Biotechnology Bulletin ›› 2021, Vol. 37 ›› Issue (8): 213-220.doi: 10.13560/j.cnki.biotech.bull.1985.2021-0055
Previous Articles Next Articles
CHEN Jian-jun1(), ZHAO Yi-di1, CAO Xiang-lin2()
Received:
2021-01-13
Online:
2021-08-26
Published:
2021-09-10
Contact:
CAO Xiang-lin
E-mail:cjjjianjun@163.com;hsdcxl@163.com
CHEN Jian-jun, ZHAO Yi-di, CAO Xiang-lin. Comprehensive Transcriptome Analysis of Intestinal Epithelial Cells of Cyprinus carpio Exposed to Lipopolysaccharide[J]. Biotechnology Bulletin, 2021, 37(8): 213-220.
Primer name | Gene bank | Oligonucleotide sequence(5'-3') |
---|---|---|
β-actin | M24113.1 | F:TCAGGACATTGAACCTCACTGTCT R:TAACACCATCACCAGAGTCCATCC |
Ferritin | XM_019064890.1 | F:ACGAGGACAGACTGAAGG R:AGCACAGATGGTCAACGA |
LC3 | XM_019072575.1 | F:GCCATCCGACAGACCCTT R:TGAGCTGCAGTCTACGCC |
Cathepsin | XM_019064744.1 | F:ACCACACGCAACCAACAC R:CTCCACCATTGCAGGAAC |
Casp9 | XM_019066459.1 | F:TGATCCCTCTGCCAGTCC R:TCTCCATCTTGTCGCAGT |
Lamin | XM_019083381.1 | F:TGGCTTTGGCTCAGGCTC R:GTCTCCGTCTCCAGCTGT |
PARP | XM_019073641.1 | F:GGTGCAGTCTCCCATGTT R:TCTGCTCTCCTTTCCCTC |
BNIP3 | XM_019071032.1 | F:CATCAGTGCAGCCTCCTT R:TGTTCCGCTTTGGCTGTT |
ULK1 | XM_019089282.1 | F:AGGGAAGCGGAAAGAGGA R:AATACCACAGCGAAGGCA |
TP53INP2 | XM_019070597.1 | F:AGAGCTGAAGGGACCGAA R:ATGCTGGGGTGCTCGATG |
LAMP | XM_019096275.1 | F:CTGCATTGGCTGACATGG R:AGCTGGAAGGTGTTGAGA |
Table 1 Primers for qRT-PCR
Primer name | Gene bank | Oligonucleotide sequence(5'-3') |
---|---|---|
β-actin | M24113.1 | F:TCAGGACATTGAACCTCACTGTCT R:TAACACCATCACCAGAGTCCATCC |
Ferritin | XM_019064890.1 | F:ACGAGGACAGACTGAAGG R:AGCACAGATGGTCAACGA |
LC3 | XM_019072575.1 | F:GCCATCCGACAGACCCTT R:TGAGCTGCAGTCTACGCC |
Cathepsin | XM_019064744.1 | F:ACCACACGCAACCAACAC R:CTCCACCATTGCAGGAAC |
Casp9 | XM_019066459.1 | F:TGATCCCTCTGCCAGTCC R:TCTCCATCTTGTCGCAGT |
Lamin | XM_019083381.1 | F:TGGCTTTGGCTCAGGCTC R:GTCTCCGTCTCCAGCTGT |
PARP | XM_019073641.1 | F:GGTGCAGTCTCCCATGTT R:TCTGCTCTCCTTTCCCTC |
BNIP3 | XM_019071032.1 | F:CATCAGTGCAGCCTCCTT R:TGTTCCGCTTTGGCTGTT |
ULK1 | XM_019089282.1 | F:AGGGAAGCGGAAAGAGGA R:AATACCACAGCGAAGGCA |
TP53INP2 | XM_019070597.1 | F:AGAGCTGAAGGGACCGAA R:ATGCTGGGGTGCTCGATG |
LAMP | XM_019096275.1 | F:CTGCATTGGCTGACATGG R:AGCTGGAAGGTGTTGAGA |
