中国农业科学 ›› 2019, Vol. 52 ›› Issue (4): 738-754.doi: 10.3864/j.issn.0578-1752.2019.04.014
金梅,张丽娟,曹倩,郭鑫英
收稿日期:
2018-09-03
接受日期:
2018-12-03
出版日期:
2019-02-16
发布日期:
2019-02-27
作者简介:
金梅,E-mail: 基金资助:
JIN MEI,ZHANG LIJUAN,CAO QIAN,GUO XinYing
Received:
2018-09-03
Accepted:
2018-12-03
Online:
2019-02-16
Published:
2019-02-27
摘要:
【目的】筛选出辽宁绒山羊皮肤成纤维细胞中与绒毛生长相关的LncRNA,为绒毛生长相关LncRNA的功能及机制研究提供基础性数据。【方法】提取MT和FGF5处理的辽宁绒山羊皮肤成纤维细胞总RNA,通过样品总RNA电泳检测、测序数据质量评估、Mapping比对、样品间相关性检查对提取的总RNA进行质量检测。筛选出差异表达的LncRNA并预测其靶基因,通过GO和KEGG富集分析,筛选出与绒毛生长相关的LncRNA,并通过Real-time PCR对目标LncRNA进行表达验证。【结果】(1)样品总RNA质量检测结果显示:RNA 完整性良好、GC含量相对较高,序列较稳定、样品间表达水平相关性均较高、符合测序要求。(2)差异表达LncRNA的筛选结果显示:1.0g·L -1 24h组差异表达LncRNA有32个,其中4个表达上调,28个表达下调;0.2g·L -1 24h组差异表达LncRNA 有10个,其中4个表达上调,6个表达下调;0.2g·L -1 72h组差异表达LncRNA有113个,其中5个表达上调,108个表达下调。10 -4g·L -1 24 h组差异表达LncRNA有164个,其中有70个上调,94个下调;10 -4g·L -1 72 h差异表达LncRNA 有189个,其中有78个上调,111个下调;10 -6g·L -1 24 h组差异表达的LncRNA有123个,其中有27个上调,96个下调 。(3) 靶基因GO富集分析结果显示:1.0g·L -1 24h组差异表达LncRNA靶基因富集在GO的negative regulation of transcription from RNA polymerase II promoter;0.2g·L -1 24h组无差异表达LncRNA靶基因富集的GO term;0.2g·L -1 72h组差异表达LncRNA靶基因富集在GO的cellular metabolic process biological_process,binding molecular_function,FGF5处理组中只有10 -4g·L -1 72 h组差异表达LncRNA靶基因富集在cell cellular_component、cell part cellular_component、intracellular cellular_component、binding molecular_function等6个条目。(4)靶基因KEGG富集分析结果显示:1.0g·L -1 24h组差异表达LncRNA靶基因富集在Steroid biosynthesis pathway;0.2g·L -1 24h组无差异表达LncRNA靶基因富集的Pathway term;0.2g·L -1 72h组差异表达LncRNA靶基因富集在Cell cycle,DNA replication,Steroid biosynthesis,TNF,Nod-like receptor,NF-kappa B等信号通路,其中TNF和NF-kappa B信号通路与绒毛生长相关。FGF5处理组中,10 -4g·L -1 72 h组差异表达的LncRNA靶基因显著富集到Fanconi anemia pathway,Huntington's disease,Metabolic pathway,Aminoacyl-tRNA biosynthesis等9个pathway term,其中Metabolic信号通路与绒毛生长相关;10 -4g·L -1 24 h组差异表达的LncRNA靶基因无显著富集的pathway term;10 -6g·L -1 24 h组差异表达的LncRNA靶基因只富集在Taste transduction pathway。(5)NF-κB和TNF两个信号通路中富集的靶基因TNFα、TNFAIP3(A20)、NFKBIA(IkBα)、NFKB2、IL8所对应的LncRNA有2个,分别为(Gene ID):XLOC_005914;XLOC_018763;Metabolic信号通路中靶基因所对应的LncRNA有4个,分别为(Gene ID):XLOC_011424、XLOC_009522、XLOC_009063、XLOC_01115。Real-time PCR结果显示:LncRNA XLOC_011424、XLOC_011157、LncRNA XLOC_005914和XLOC_018763与高通量测序结果一致。 【结论】LncRNA XLOC_011424、XLOC_011157、LncRNA XLOC_005914和XLOC_018763可能通过调控与绒毛生长相关的NF-κB 、TNF或Metabolic信号通路,提高羊绒密度和长度,进而提高辽宁绒山羊绒产量及品质。
金梅,张丽娟,曹倩,郭鑫英. MT和FGF5调控辽宁绒山羊绒毛生长相关LncRNA的筛选及鉴定[J]. 中国农业科学, 2019, 52(4): 738-754.
