冷应激后民猪背脂中差异lncRNA的筛选与分析

doi:10.11843/j.issn.0366-6964.2021.04.009

Abstract

Abstract: The study aimed to analyze the effect of cold stress on the expression of lncRNA in adipose tissue of pigs, and discuss the effects of lncRNA and their target genes change on fat meta-bolism and body. In this study, six 6-month-old female Min pigs were randomly divided into two groups. The first group was raised in a normal house and the temperature was controlled at (18±2) ℃ and set as the control group. The second group was raised in an outdoor semi-convertible house with the temperature controlled at (-18±5) ℃ and set as the experimental group. After 24 h of treatment, the subcutaneous fat of back was taken as the experimental material after slaughter. lncRNAs and their target genes induced by low temperature were screened out through transcriptomic sequencing, and the biological function analysis of the differentially expressed genes was carried out, the regulatory network between them was constructed. The results showed that, 166 differentially expressed lncRNAs and 269 genes were induced by cold stress, of which only 2 were known lncRNAs. Among the differentially expressed genes, some genes were related to immune system, such as interferon stimulating genes, DHX58, PTX3 and OASL, some genes were related to respiration, oxidative stress and blood circulation, such as KCNK3, CCDC38, GAS2L2, KNDC1, LIPG and C1QL3, and some genes were related to lipid metabolism, such as ANGPTL4, KLF11, NUPR1 and HERC5, these genes were all significantly up-regulated. However, some genes related to nervous system, such as SLIT1, MAP6, TREM2 and IRFN2, were significantly down-regulated. The differentially expressed genes mainly involved in defense response, response to biological stimulation and response to virus. One hundred and forty four lncRNAs were found coexpression with 208 target genes by correlation coefficient analysis, the main accommodation mode between them was trans-regulation, there was a complex regulatory relationship between them. The screened target genes were significantly enriched in the ribosome biogenesis in eukaryotes and basal cell carcinoma pathways. It is speculated that the innate immune system, respiration, oxidative stress, blood circulation and sensitivity of nervous system were all affected by cold stress, and lipid metabolism was changed.

Key words: Min pig, lncRNA, mRNA, cold stress, regulatory network

CLC Number:

S828.2

MA Junjie, WANG Liang, LIU Di, ZHANG Dongjie, YANG Xiuqin. Screening and Analysis of Differentially Expressed lncRNA in Min Pig Back Fat after Cold Stress[J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(4): 932-942.