Sample | CON_1 | CON_2 | CON_3 | LPS_1 | LPS_2 | LPS_3 |
---|---|---|---|---|---|---|
Total reads/M | 52.55 | 54.38 | 50.14 | 50.75 | 54.24 | 51.36 |
Mapped reads/M | 43.22 | 44.32 | 41.35 | 41.31 | 44.24 | 42.00 |
Mapped ratio/% | 82.25 | 81.50 | 82.48 | 81.39 | 81.57 | 81.78 |
Clean bases/G | 7.56 | 7.72 | 7.25 | 7.18 | 7.72 | 7.34 |
Q30/% | 93.88 | 93.35 | 93.56 | 94.00 | 93.89 | 93.83 |
GC/% | 46.91 | 46.27 | 46.45 | 46.50 | 47.62 | 47.38 |
Table 2 Quality analysis of transcriptome data
Sample | CON_1 | CON_2 | CON_3 | LPS_1 | LPS_2 | LPS_3 |
---|---|---|---|---|---|---|
Total reads/M | 52.55 | 54.38 | 50.14 | 50.75 | 54.24 | 51.36 |
Mapped reads/M | 43.22 | 44.32 | 41.35 | 41.31 | 44.24 | 42.00 |
Mapped ratio/% | 82.25 | 81.50 | 82.48 | 81.39 | 81.57 | 81.78 |
Clean bases/G | 7.56 | 7.72 | 7.25 | 7.18 | 7.72 | 7.34 |
Q30/% | 93.88 | 93.35 | 93.56 | 94.00 | 93.89 | 93.83 |
GC/% | 46.91 | 46.27 | 46.45 | 46.50 | 47.62 | 47.38 |
Gene name | Gene description | LPS -vs- CON Log2(fold change) | |
---|---|---|---|
自噬 | LC3 | 微管相关蛋白轻链3 | 2.111361109 |
BNIP3 | B淋巴细胞瘤-2基因/腺病毒E1B相互作用蛋白3 | 3.959358016 | |
ULK1 | 自噬启动激酶ULK1 | 1.590396387 | |
TP53INP2 | 肿瘤蛋白p53诱导核蛋白2 | 3.655351829 | |
LAMP | 溶酶体相关膜蛋白 | 3.987927168 | |
ATG16 | 自噬相关蛋白16 | 1.900464326 | |
凋亡 | Casp9 | 半胱氨酸天冬氨酸蛋白酶 | 3.774933444 |
Cathepsin | 组织蛋白酶 | 2.158941208 | |
Gadd45 | 生长阻滞和DNA损伤诱导蛋白45 | 2.436517227 | |
PARP | 多聚ADP-核糖聚合酶 | -3.684498174 | |
Lamin | 核纤层蛋白 | -4.006426269 | |
AP-1 | 激活蛋白1 | 2.264738712 | |
细胞周期 | PCNA | 增殖细胞核抗原 | -2.80580447 |
Cdc14 | 细胞分裂周期蛋白 | -1.920565533 | |
CycB | 细胞周期调节蛋白B | -3.421463768 | |
CDK2 | 细胞周期蛋白依赖性激酶2 | -2.038135129 | |
MCM2 | 微染色体维持蛋白2 | -4.143929793 | |
PLK1 | 丝氨酸/苏氨酸蛋白激酶PLK1 | -3.602036014 | |
TGF-β | 转化生长因子-β | -2.509819643 |
Table 3 Differentially expressed genes of autophagy,apoptosis and cell cycle
Gene name | Gene description | LPS -vs- CON Log2(fold change) | |
---|---|---|---|
自噬 | LC3 | 微管相关蛋白轻链3 | 2.111361109 |
BNIP3 | B淋巴细胞瘤-2基因/腺病毒E1B相互作用蛋白3 | 3.959358016 | |
ULK1 | 自噬启动激酶ULK1 | 1.590396387 | |
TP53INP2 | 肿瘤蛋白p53诱导核蛋白2 | 3.655351829 | |
LAMP | 溶酶体相关膜蛋白 | 3.987927168 | |
ATG16 | 自噬相关蛋白16 | 1.900464326 | |
凋亡 | Casp9 | 半胱氨酸天冬氨酸蛋白酶 | 3.774933444 |