JIN MEI,ZHANG LIJUAN,CAO QIAN,GUO XinYing. The Screening and Identification of LncRNA Related to Villus Growth in Liaoning Cashmere Goats by MT and FGF5[J]. Scientia Agricultura Sinica, 2019, 52(4): 738-754.
表1
RT-PCR引物序列"
基因 Gene | 引物 Primer | 引物序列(5'→3') Primer sequence(5'→3') | 产物 Products |
---|---|---|---|
β-actin | β-actin -F β-actin -R | GATGGCTACTGCTGCGTCG GGCATACAGGTCCTTTCGG | 208bp |
LncRNA XLOC_005914 | LncRNA XLOC_005914 -F LncRNA XLOC_005914-R | CAGACCTTGCCACACCGA CAGTCCCGAACAAAATCAGC | 143bp |
LncRNA XLOC_018763 | LncRNA XLOC_018763 -F LncRNA XLOC_018763-R | CAGCAGAGAAAGGAGAAAATGG GTGATGTAGGTGAGAGGCGAG | 299bp |
LncRNA XLOC_011424 | LncRNA XLOC_011424 -F LncRNA XLOC_011424-R | AAAAGCACATTAGAGGCTGGAG GCAAGCAAATTCATGGCACA | 116 bp |
LncRNA XLOC_009522 | LncRNA XLOC_018763 -F LncRNA XLOC_018763-R | GGGCGTGACATTTTCAGATT TCAGGGGACCTTTGGACTTG | 289 bp |
LncRNA XLOC_009063 | LncRNA XLOC_009063-F LncRNA XLOC_009063-R | GCATCATTTCTTCCGCATTC TGGGTTACCATTTCCTTCTCC | 220 bp |
LncRNA XLOC_011157 | LncRNA XLOC_011157-F LncRNA XLOC_011157-R | CTTTGGAAATGGTTCTGTGCTG GGAAGTAGGAGATGCTGGGTAA | 140 bp |
表2
RNA-Seq数据一览表"
样本 Sample | 原始序列 Raw reads | 过滤后序列 Clean reads | 错误率 Error rate (%) | Q20 Q20 (%) | Q30 Q30 (%) | GC含量 GC content(%) |
---|---|---|---|---|---|---|
C_1 | 48045300 | 46275212 | 0.03 | 96.86 | 93.68 | 48.39 |
C_2 | 48045300 | 46275212 | 0.04 | 94.99 | 90.67 | 48.37 |
M2_72H_1 | 42277089 | 40464850 | 0.03 | 96.34 | 92.55 | 51.77 |
M2_72H_2 | 42277089 | 40464850 | 0.04 | 93.42 | 87.84 | 51.95 |
M2_24H_1 | 50302056 | 48536611 | 0.03 | 96.75 | 93.50 | 48.03 |
M2_24H_2 | 50302056 | 48536611 | 0.03 | 95.04 | 90.73 | 48.03 |
M1_24H_1 | 48057476 | 46336801 | 0.03 | 96.80 | 93.55 | 48.90 |
M1_24H_2 | 48057476 | 46336801 | 0.04 | 94.99 | 90.66 | 48.92 |
F4_24H_1 | 51394058 | 49453178 | 0.03 | 96.82 | 93.65 | 47.67 |
F4_24H_2 | 51394058 | 49453178 | 0.03 | 95.31 | 91.23 | 47.57 |
F4_72H_1 | 49418892 | 47713121 | 0.03 | 96.72 | 93.27 | 52.04 |
F4_72H_2 | 49418892 | 47713121 | 0.04 | 94.71 | 90.09 | 52.26 |
F6_24H_1 | 46346088 | 44739804 | 0.03 | 96.88 | 93.73 | 48.58 |
F6_24H_2 | 46346088 | 44739804 | 0.04 | 94.92 | 90.55 | 48.55 |
表3
M2_72H vs C组差异表达LncRNA靶基因GO term分类"
条目类型 Term_type | 功能 Features | 过表达的P值 Over_represented P value | 校正的P值 Corrected P value |
---|---|---|---|
生物过程 Biological_process (BP) | 细胞代谢过程 Cellular metabolic process | 7.15E-06 | 0.003923 |
氮化合物代谢过程 Nitrogen compound metabolic process | 8.48E-06 | 0.0039252 | |
