留言板

尊敬的读者、作者、审稿人, 关于本刊的投稿、审稿、编辑和出版的任何问题, 您可以本页添加留言。我们将尽快给您答复。谢谢您的支持!

姓名
邮箱
手机号码
标题
留言内容
验证码

低氧胁迫下斑马鱼鳃microRNAs差异分析

林枫 贾若南 王法祥 许强华

林枫, 贾若南, 王法祥, 许强华. 低氧胁迫下斑马鱼鳃microRNAs差异分析[J]. 南方水产科学. doi: 10.12131/20210124
引用本文: 林枫, 贾若南, 王法祥, 许强华. 低氧胁迫下斑马鱼鳃microRNAs差异分析[J]. 南方水产科学. doi: 10.12131/20210124
Feng LIN, Ruonan JIA, Faxiang WANG, Qianghua XU. Differential analysis of microRNAs in zebrafish gills under hypoxic stress[J]. South China Fisheries Science. doi: 10.12131/20210124
Citation: Feng LIN, Ruonan JIA, Faxiang WANG, Qianghua XU. Differential analysis of microRNAs in zebrafish gills under hypoxic stress[J]. South China Fisheries Science. doi: 10.12131/20210124

低氧胁迫下斑马鱼鳃microRNAs差异分析

doi: 10.12131/20210124
基金项目: 国家重点研发计划项目 (2018YFD0900601);国家自然科学基金面上项目 (31772826);上海市教委重点科技创新项目 (2017-01-07-00-10-E00060)
详细信息
    作者简介:

    林枫:林 枫 (1995—),男,硕士研究生,研究方向为鱼类分子生物学. E-mail: 1156630936@qq.com

    通讯作者:

    许强华 (1974—),女,博士,教授,从事鱼类生物学、功能基因组学研究。E-mail: qhxu@shou.edu.cn

  • 中图分类号: S 917.4

Differential analysis of microRNAs in zebrafish gills under hypoxic stress

  • 摘要: 为研究microRNAs (miRNAs) 应对低氧胁迫的生物学功能,对低氧胁迫和常氧条件下斑马鱼 (Danio rerio) 鳃组织进行高通量miRNAs测序,分析了低氧胁迫与常氧条件下斑马鱼鳃中miRNAs的表达差异。结果表明,低氧胁迫和常氧条件下斑马鱼鳃中,共有15个miRNAs呈显著差异表达,其中13个miRNAs在低氧胁迫斑马鱼鳃中的表达量显著上调,2个miRNAs表达量显著下调。对miRNAs测序和斑马鱼鳃转录组进行关联分析,针对前期筛选获得的低氧胁迫与常氧条件下显著差异表达的28个热休克蛋白基因,进行靶基因预测,结果显示,低氧胁迫下显著低表达的miR-455-3p同时靶向提高热休克蛋白基因 (hspa14和dnajb6b) 的表达,以增强对低氧的适应能力。另外,低氧胁迫下显著高表达的miR-194a和miR-155可以分别靶向5个热休克蛋白基因 (hspa12a, dnajc5aa, hspb7, hsp70.3, dnajb2) 和4个热休克蛋白基因 (hspa12a, hspg2, hspa13, dnajb2) 来调控斑马鱼对低氧环境的适应。
  • 图  1  常氧与低氧中鳃组织miRNA占小RNA的比例

    Figure  1.  Proportion of miRNA in whole small RNAs sequence in normal and hypoxic gill tissues

    图  2  常氧和低氧鳃组织差异miRNAs火山图

    横坐标代表miRNAs不同样品中表达倍数变化,纵坐标代表miRNAs表达量变化的统计学显著程度,图中的散点代表各个miRNAs,灰色圆点表示无显著性差异的miRNAs,蓝色圆点表示显著上调的差异miRNAs,红色圆点表示显著下调的差异miRNAs

    Figure  2.  Differential miRNAs volcano map of normoxic and hypoxic gill tissues

    The horizontal axis represents the variation of miRNAs expression multiple in different samples; the vertical axis represents the statistically significant degree of miRNAs expression change; the scattered dots represent each miRNAs; the gray dots represent the miRNAs without significant difference; the blue dots represent the significantly upregulated differential miRNAs; and the red dots represent the significantly down-regulated differential miRNAs.