Cathepsin | 组织蛋白酶 | 2.158941208 | |
Gadd45 | 生长阻滞和DNA损伤诱导蛋白45 | 2.436517227 | |
PARP | 多聚ADP-核糖聚合酶 | -3.684498174 | |
Lamin | 核纤层蛋白 | -4.006426269 | |
AP-1 | 激活蛋白1 | 2.264738712 | |
细胞周期 | PCNA | 增殖细胞核抗原 | -2.80580447 |
Cdc14 | 细胞分裂周期蛋白 | -1.920565533 | |
CycB | 细胞周期调节蛋白B | -3.421463768 | |
CDK2 | 细胞周期蛋白依赖性激酶2 | -2.038135129 | |
MCM2 | 微染色体维持蛋白2 | -4.143929793 | |
PLK1 | 丝氨酸/苏氨酸蛋白激酶PLK1 | -3.602036014 | |
TGF-β | 转化生长因子-β | -2.509819643 |
[1] |
Chen J, Liu N, Zhang H, et al. The effects of Aeromonas hydrophila infection on oxidative stress, nonspecific immunity, autophagy, and apoptosis in the common carp[J]. Dev Comp Immunol, 2020, 105:103587.
doi: 10.1016/j.dci.2019.103587 URL |
[2] | Rasmussen-Ivey CR, Hossain MJ, Odom SE, et al. Classification of a hypervirulent aeromonas hydrophila pathotype responsible for epidemic outbreaks in warm-water fishes[J]. Front Microbiol, 2016, 18(7):1615. |
[3] | 唐黎标. 鲤鱼养殖的常见病害防治[J]. 渔业致富指南, 2019, 510(6):50-51. |
Tang LB. Common disease control of carp culture[J]. Fisheries Rich Guide, 2019, 510(6):50-51. | |
[4] | Pulido-Salgado M, Vidal-Taboada JM, Barriga GG, et al. RNA-Seq transcriptomic profiling of primary murine microglia treated with LPS or LPS + IFNγ[J]. Sci Rep, 2018, 318(1):16096. |
[5] | Kong S, Zhang YH, Zhang W. Regulation of intestinal epithelial cells properties and functions by amino acids[J]. Biomed Res Int, 2018, 2018:2819154. |
[6] |
Pesonen M, Andersson TB. Fish primary hepatocyte culture;an important model for xenobiotic metabolism and toxicity studies[J]. Aquatic Toxicology, 1997, 37(2/3):253-267.
doi: 10.1016/S0166-445X(96)00811-9 URL |
[7] |
Yin G, Cao L, Xu P, et al. Hepatoprotective and antioxidant effects of glycyrrhiza glabra extract against carbon tetrachloride(CCl4)-Induced hepatocyte damage in common carp(Cyprinus carpio)[J]. Fish Physiol Biochem, 2011, 37:209-216.
doi: 10.1007/s10695-010-9436-1 URL |
[8] |
Wang Z, Gerstein M, Snyder M. RNA-seq:a revolutionary tool for transcriptomics[J]. Nat Rev Genet, 2009, 10(1):57-63.
doi: 10.1038/nrg2484 URL |
[9] |
López-Nieva P, Fernández-Navarro P, Graña-Castro O, et al. Detection of novel fusion-transcripts by RNA-Seq in T-cell lymphoblastic lymphoma[J]. Sci Rep, 2019, 9(1):5179.
