中国农业科学 ›› 2020, Vol. 53 ›› Issue (10): 2122-2136.doi: 10.3864/j.issn.0578-1752.2020.10.018
• 畜牧·兽医·资源昆虫 • 上一篇
周丁丁,史小玉,王杰,范元婵,祝智威,蒋海宾,范小雪,熊翠玲,郑燕珍,付中民,徐国钧,陈大福,郭睿()
收稿日期:
2019-10-23
接受日期:
2019-11-26
出版日期:
2020-05-16
发布日期:
2020-05-22
通讯作者:
郭睿
作者简介:
周丁丁,E-mail:zdd03569981@163.com。|史小玉,E-mail:2395965008@qq.com。
基金资助:
ZHOU DingDing,SHI XiaoYu,WANG Jie,FAN YuanChan,ZHU ZhiWei,JIANG HaiBin,FAN XiaoXue,XIONG CuiLing,ZHENG YanZhen,FU ZhongMin,XU GuoJun,CHEN DaFu,GUO Rui()
Received:
2019-10-23
Accepted:
2019-11-26
Online:
2020-05-16
Published:
2020-05-22
Contact:
Rui GUO
摘要:
【背景】 长链非编码RNA(long non-coding RNA,lncRNA)是一类长度>200 nt且不具有编码能力的转录本,能够在真核生物的转录水平和转录后水平通过顺式(cis)、反式(trans)或竞争性内源RNA(competing endogenous RNA,ceRNA)机制调控基因的表达,已被证明在生物体的生长和发育等生物学过程中发挥重要的调控作用。【目的】 结合测序得到的东方蜜蜂微孢子虫(Nosema ceranae)纯化孢子的small RNA(sRNA)组学数据和前期获得的lncRNA组学数据对lncRNA的调控方式进行深入细致的分析和探讨,揭示lncRNA在东方蜜蜂微孢子虫孢子中的潜在功能。【方法】 利用small RNA-seq(sRNA-seq)技术对东方蜜蜂微孢子虫纯化孢子进行测序,通过相关的生物信息学软件对测序数据进行质控。根据lncRNA与mRNA的位置关系预测lncRNA的上下游基因;使用Blast软件比对GO和KEGG数据库,对上下游基因进行功能和代谢通路注释;利用Target Finder软件预测lncRNA-miRNA及lncRNA-miRNA-mRNA调控网络,进而通过Cytoscape v3.7.2软件对调控网络进行可视化;利用RT-PCR对调控网络中的部分lncRNA、miRNA和mRNA的表达进行验证。【结果】 东方蜜蜂微孢子虫纯化孢子样品的sRNA-seq分别得到16 597 883、15 451 791和12 248 316条raw reads,经质控分别得到15 608 370、14 249 255和11 440 684条clean reads,各样品的Q30≥98.58%。共预测出lncRNA的上下游基因310个,它们可注释到代谢进程、细胞进程、催化活性、结合和细胞等相关的35个功能条目;此外还可注释到56条代谢通路,涉及嘌呤代谢、碳代谢和丙酮酸代谢等物质代谢通路,以及甲烷代谢、氧化磷酸化和糖酵解/糖异生等能量代谢通路。上述结果表明相应的lncRNA可能通过cis作用调节上下游基因的表达,从而参与调控东方蜜蜂微孢子虫孢子中的物质和能量代谢以及细胞生命活动。进一步构建lncRNA-miRNA调控网络,分析结果显示MSTRG.3636.1、MSTRG.4498.1和MSTRG.4883.1可靶向结合4个miRNA(nce-miR-7729、nce-miR-7502、nce-miR-8639和nce-miR-8565),说明此3个lncRNA可作为ceRNA在东方蜜蜂微孢子虫孢子中发挥潜在作用。LncRNA-miRNA-mRNA调控网络分析结果显示,三者之间形成较为复杂的调控网络关系,miRNA处于调控网络的中心并联系lncRNA和mRNA,nce-miR-7502和nce-miR-8639结合的mRNA最多,达到28个;与MSTRG.3636.1、MSTRG.4498.1和MSTRG.4883.1存在靶向关系的miRNA结合多个mRNA,表明上述3个lncRNA可能通过ceRNA机制发挥作用,从而影响东方蜜蜂微孢子虫孢子中的新陈代谢和生命活动。【结论】 lncRNA可能通过cis作用调控上下游基因的表达,以及作为ceRNA通过吸附miRNA间接影响靶基因的表达,从而参与调节东方蜜蜂微孢子虫孢子中的物质和能量代谢等基本生命活动。
周丁丁,史小玉,王杰,范元婵,祝智威,蒋海宾,范小雪,熊翠玲,郑燕珍,付中民,徐国钧,陈大福,郭睿. 东方蜜蜂微孢子虫孢子中长链非编码RNA的竞争性内源RNA调控网络及潜在功能[J]. 中国农业科学, 2020, 53(10): 2122-2136.