    图  3  常氧和低氧鳃组织差异miRNAs聚类图

    图中的颜色代表了不同基因在低氧胁迫后的表达量,颜色由蓝到黄到红表示表达量依次增加

    Figure  3.  Clustering map of miRNAs differences between normal and hypoxic gill tissues

    The colors in the figure represent the expression levels of different genes under hypoxic stress; the colors from blue to yellow to red represent the increased expression levels successively.

    图  4  差异miRNAs靶基因数量统计分析

    Figure  4.  Statistical analysis of number of differential miRNAs target genes

    图  5  差异microRNAs靶向的热休克蛋白基因GO富集

    Figure  5.  GO enrichment of differential microRNA-targeted heat shock protein genes

    表  1  斑马鱼低氧与常氧鳃中下调miRNAs靶基因预测

    Table  1.   Prediction of down-regulated miRNAs target genes in hypoxic and normoxic gills of Danio rerio

    miRNA名称
    miRNA name
    靶基因
    Gene binding
    结合位点
    Site
    目标区域的预测配对
    Predicted pairing of target region
    dre-miR-455-3p hspa14 935—941
    dnajb6b 1157—1163
    1829—1835
    下载: 导出CSV

    表  2  斑马鱼低氧与常氧鳃中上调miRNAs靶基因预测

    Table  2.   Prediction of up-regulated miRNAs target genes in hypoxic and normoxic gills of Danio rerio