doi: 10.1038/s41598-019-41675-3 pmid: 30914738 |
[10] | 吕钧惠, 王悦, 周蕾, 等. 雌二醇暴露中国青鳉原代肝细胞转录组分析[J]. 生态毒理学报, 2021, 15:1-15. |
Lv JH, Wang Y, Zhou L, et al. Transcriptome analysis of Oryzias sinensis primary hepatocytes under the exposure of estradiol[J]. Asian Journal of Ecotoxicology, 2020, 15:1-15. | |
[11] | 岳影星, 杨舟鑫, 卢艳, 等. 脂多糖调控对大鼠心脏微血管内皮细胞的转录组分析[J]. 中华细胞与干细胞杂志, 2020, 10(6):328-335. |
Yue XX, Yang ZX, Lu Y, et al. Transcriptomic characteristics of lipopolysaccharide-induced cardiac microvascular endothelial cells[J]. Chin J Cell Stem Cell, 2020, 10(6):328-335. | |
[12] |
Kim D, Langmead B, Salzberg SL. HISAT:a fast spliced aligner with low memory requirements[J]. Nat Meth, 2015, 12(4):357.
doi: 10.1038/nmeth.3317 URL |
[13] |
Roberts A, Trapnell C, Donaghey J, et al. Improving RNA-Seq expression estimates by correcting for fragment bias[J]. Genome Biology, 2011. DOI: 10.1186/gb-2011-12-3-r22.
doi: 10.1186/gb-2011-12-3-r22 |
[14] | Anders S, Huber W. Differential expression of RNA-Seq data at the gene level-the DESeq package[J]. European Molecular Biology Laboratory, 2012. |
[15] |
Kanehisa M, Araki M, Goto S, et al. KEGG for linking genomes to life and the environment[J]. Nucleic Acids Research, 2008, 36:480-484.
pmid: 18077471 |
[16] |
Chai L, Yang Y, Yang H, et al. Transcriptome analysis of genes expressed in the earthworm Eisenia fetida in response to cadmium exposure[J]. Chemosphere, 2020, 240:124902.
doi: 10.1016/j.chemosphere.2019.124902 URL |
[17] |
Satsu H. Molecular and cellular studies on the absorption, function, and safety of food components in intestinal epithelial cells[J]. Biosci Biotechnol Biochem, 2017, 81(3):419-425.
doi: 10.1080/09168451.2016.1259552 URL |
[18] |
Biswas G, Korenaga H, Takayama H, et al. Cytokine responses in the common carp, Cyprinus carpio L. treated with baker’s yeast extract[J]. Aquaculture, 2012, 356-357:169-175.
doi: 10.1016/j.aquaculture.2012.05.019 URL |
[19] |
Low C, Wadsworth S, Burrells C, et al. Expression of immune genes in turbot(Scophthalmus maximus)fed a nucleotide-supplemented diet[J]. Aquaculture, 2003, 221(1-4):23-40.
doi: 10.1016/S0044-8486(03)00022-X URL |
[20] |
Grayfer L, Belosevic M. Molecular characterization, expression and functional analysis of goldfish(Carassius aurutus L.)interferon gamma[J]. Dev Comp Immunol, 2009, 33(2):235-246.
doi: 10.1016/j.dci.2008.09.001 pmid: 18831986 |
[21] |
Salvador JM, Brown-Clay JD, Fornace AJ Jr. Gadd45 in stress signaling, cell cycle control, and apoptosis[J]. Adv Exp Med Biol, 2013, 793:1-19.
doi: 10.1007/978-1-4614-8289-5_1 pmid: 24104470 |
[22] |
Zhan Q, Antinore MJ, Wang XW, et al. Association with Cdc2 and inhibition of Cdc2/Cyclin B1 kinase activity by the p53-regulated protein Gadd45[J]. Oncogene, 1999, 18(18):2892-2900.
pmid: 10362260 |
[23] |
Dong ML, Zhu YC, Hopkins JV. Oil A induces apoptosis of pancreatic cancer cells via caspase activation, redistribution of cell cycle and GADD expression[J]. World J Gastroenterol, 2003, 9(12):2745-2750.