细胞氮化合物代谢过程 Cellular nitrogen compound metabolic process | 1.67E-05 | 0.0063413 | |
有机氮化合物代谢过程 Organonitrogen compound metabolic process | 8.12E-05 | 0.019891 | |
细胞芳香化合物代谢过程 Cellular aromatic compound metabolic process | 3.26E-05 | 0.0097043 | |
杂环代谢过程 Heterocycle metabolic process | 5.36E-05 | 0.013956 | |
有机环状化合物代谢过程 Organic cyclic compound metabolic process | 3.84E-05 | 0.01066 | |
染色体组织 Chromosome organization | 9.55E-05 | 0.022102 | |
含核碱基的化合物代谢过程 Nucleobase-containing compound metabolic process | 0.00011221 | 0.024598 | |
染色质修饰 Chromatin modification | 0.00025719 | 0.04581 | |
细胞成分组织或生物发生 Cellular component organization or biogenesis | 0.00026397 | 0.04581 | |
细胞组分Cellular_component (CC) | 核 Nucleus | 1.48E-06 | 0.0031426 |
膜结合的细胞器 Membrane-bounded organelle | 3.52E-06 | 0.003923 | |
细胞内膜结合细胞器 Intracellular membrane-bounded organelle | 4.25E-06 | 0.003923 | |
染色体 Chromosome | 0.00022214 | 0.042055 | |
分子功能Molecular_function (MF) | 核酸酶活性 Nuclease activity | 1.51E-06 | 0.0031426 |
腺苷酸核苷酸结合 Adenyl nucleotide binding | 5.49E-06 | 0.003923 | |
腺苷核糖核苷酸结合 Adenyl ribonucleotide binding | 7.54E-06 | 0.003923 | |
ATP结合 ATP binding | 6.43E-06 | 0.003923 | |
蛋白质结合 Protein binding | 1.65E-05 | 0.0063413 | |
细胞因子活性 Cytokine activity | 3.00E-05 | 0.0096034 | |
水解酶活性,作用于酯键 Hydrolase activity, acting on ester bonds | 0.00012043 | 0.02508 | |
催化活性 Catalytic activity | 0.00021879 | 0.042055 | |
结合物 Binding | 1.90E-05 | 0.0065865 |
表4
F4_72H vs C组差异表达LncRNA靶基因的GO term分类"
条目类型 Term_type | 功能 Features | 过表达的P值 Over_represented P value | 校正的P值 Corrected P value | |
---|---|---|---|---|
生物过程Biological_process (BP) | 细胞代谢过程 Cellular metabolic process | 1.22E-06 | 0.002285 | |
生物合成过程 Biosynthetic process | 3.29E-06 | 0.002285 | ||
有机物生物合成过程 Organic substance biosynthetic process | 6.96E-06 | 0.0034462 | ||
细胞生物合成过程 Cellular biosynthetic process | 8.88E-06 | 0.0034462 | ||
细胞大分子代谢过程 Cellular macromolecule metabolic process | 9.10E-06 | 0.0034462 | ||
基因表达 Gene expression | 1.87E-05 | 0.0051872 | ||
细胞蛋白质代谢过程 Cellular protein metabolic process | 2.03E-05 | 0.0052866 | ||
翻译 Translation | 3.43E-05 | 0.0071461 | ||
高分子生物合成过程 Macromolecule biosynthetic process | 7.00E-05 | 0.013255 | ||
细胞大分子生物合成过程 Cellular macromolecule biosynthetic process | 8.41E-05 | 0.015233 | ||
有机环状化合物代谢过程 Organic cyclic compound metabolic process | 9.81E-05 | 0.017021 | ||
细胞氮化合物代谢过程 Cellular nitrogen compound metabolic process | 0.0001207 | 0.019468 | ||