ZHOU DingDing,SHI XiaoYu,WANG Jie,FAN YuanChan,ZHU ZhiWei,JIANG HaiBin,FAN XiaoXue,XIONG CuiLing,ZHENG YanZhen,FU ZhongMin,XU GuoJun,CHEN DaFu,GUO Rui. Investigation of Competing Endogenous RNA Regulatory Network and Putative Function of Long Non-Coding RNAs in Nosema ceranae Spore[J]. Scientia Agricultura Sinica, 2020, 53(10): 2122-2136.
表1
本研究使用的引物"
核酸ID Nucleotide ID | 引物名称 Primer name | 引物序列 Primer sequence (5′-3′) | 预期目的片段 Product size (bp) |
---|---|---|---|
gene1439 | 1-F | ATGTATCTTATGCCAACGC | 382 |
1-R | TGAATCTTTCCTACACCCT | ||
gene565 | 2-F | TCAAGCCTGTTAAGATGAC | 499 |
2-R | ACTACTTCTGGCGGTTTAT | ||
gene1719 | 3-F | ATAGGAGGTAAACATCAG | 438 |
3-R | ATAGTAAAGTTCAGTGCC | ||
gene1366 | 4-F | TTGAAGAAGGTGTCGCAGAAC | 182 |
4-R | AGCAGAGCCACATAAACAAGC | ||
gene1360 | 5-F | AAGAAGCCGAAACAACCC | 101 |
5-R | GTTAGCCGCATCCATAGC | ||
gene1134 | 6-F | TGTACGGTCTGGCTGCTTC | 352 |
6-R | GGACTTGGCTTTCCACTAA | ||
gene1695 | 7-F | GATACAGCCTCTTTGG | 138 |
7-R | GGAACAATAACCCTAAA | ||
gene1563 | 8-F | TGCCTACAATCAACTCTAAT | 384 |
8-R | CACCCAATACTTCAAATAAC | ||
MSTRG.3636.1 | 9-F | TAACTAGCCTACTCTATCCC | 257 |
9-R | TAAAAGCACTAACTACAACC | ||
MSTRG.4883.1 | 10-F | CTGACAGACCATAGTCGGCATA | 128 |
10-R | TCTACAATGATGGGCACAGGA | ||
nce-miR-8565 | 11-L | CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGCCTAAAGA | 67 |
11-F | CGCGCCTTTAATTGTGAAACATG | ||
nce-miR-7502 | 12-L | CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGAACTTGTC | 66 |
12-F | CGCGCCTAAAAACAAAAATGTA | ||
nce-miR-7729 | 13-L | CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGTCTAGGCC | 62 |
13-F | CGCGCCTAGTGATGGCTGT | ||
- | R | CTCAACTGGTGTCGTGGA |
表4
东方蜜蜂微孢子虫孢子中lncRNA靶向miRNA的靶mRNA的Swissprot和Nr数据库注释"
核酸ID Nucleotide ID | Swissprot 数据库注释 Swissprot database annotation | Nr数据库注释 Nr database annotation |
---|---|---|
gene986 | 液泡氨基酸转运体5 Vacuolar amino acid transporter 5 | 假定蛋白NCER_101697 Hypothetical protein NCER_101697 |
gene783 | 负辅因子2复合亚基 Negative cofactor 2 complex subunit beta | 假定蛋白NCER_101896 Hypothetical protein NCER_101896 |
gene565 | 丝氨酸/苏氨酸多聚蛋白激酶1 Serine/threonine-protein kinase plo1 | 假定蛋白NCER__102113 Hypothetical protein NCER_102113 |
gene2596 | 含C1778.09蛋白的TBC结构域 TBC domain-containing protein C1778.09 | 假定蛋白NCER_100108 Hypothetical protein NCER_100108 |
gene2543 | TATA结合蛋白相关因子MOT1 TATA-binding protein-associated factor MOT1 | 假定蛋白NCER_100152 Hypothetical protein NCER_100152 |
gene2397 | 丝氨酸/苏氨酸蛋白激酶CDC5同源物 Cell cycle serine/threonine-protein kinase CDC5 homolog | 假定蛋白NCER_100270 Hypothetical protein NCER_100270 |
gene2312 | ERAD-相关E3泛素蛋白连接酶doa10 ERAD-associated E3 ubiquitin-protein ligase doa10 | 假定蛋白NCER_100375 Hypothetical protein NCER_100375 |
gene2178 | 转运蛋白sec24 Transport protein sec24 | 假定蛋白NCER_100510 Hypothetical protein NCER_100510 |