doi: 10.3748/wjg.v9.i12.2745 URL |
[24] |
Du WW, Yang W, Liu E, et al. Foxo3 circular RNA retards cell cycle progression via forming ternary complexes with p21 and CDK2[J]. Nucleic Acids Res, 2016, 44(6):2846-2858.
doi: 10.1093/nar/gkw027 URL |
[25] |
Pietenpol JA, Stewart ZA. Cell cycle checkpoint signaling:cell cycle arrest versus apoptosis[J]. Toxicology, 2002, 181-182:475-481.
pmid: 12505356 |
[26] |
Lamkanfi M. Caspases in cell death, inflammation, and disease[J]. Immunity, 2019, 50(6):1352-1364.
doi: 10.1016/j.immuni.2019.05.020 URL |
[27] |
Okinaga T, Kasai H, Tsujisawa T, et al. Role of caspases in cleavage of lamin A/C and PARP during apoptosis in macrophages infected with a periodontopathic bacterium[J]. J Med Microbiol, 2007, 56:1399-1404.
doi: 10.1099/jmm.0.47193-0 URL |
[28] |
Yang Y, Dong F, Liu X, et al. Crosstalk of oxidative damage, apoptosis, and autophagy under endoplasmic reticulum(ER)stress involved in thifluzamide-induced liver damage in zebrafish(Danio rerio)[J]. Environ Pollut, 2018, 243:1904-1911.
doi: S0269-7491(18)32400-X pmid: 30408879 |
[29] | Zhang Y, Liu D, et al. HIF-1α/BNIP3 signaling pathway-induced-autophagy plays protective role during myocardial ischemia-reperfusion injury[J]. Biom Phar, 2019, 120:109464. |
[30] |
Zhu Y, Ji JJ, Yang R, et al. Lactate accelerates calcification in VSMCs through suppression of BNIP3-mediated mitophagy[J]. Cell Signal, 2019, 58:53-64.
doi: S0898-6568(19)30049-X pmid: 30851408 |
[31] |
You Z, Xu Y, Wan W, et al. TP53INP2 contributes to autophagosome formation by promoting LC3-ATG7 interaction[J]. Autophagy, 2019, 15(8):1309-1321.
doi: 10.1080/15548627.2019.1580510 URL |
[32] |
Huang R, Liu W. Identifying an essential role of nuclear LC3 for autophagy[J]. Autophagy, 2015, 11(5):852-853.
doi: 10.1080/15548627.2015.1038016 pmid: 25945743 |
[33] |
Singh PK, Kumar R, Sharma A, et al. Podophyllum hexandrum fraction(REC-2006)shows higher radioprotective efficacy in the p53-carrying hepatoma cell line:a role of cell cycle regulatory proteins[J]. Integr Cancer Ther, 2009, 8(3):261-272.
doi: 10.1177/1534735409343589 URL |
[34] |
Reynaud K, Driancourt MA. Oocyte attrition[J]. Mol Cell Endocrinol, 2000, 163(1-2):101-108.
pmid: 10963881 |
[35] |
Xing Y, Li J, Li SP, et al. MiR-27a-5p regulates apoptosis of liver ischemia-reperfusion injury in mice by targeting Bach1[J]. J Cell Biochem, 2018, 119(12):10376-10383.