细胞芳香化合物代谢过程 Cellular aromatic compound metabolic process | 0.00012153 | 0.019468 | ||
细胞芳香化合物代谢过程 Nitrogen compound metabolic process | 0.00013872 | 0.021399 | ||
蛋白质定位 Protein localization | 0.00015944 | 0.023716 | ||
杂环代谢过程 Heterocycle metabolic process | 0.00018062 | 0.025736 | ||
DNA复制,合成RNA引物 DNA replication, synthesis of RNA primer | 0.00023573 | 0.031671 | ||
含核碱基的化合物代谢过程 Nucleobase-containing compound metabolic process | 0.00038174 | 0.045427 | ||
胞组分Cellular_component (CC) | 细胞内部分 Intracellular part | 9.95E-08 | 0.00041428 | |
细胞质 Cytoplasm | 1.93E-06 | 0.002285 | ||
细胞内膜结合细胞器 Intracellular membrane-bounded organelle | 2.49E-06 | 0.002285 | ||
膜结合的细胞器 Membrane-bounded organelle | 3.16E-06 | 0.002285 | ||
细胞 Cell | 7.88E-06 | 0.0034462 | ||
细胞部分 Cell part | 7.88E-06 | 0.0034462 | ||
细胞内 Intracellular | 1.34E-05 | 0.0046662 | ||
细胞质部分 Cytoplasmic part | 1.65E-05 | 0.0049423 | ||
核 Nucleus | 1.66E-05 | 0.0049423 | ||
细胞内细胞器 Intracellular organelle | 2.56E-05 | 0.0061674 | ||
细胞器 Organelle | 2.69E-05 | 0.0061674 | ||
大分子复合物 Macromolecular complex | 2.81E-05 | 0.0061674 | ||
核部分 Nuclear part | 4.41E-05 | 0.0087498 | ||
膜封闭的管腔 Membrane-enclosed lumen | 0.00018537 | 0.025736 | ||
细胞器腔 Organelle lumen | 0.00025929 | 0.032725 | ||
细胞内细胞器腔 Intracellular organelle lumen | 0.00025929 | 0.032725 | ||
内膜系统 Endomembrane system | 0.00031133 | 0.038138 | ||
蛋白质复合物 Protein complex | 0.00047111 | 0.049055 | ||
核腔 Nuclear lumen | 0.00048565 | 0.049335 | ||
分子功能Molecular_function (MF) | 连接酶活性,形成碳 - 氧键 Ligase activity, forming carbon-oxygen bonds | 0.00040555 | 0.045652 | |
连接酶活性,形成氨酰-tRNA和相关化合物 Ligase activity, forming aminoacyl-tRNA and related compounds | 0.00040555 | 0.045652 | ||
腺苷酸核苷酸结合 Adenyl nucleotide binding | 0.00043007 | 0.047138 | ||
结合物 Binding | 0.00046 | 0.049055 |
表5
M2_72H vs C组Pathways富集数据表"
通路 Pathway | 通路ID Pathway ID | 样本编号 Sample number | 背景编号 Background number | 校正的P值 Corrected P value |
---|---|---|---|---|
细胞周期 Cell cycle | chx04110 | 62 | 116 | 1.30736872661e-07 |
DNA复制 DNA replication | chx03030 | 26 | 34 | 1.97822480896e-07 |
范可尼贫血症 Fanconi anemia | chx03460 | 29 | 50 | 0.000199893004074 |
错配修复 Mismatch repair | chx03430 | 15 | 22 | 0.00320771571904 |
赖氨酸降解 Lysine degradation | chx00310 | 25 | 50 | 0.0157486842455 |
癌症中的微小RNA MicroRNAs in cancer | chx05206 | 50 | 127 | 0.0399507008006 |
阿尔茨海默氏病 Alzheimer's disease | chx05010 | 61 | 164 | 0.0467892160603 |