gene2014 | 转录相关蛋白1 Transcription-associated protein 1 | 假定蛋白NCER_100665 Hypothetical protein NCER_100665 |
gene1870 | ERAD-相关E3泛素蛋白连接酶doa10 ERAD-associated E3 ubiquitin-protein ligase doa10 | 假定蛋白NCER_100805 Hypothetical protein NCER_100805 |
gene1766 | 赖氨酸- tRNA连接酶 Lysine-tRNA ligase | 假定蛋白NCER_100909 Hypothetical protein NCER_100909 |
gene1719 | T-复合体蛋白1亚基 T-complex protein 1 subunit alpha | 假定蛋白NCER_100958 Hypothetical protein NCER_100958 |
gene1687 | DNA-锚定 RNA 聚合酶 II 亚基RPB2 DNA-directed RNA polymerase II subunit RPB2 | 假定蛋白NCER_100983 Hypothetical protein NCER_100983 |
gene1678 | 锰-ATP转运酶4 Manganese-transporting ATPase 4 | 假定蛋白NCER_101005 Hypothetical protein NCER_101005 |
gene1677 | 3型蛋白酶体亚基 Probable proteasome subunit beta type-3 | 假定蛋白NCER_101004 Hypothetical protein NCER_101004 |
gene1662 | 微管蛋白γ链 Tubulin gamma chain | 假定蛋白NCER_101024 Hypothetical protein NCER_101024 |
gene1563 | 核输出蛋白BRL1 Nucleus export protein BRL1 | 假定蛋白NCER_101114 Hypothetical protein NCER_101114 |
gene1383 | V型质子ATP酶催化亚基A V-type proton ATPase catalytic subunit A | 假定蛋白NCER_101294 Hypothetical protein NCER_101294 |
gene1366 | 长链脂肪酸CoA链2 Long chain fatty acid CoA ligase 2 | 假定蛋白NCER_101315 Hypothetical protein NCER_101315 |
gene1360 | 热休克蛋白hsp98 Heat shock protein hsp98 | 假定蛋白NCER_101322 Hypothetical protein NCER_101322 |
gene1348 | 丝氨酸/苏氨酸蛋白激酶MEC1同源物 Serine/threonine-protein kinase MEC1 homolog | 假定蛋白NCER_101332 Hypothetical protein NCER_101332 |
gene1190 | 泛素羧基末端水解酶5 Ubiquitin carboxyl-terminal hydrolase 5 | 假定蛋白NCER_101487 Hypothetical protein NCER_101487 |
gene1180 | 苯丙氨酸-tRNA连接酶亚基 Phenylalanine-tRNA ligase beta subunit | 假定蛋白NCER_101490 Hypothetical protein NCER_101490 |
gene1134 | 二磷酸异戊基丁二醇异构酶 Isopentenyl-diphosphate Delta-isomerase | 假定蛋白NCER_101544 Hypothetical protein NCER_101544 |
newGene_142 | 60S核糖体蛋白L40(前体) 60S ribosomal protein L40 (precursor) | 假定蛋白NCER_102067 Hypothetical protein NCER_102067 |
图5
东方蜜蜂微孢子虫孢子中lncRNA、靶miRNA和靶mRNA的RT-PCR验证 M:DNA marker;1:假定蛋白NCER_101243编码基因Hypothetical protein NCER_101243 coding gene;2:假定蛋白NCER_102113编码基因Hypothetical protein NCER_102113 coding gene;3:假定蛋白NCER_100958编码基因Hypothetical protein NCER_100958 coding gene;4:假定蛋白NCER_101315编码基因Hypothetical protein NCER_101315 coding gene;5:假定蛋白NCER_101322编码基因Hypothetical protein NCER_101322 coding gene;6:假定蛋白NCER_101544编码基因Hypothetical protein NCER_101544 coding gene;7:假定蛋白NCER_100991编码基因Hypothetical protein NCER_100991 coding gene;8:假定蛋白NCER_1011114编码基因Hypothetical protein NCER_101114 coding gene;9:MSTRG.3636.1;10:MSTRG.4883.1;11:nce-miR-8565;12:nce-miR-7502;13:nce-miR-7729;N1、N2:阴性对照(无菌水)Negative control (sterile water);N3:阴性对照(DEPC水)Negative control (DEPC water)"
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