doi: 10.1002/jcb.27383 pmid: 30145824 |
[1] | XIONG He-li, SHA Qian, LIU Shao-na, XIANG De-cai, ZHANG Bin, ZHAO Zhi-yong. Application of Single-cell Transcriptome Sequencing in Animals [J]. Biotechnology Bulletin, 2022, 38(3): 226-233. |
[2] | KOU Jia-yi, WANG Yu-ling, ZENG Rui-lin, LAN Dao-liang. Application of Single-cell Transcriptome Sequencing in Mammalian [J]. Biotechnology Bulletin, 2022, 38(11): 41-48. |
[3] | XU Yuan-yuan, ZHAO Guo-chun, HAO Ying-ying, WENG Xue-huang, CHEN Zhong, JIA Li-ming. Reference Genes Selection and Validation for RT-qPCR in Sapindus mukorossi [J]. Biotechnology Bulletin, 2022, 38(10): 80-89. |
[4] | HUANG Bao-song, LI Jin-feng, ZHANG Ye, CAO Dan-yu, LU Xiao-ying, GHEN Gang, WANG Zhong-liang. Cloning and Expression Analysis of Prolactin Receptor 1 in Rachycentron canadum at Different Water Salinities [J]. Biotechnology Bulletin, 2020, 36(3): 183-192. |
[5] | MA Yan-jun, DUAN Hui-rong, WEI Jia, RICHARD John Tiika, SHAN Li-shan, MA Rui. Transcriptome Sequencing Analysis of Lycium ruthenicum Murr. Under NaCl Stress [J]. Biotechnology Bulletin, 2020, 36(2): 100-109. |
[6] | KONG Chun-yan, CHEN Yong-kun, WANG Sha-sha, HAO Da-hai, YANG Yu, GONG Ming. Screening and Comparison of Reference Genes for microRNA Quantitative Real-time PCR in Jatropha curcas Under Chilling Stress [J]. Biotechnology Bulletin, 2019, 35(7): 25-32. |
[7] | ZHAO Yang-yang, GUO Yu-xiao, ZHANG Ling-yun. Transcriptome Sequencing and Analysis of Xanthoceras sorbifolia Bunge Fruit [J]. Biotechnology Bulletin, 2019, 35(6): 24-31. |
[8] | ZHANG Zhao-yang, PANG Jun-ling, HAN Mei, LENG Peng-fei, ZHAO Jun. Characterization of the Salt Tolerance of Transgenic Maize Line Expressing ABP9 [J]. Biotechnology Bulletin, 2019, 35(5): 48-57. |
[9] | GENG Hui-jun, ZOU Wei, CUI Hui-jing, LI Xiao-yu, WANG Li-li, XU Yong-ping. Safety Evaluation of Staphylococcus aureus Bacteriophage Based on Transcriptome [J]. Biotechnology Bulletin, 2019, 35(12): 64-75. |
[10] | DUAN Min-jie, YI Hong-wei, WANG Jin, WU Zheng. Cloning and Expression Analysis of the Pear Black Spot Resistant Gene PpEMS1 [J]. Biotechnology Bulletin, 2019, 35(11): 16-21. |
[11] | LIU Si-jia, TIAN Fei, ZHANG Cun-fang, QIAO Zhi-gang, ZHAO Kai. Transcriptome Sequencing and Analysis of Hepatopancreas from Carps Under Cold Stress [J]. Biotechnology Bulletin, 2018, 34(11): 168-178. |
[12] | LIU Wen-rong ,DING Ruo-fan, ZHANG Yi-ming ,LI Yu-peng, LI Ling ,GUO Zhi-yun. Transcriptome Sequencing Analysis of Hepatocellular Carcinoma HepG2 Cells Induced by Antitumor Peptide 9R-P201 [J]. Biotechnology Bulletin, 2017, 33(7): 210-215. |
[13] | HAO Wei-wei, GAO Chang-fu, QIU Xue-mei, JIANG Zhi-qiang, WANG Xiu-li. The Expression of Transcription Factor GATA4 Gene in Takifugu rubripes [J]. Biotechnology Bulletin, 2016, 32(6): 155-160. |
[14] | LUO Yan,LIU Xiao-gang,ZHOU Zhi-qin. Research Progress on Methods for Isolating the Gene of Plant Glycosyltransferase,and Its Biological Functions [J]. Biotechnology Bulletin, 2016, 32(12): 34-39. |
[15] | QIAN Jing-hua, ZHOU Bu-jin, KONG Xiang-jun, LI Zeng-qiang, SHI Qi-qi, LIAO Xiao-fang, ZHOU Rui-yang, CHEN Peng. Cloning,Expression Analysis and Vector Construction of MYB21 Gene in Kenaf [J]. Biotechnology Bulletin, 2016, 32(11): 170-179. |
Viewed | ||||||
Full text |
|
|||||
Abstract |
|
|||||