类固醇生物合成 Steroid biosynthesis | chx00100 | 12 | 20 | 0.0467892160603 |
TNF | chx04668 | 39 | 97 | 0.0467892160603 |
Nod样受体 Nod-like receptor | chx04621 | 22 | 47 | 0.0467892160603 |
嘧啶代谢 Pyrimidine metabolism | chx00240 | 37 | 91 | 0.0467892160603 |
RNA转运 RNA transport | chx03013 | 54 | 144 | 0.0467892160603 |
柠檬酸循环 Citrate cycle | chx00020 | 16 | 31 | 0.0467892160603 |
同源重组 Omologous recombination | chx03440 | 14 | 26 | 0.0467892160603 |
NF-kappa B | chx04064 | 32 | 77 | 0.0467892160603 |
表6
M2_72H vs C组差异表达基因富集的绒毛生长相关信号通路"
通路 Pathway | 基因ID Gene ID | 基因名称 Gene name | 方式 Style |
---|---|---|---|
TNF NF-kB | 100861232 102169137 102172758 102186424 100861171 102182977 100860785 102188524 100861236 102185051 100861232 102182977 102169137 102191581 102178438 | TNFα NFKBIA PIK3R5 NOD2 MT1MMP TNFAIP3 IL6 LIF IL18R1 CSF1 TNFα TNFAIP3(A20) NFKBIA(IKBα) NFKB2 IL8 | UP UP UP UP UP UP UP UP UP UP UP UP UP UP UP |
表7
FGF处理组,KEGG富集分析"
样本名称 Sample name | 显著富集的信号通路 Significantly enriched signaling pathway | Q值 Qvalue | |
---|---|---|---|
F4_24H vs C | cis靶基因 cis target gene | 无 No | - |
trans靶基因 trans target gene | 无 No | - | |
F4_72H vs C | cis靶基因 cis target gene | 无 No | - |
trans靶基因 trans target gene | 核糖体 Ribosome RNA转运 RNA transport 范可尼贫血途径 Fanconi anemia pathway 亨廷顿氏病 Huntington's disease 代谢途径 Metabolic pathway 氨酰基-tRNA生物合成 Aminoacyl-tRNA biosynthesis 柠檬酸循环(TCA循环) Citrate cycle (TCA cycle) 阿尔茨海默氏病 Alzheimer's disease 泛素介导的蛋白水解 Ubiquitin mediated proteolysis | 0.001 0.018 0.018 0.018 0.025 0.029 0.033 0.033 0.037 | |
F6_24H vs C | Cis靶基因 Cis target gene | 味觉转导 Taste transduction | 0.022 |
Trans靶基因 Trans target gene | 无 No | - |
表8
FGF处理组,Pathways显著性富集数据表"
通路 Pathway | 通路ID Pathway ID | 样本编号 Sample number | 背景编号 Background number | 校正后的P值 Corrected P-value |
---|---|---|---|---|
核糖体 Ribosome | chx03010 | 36 | 129 | 0.001 |
RNA转运 RNA transport | chx03013 | 34 | 144 | 0.018 |
范可尼贫血途径 Fanconi anemia pathway | chx03460 | 16 | 50 | 0.018 |
亨廷顿氏病 Huntington's disease | chx05016 | 38 | 171 | 0.018 |
代谢途径 Metabolic pathway | chx01100 | 178 | 1126 | 0.025 |
氨酰基-tRNA生物合成 Aminoacyl-tRNA biosynthesis | chx00970 | 14 | 44 | 0.029 |
柠檬酸循环(TCA循环) Citrate cycle (TCA cycle) | chx00020 | 11 | 31 | 0.033 |
阿尔茨海默氏病 Alzheimer's disease | chx05010 | 35 | 164 | 0.033 |
泛素介导的蛋白水解 Ubiquitin mediated proteolysis | chx04120 | 28 | 124 | 0.037 |
味觉转导 Taste transduction | chx04742 | 2 | 35 | 0.022 |
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