-β/Smad Signaling Pathway [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(8): 3335-3347.
[6]	HAN Xiuyuan, ZHAO Liang, WANG Chuang, QI Meiyu, YAO Yuchang. Nicotinic Acid Enhances Low Temperature Preservation of Sheep Sperm by Reducing Oxidative Stress Levels [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(5): 1979-1989.
[7]	YANG Chulei, ZHANG Yiyuan, TANG Hong, GUO Yanhua, REN Xiumeiao, WANG Limin, ZHOU Ping. Research Progress of FecB Gene on Reproductive Performance of Sheep [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(4): 1370-1380.
[8]	LI Yu, DUAN Chunhui, SONG Zhipan, YUE Sicong, WANG Yuan, ZHANG Yingjie, LIU Yueqin. Effects of PGF2α on Luteal Tissue Morphology, Expression of PGF2α Receptors and Necroptosis-associated Genes During Luteal Phase in Hu Sheep [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(4): 1500-1510.
[9]	WANG Yahan, ZHENG Yujing, ZHONG Pei, LI Xiaodan, WANG Feng. Expression Patterns and Functional Analysis of YAP1 in Endometrium of Hu Sheep with Different Fertility during Estrus [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(1): 189-200.
[10]	WANG Mengyao, ZHAI Zhenhan, ZHAO Lu, WANG Saiqiao, WANG Yuqin. Identification and Functional Analysis of lncRNA in Ovaries of Sheep at Different Stages of Estrus Cycle [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(12): 4221-4231.
[11]	LIU Xinjie, WU Xiaoxue, LIU Suping, YUAN Liming, CHEN Ning, SAIWU Jiafu. Preparation of Polyclonal Antibody against PLC-γ1 and Preliminary Study on Its Effect on Early Embryo Development in Sheep [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(11): 3842-3855.
[12]	LIU Xinjie,WU Xiaoxue,LIU Suping,YUAN Liming,CHEN Ning,SAIWU Jiafu. Effects of Sheep Phospholipase C-γ1 on in vitro Maturation of Sheep Oocytes [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(10): 3459-3469.
[13]	WU Xiaoxue, YUAN Liming, LIU Xinjie, LIU Suping, CHEN Ning, SAIWU Jiafu. Effect of PLCγ1 Gene on the Development of Sheep Early Embryo in vitro [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(8): 2578-2585.
[14]	YAN Shuo, ZHAO Shanshan, ZHU Zhendong, PAN Qingjie, DONG Huansheng. Study on Nuclear-plasma Transporter KPNA4 of Sheep Sperm Cell [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(7): 2194-2201.
[15]	LI Yu, DUAN Chunhui, SONG Zhipan, YUE Sicong, WANG Yuan, ZHANG Yingjie, LIU Yueqin. Effects of PGF2α on Reproductive Hormones and Related Cytokines during Luteal Phase in Ewes [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(6): 1807-1818.