    miRNA名称
    miRNA name
    靶基因
    Gene binding
    结合位点
    Site
    目标区域的预测配对
    Predicted pairing of target region
    dre-miR-194a hspa12a 2262—2268
    dnajc5aa 4114—4120
    hspb7 1644—1650
    hsp70.3 245—251
    dnajb2 3834—3840
    Dre-miR-155 hspa12a 2771—2777
    hspg2 3611—3617
    hspa13 308—314
    903—910
    dnajb2 1484—1490
    3420—3426
    dre-miR-130c hspa12a 3219—3225
    4709—4715
    dnajb2 920—926
    dre-miR-9 dnajc5aa 2348—2354
    dnajb2 5033—5039
    dre-miR-29a hspg2 2832—2839
    dre-miR-96-5p dnajb2 2290—2296
    5045—5051
    5094—5100
    下载: 导出CSV
  • [1] RICHARDS J G. Physiological, behavioral and biochemical adaptations of intertidal fishes to hypoxia[J]. J Exp Biol, 2011, 214(2): 191-199. doi: 10.1242/jeb.047951
    [2] 赵文文, 曹振东, 付世建. 溶氧水平对鳊鱼, 中华倒刺鲃幼鱼游泳能力的影响[J]. 水生生物学报, 2013, 37(2): 314-320. doi: 10.7541/2013.20
    [3] 钟雪萍, 王丹, 张义兵, 等. 鲫鱼低氧相关基因差减cDNA文库的构建与分析[J]. 水生生物学报, 2009, 33(1): 113-118.
    [4] BEST C, IKERT H, KOSTYNIUK D J, et al. Epigenetics in teleost fish: from molecular mechanisms to physiological phenotypes[J]. Comp Biochem Physiol B, 2018, 224: 210-244. doi: 10.1016/j.cbpb.2018.01.006
    [5] 刘昌盛, 穆宇, 杜久林. 斑马鱼在生命科学研究中的应用[J]. 生命科学, 2007(4): 33-37.
    [6] SARASAMMA S, VARIKKODAN M M, LIANG S T, et al. Zebrafish: a premier vertebrate model for biomedical research in Indian scenario[J]. Zebrafish, 2017, 14(6): 589-605. doi: 10.1089/zeb.2017.1447
    [7] 刘春晓, 吕为群, 杨志刚, 等. TGF-β/Smad信号通路响应光周期变化参与调控斑马鱼卵巢发育[J]. 南方水产科学, 2019, 15(3): 69-75.
    [8] SANTHAKUMAR K, JUDSON E C, ELKS P M, et al. A zebrafish model to study and therapeutically manipulate hypoxia signaling in tumorigenesis[J]. Cancer Res, 2012, 72(16): 4017-4027. doi: 10.1158/0008-5472.CAN-11-3148
    [9] 张凡, 黄秋花, 陈赛娟, 等. 用斑马鱼模型研究低氧应激在造血和血液疾病中的作用[J]. 上海交通大学学报:医学版, 2016, 36(8): 1237-1241.
    [10] 狄治朝, 周涛, 许强华. 低氧胁迫与常氧条件下斑马鱼鳃中热休克蛋白基因家族的表达差异比较[J]. 大连海洋大学学报, 2018, 33(6): 11-16.
    [11] 徐湛宁. 草鱼在低氧胁迫下鳃的差异蛋白质组学及热休克诱导草鱼四倍体育种研究[D]. 上海: 上海海洋大学, 2018: 11-12.
    [12] 陈世喜, 王鹏飞, 区又君, 等. 急性和慢性低氧胁迫对卵形鲳鲹鳃器官的影响[J]. 南方水产科学, 2017, 13(1): 124-130. doi: 10.3969/j.issn.2095-0780.2017.01.016
    [13] 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. doi: 10.1038/35002607
    [14] 曾幼玲, 杨瑞瑞. 植物miRNA的生物学特性及在环境胁迫中的作用[J]. 中国农业科学, 2016, 49(19): 3671-3682. doi: 10.3864/j.issn.0578-1752.2016.19.001
    [15] QIAN M, WANG S, GUO X, et al. Hypoxic glioma-derived exosomes deliver microRNA-1246 to induce M2 macrophage polarization by targeting TERF2IP via the STAT3 and NF-κB pathways[J]. Oncogene, 2020, 39(2): 428-442. doi: 10.1038/s41388-019-0996-y
    [16] ZHAO Y, ZHU C D, YAN B, et al. miRNA-directed regulation of VEGF in tilapia under hypoxia condition[J]. Biochem Bioph Res Commun, 2014, 454: 183-188. doi: 10.1016/j.bbrc.2014.10.068
    [17] SUN X H, WANG X, ZHANG Y, et al. Exosomes of bone-marrow stromal cells inhibit cardiomyocyte apoptosis under ischemic and hypoxic conditions via miR-486-5p targeting the PTEN/PI3K/AKT signaling pathway[J]. Thromb Res, 2019, 177: 23-32. doi: 10.1016/j.thromres.2019.02.002
    [18] 曲凌云, 孙修勤, 相建海, 等. 热休克蛋白研究进展[J]. 海洋科学进展, 2004, 22(3): 385-391. doi: 10.3969/j.issn.1671-6647.2004.03.019
    [19] 黄勇, 龚望宝, 陈海刚, 等. 基于RNA-Seq高通量测序技术的大口黑鲈转录组分析[J]. 南方水产科学, 2019, 15(1): 106-112. doi: 10.12131/20180066
    [20] NAORA H. Involvement of ribosomal proteins in regulating cell growth and apoptosis: translational modulation or recruitment for extraribosomal activity[J]. Immunol Cell Biol, 1999, 77(3): 197-205. doi: 10.1046/j.1440-1711.1999.00816.x
    [21] ZHI F, SHAO N, XUE L, et al. Characteristic MicroRNA expression induced by δ-Opioid receptor activation in the rat liver under prolonged hypoxia[J]. Cell Physiol Biochem, 2017, 44(6): 2296-309. doi: 10.1159/000486067
    [22] CHEN P J, WENG J Y, PANG-HUNG J Y, et al. NPGPx modulates CPEB2-controlled HIF-1α RNA translation in response to oxidative stress[J]. Nucleic Acids Res, 2015, 43(19): 9393-9404. doi: 10.1093/nar/gkv1010
    [23] CAI Y H, LI Y P. Upregulation of miR-29b-3p protects cardiomyocytes from hypoxia-induced apoptosis by targeting TRAF5[J]. Cell Mol Biol Lett, 2019, 24(1): 27. doi: 10.1186/s11658-019-0151-3
    [24] ZHANG H, LI H, GE A, et al. Long non-coding RNA TUG1 inhibits apoptosis and inflammatory response in LPS-treated H9c2 cells by down-regulation of miR-29b[J]. Biomed Pharmacother, 2018, 101: 663-669. doi: 10.1016/j.biopha.2018.02.129
    [25] DING S, MIERADILIJIANG A, ZHOU Z, et al. Histamine deficiency aggravates cardiac injury through miR-206/216b-Atg13 axis-mediated autophagic-dependant apoptosis[J]. Cell Death Dis, 2018, 9(6): 694. doi: 10.1038/s41419-018-0723-6
    [26] YAN Y, CHENG W, ZHOU W, et al. Elevation of circulating miR-210-3p in high-altitude hypoxic environment[J/OL]. Front Physiol, 2016, 7(84)[2021-04-22]. https://www.frontiersin.org/articles/10.3389/fphys.2016.00084/full. DOI: https://doi.org/10.3389/fphys.2016.00084.
    [27] SHEN Y, ZHAO Y, WANG L, et al. MicroRNA-194 overexpression protects against hypoxia/reperfusion-induced HK-2 cell injury through direct targeting Rheb[J]. J Cell Biochem, 2018, 120(5): 8311-8318.
    [28] MATSUURA Y, WADA H, EGUCHI H, et al. Exosomal miR-155 derived from hepatocellular carcinoma cells under hypoxia promotes angiogenesis in endothelial cells[J]. 2019, 64(3): 792-802.
    [29] YAN J R, XUE H J, WU S Q, et al. Ginsenoside-Rb1 protects hypoxic- and ischemic-damaged cardiomyocytes by regulating expression of miRNAs[J/OL]. EVID-Based Compl Alt, 2015, 171306[2021-04-22]. https://doi.org/10.1155/2015/171306.
    [30] SHAN F, LI J, HUANG Q Y. HIF-1 alpha-induced up-regulation of miR-9 contributes to phenotypic modulation in pulmonary artery smooth muscle cells during hypoxia[J]. J Cell Physiol, 2014, 229(10): 1511-1520. doi: 10.1002/jcp.24593
    [31] TIAN L, CAI D, ZHUANG D, et al. miR-96-5p regulates proliferation, migration, and apoptosis of vascular smooth muscle cell induced by angiotensin II via targeting NFAT5[J]. J Vasc Res, 2020, 57(2): 1-11.
    [32] 郭伟, 许万福, 赵俊红, 等. microRNA-1和热休克蛋白90在心肌缺氧复氧中的关系[J]. 中国分子心脏病学杂志, 2019, 108(05): 57-61.
    [33] 苑洁, 邹云增. 压力超负荷致小鼠心肌肥厚中miR-378对热休克转录因子−1的调节作用[J]. 中国临床医学, 2019, 26(40): 543-648.
    [34] CLAEYS K G, SOZANSKA M, MARTIN J J, et al. DNAJB2 expression in normal and diseased human and mouse skeletal muscle[J]. Am J Pathol, 2010, 176(6): 2901-2910. doi: 10.2353/ajpath.2010.090663
    [35] VINCENZO L, CARMEN A, ERWIN K, et al. Chaperonopathies: spotlight on hereditary motor neuropathies[J/OL]. Front Mol Biosci, 2016, 3[2021-04-22]. https://www.frontiersin.org/articles/10.3389/fmolb.2016.00081/full. DOI: https://doi.org/10.3389/fmolb.2016.00081.
    [36] ZHU Y, ZHOU H, ZHU Y, et al. Gene expression of Hsp70, Hsp90, and Hsp110 families in normal and abnormal embryonic development of mouse forelimbs[J]. Drug Chem Toxicol, 2012, 35(4): 432-444. doi: 10.3109/01480545.2011.640683
    [37] DING Y, LIU W, GORE B, et al. Abstract 41: Dnajb6b is a novel genetic modifier for cardiomyopathy that regulates ER stress response[J]. Circul Res, 2014, 115(Suppl1): A41.
    [38] TRANLUNDMARK K, CHANG Y T, TANNENBERG P, et al. Lack of perlecan heparan sulfate impairs pulmonary vascular development and is protective in hypoxia induced pulmonary hypertension[J]. Cardiovasc Res, 2015, 107(1): 20-31. doi: 10.1093/cvr/cvv143
  • 加载中
计量
  • 文章访问数:  8
  • 被引次数: 0
出版历程
  • 收稿日期:  2021-04-22
  • 修回日期:  2021-06-21
  • 录用日期:  2021-07-22
  • 网络出版日期:  2021-08-31

目录

    /

    返回文章
    返回