References 40

[1]	IK HEIMO T M.Cardiovascular diseases,cold exposure and exercise[J].Temperature,2018,5(2):123-146.
[2]	JONES D M,BAILEY S P,ROELANDS B,et al.Cold acclimation and cognitive performance:a review[J].Auton Neurosci, 2017,208:36-42.
[3]	XU D D,ZHANG Y,WANG B,et al.Acute effects of temperature exposure on blood pressure:an hourly level panel study[J].Environ Int,2019,124:493-500.
[4]	QIANG L,WANG L H,KON N,et al.Brown remodeling of white adipose tissue by SirT1-dependent deacetylation of Pparγ[J].Cell,2012,150(3):620-632.
[5]	BAUDIER J,GENTIL B J.The S100B protein and partners in adipocyte response to cold stress and adaptive thermogenesis:facts,hypotheses,and perspectives[J].Biomolecules,2020,10(6):843.
[6]	BARTNESS T J,RYU V.Neural control of white,beige and brown adipocytes[J].Int J Obes Suppl,2015,5(S1):S35-S39.
[7]	JIANG H C,DING X F,CAO Y,et al.Dense intra-adipose sympathetic arborizations are essential for cold-induced beiging of mouse white adipose tissue[J].Cell Metab,2017,26(4):686-692.e3.
[8]	BACHMAN E S,DHILLON H,ZHANG C Y,et al.βAR signaling required for diet-induced thermogenesis and obesity resistance[J]. Science,2002,297(5582):843-845.
[9]	BERG F,GUSTAFSON U,ANDERSSON L.The uncoupling protein 1 gene (UCP1) is disrupted in the pig lineage:a genetic explanation for poor thermo-regulation in piglets[J].PLoS Genet,2006,2(8):e129.
[10]	LIN J,CAO C W,TAO C,et al.Cold adaptation in pigs depends on UCP3 in beige adipocytes[J].J Mol Cell Biol,2017,9(5):364-375.
[11]	HOU L J,XIE M Y,CAO L B,et al.Browning of pig white preadipocytes by co-overexpressing pig PGC-1α and mice UCP1[J]. Cell Physiol Biochem,2018,48(2):556-568.
[12]	刘自广,刘娣,王文涛,等.寒冷条件下民猪耐寒表现的比较研究[J].黑龙江畜牧兽医,2019(16):60-62,179.LIU Z G,LIU D,WANG W T,et al.A comparative study on the cold-resistant performance of civilian pigs under cold conditions[J].Heilongjiang Animal Science and Veterinary Medicine,2019(16):60-62,179.(in Chinese)
[13]	TRAPNELL C,WILLIAMS B A,PERTEA G,et al.Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation[J].Nat Biotechnol,2010,28(5):511-515.
[14]	HUANG W L,ZHANG X X,LI A,et al.Genome-wide analysis of mRNAs and lncRNAs of intra-muscular fat related to lipid metabolism in two pig breeds[J].Cell Physiol Biochem,2018,50(6):2406-2422.
[15]	RAN M L,CHEN B,LI Z,et al.Systematic identification of long noncoding RNAs in immature and mature porcine testes[J].Biol Reprod,2016,94(4):77.
[16]	WANG F,LI L P,XU H M,et al.Characteristics of long non-coding RNAs in the Brown Norway rat and alterations in the Dahl salt-sensitive rat[J].Sci Rep,2014,4:7146.
[17]	CABILI M N,TRAPNELL C,GOFF L,et al.Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses[J].Genes Dev,2011,25(18):1915-1927.
[18]	SUN L,GOFF L A,TRAPNELL C,et al.Long noncoding RNAs regulate adipogenesis[J].Proc Natl Acad Sci U S A,2013,110(9):3387-3392.
[19]	ALVAREZ-DOMINGUEZ J R,BAI Z Q,XU D,et al.De novo reconstruction of adipose tissue transcriptomes reveals long non-coding RNA regulators of brown adipocyte development[J].Cell Metab,2015,21(5):764-776.
[20]	CUI X W,YOU L H,LI Y,et al.A transcribed ultraconserved noncoding RNA,uc.417,serves as a negative regulator of brown adipose tissue thermogenesis[J].FASEB J,2016,30(12):4301-4312.
[21]	张悫,蔡瑞,庞卫军.长链非编码RNA调控动物脂肪沉积研究进展与趋势[J].家畜生态学报,2020,41(7):1-6.ZHANG Q,CAI R,PANG W J.Progress and tendency in the regulation of animal fat deposition by long non-coding RNA[J].Acta Ecologae Animalis Domastici,2020,41(7):1-6.(in Chinese)
[22]	肖芳,嵇辛勤,李基棕,等.山羊副流感病毒3型感染MDBK细胞和BECs后7种ISGs mRNA变化分析[J].中国预防兽医学报,2019,41(11):1147-1153.XIAO F,JI X Q,LI J Z,et al.Analysis on the change of seven ISGs transcription in MDBK cells and BECs infected with Caprine parainfluenza virus type 3[J].Chinese Journal of Preventive Veterinary Medicine,2019,41(11):1147-1153.(in Chinese)
[23]	LI X Y,HAN C M,WANG Y,et al.Expression patterns and association analysis of the porcine DHX58 gene[J].Anim Genet,2010, 41(5):537-540.
[24]	DAIGO K,HAMAKUBO T.Expression and purification of full-length and domain-fragment recombinant pentraxin 3(PTX3) proteins from mammalian and bacterial cells[J].Methods Mol Biol,2020,2132:65-74.
[25]	李连峰.干扰素诱导的2'-5'寡腺苷酸合成酶样蛋白通过增强MDA5介导的Ⅰ型干扰素信号通路抑制猪瘟病毒复制[D].北京:中国农业科学院哈尔滨兽医研究所,2019.LI L F.Interferon-inducible oligoadenylate synthetase-like protein acts as an antiviral effector against classical swine fever virus via the MDA5-mediated type I interferon-signaling pathway[D].Beijing:Harbin Institute of Veterinary Medicine,Chinese Academy of Agricultural Sciences,2019.(in Chinese)
[26]	张文娟.低温下脂肪细胞免疫相关基因的差异表达及其对贝尔麻痹病因的启示[D].太原:山西医科大学,2019.ZHANG W J.Different immune-related gene expression profiles of hypothermia adipocytes:implications for Bell's Palsy[D]. Taiyuan:Shanxi Medical University,2019.(in Chinese)
[27]	LAMBERT M,CAPUANO V,BOET A,et al.Characterization of Kcnk3-mutated rat,a novel model of pulmonary hypertension[J].Circ Res,2019,125(7):678-695.
[28]	WAIN L V,SAYERS I,ARTIGAS M S,et al.Whole exome re-sequencing implicates CCDC38 and cilia structure and function in resistance to smoking related airflow obstruction[J].PLoS Genet,2014,10(5):e1004314.
[29]	BUSTAMANTE-MARIN X M,YIN W N,SEARS P R,et al.Lack of GAS2L2 causes PCD by impairing cilia orientation and mucociliary clearance[J].Am J Hum Genet,2019,104(2):229-245.
[30]	JI J R,HAO Z X,LIU H L,et al.Effect of KNDC1 overexpression on the senescence of human umbilical vein endothelial cells[J]. Mol Med Rep,2018,17(5):7037-7044.
[31]	LEONHARDT G.LIPG supports adaption to oxidative stress[J].EXCLI J,2019,18:499-500.
[32]	LI A D,TONG L,XU N,et al.miR-124 regulates cerebromicrovascular function in APP/PS1 transgenic mice via C1ql3[J].Brain Res Bull,2019,153:214-222.
[33]	NUMATA M,GELTINK R I K,GROSVELD G C.Establishment of a transgenic mouse to model ETV7 expressing human tumors[J].Transgenic Res,2019,28(1):115-128.
[34]	张彩彩,赵久红,谭晓红,等.siRNA沉默卫星胶质细胞轴突导向因子Slit1对共培养的神经元突起生长的影响[J].海南医学,2018,29(17):2369-2372.ZHANG C C,ZHAO J H,TAN X H,et al.Effect of siRNA-mediated gene silencing of Slit1 in satellite glial cells on growth of neurite[J].Hainan Medical Journal,2018,29(17):2369-2372.(in Chinese)
[35]	CUVEILLIER C,DELAROCHE J,SEGGIO M,et al.MAP6 is an intraluminal protein that induces neuronal microtubules to coil[J].Sci Adv,2020,6(14):eaaz4344.
[36]	FITZ N F,WOLFE C M,PLAYSO B E,et al.Trem2 deficiency differentially affects phenotype and transcriptome of human APOE3 and APOE4 mice[J].Mol Neurodegener,2020,15(1):41.
[37]	LI Y,KIM R,CHO Y S,et al.Lrfn2-mutant mice display suppressed synaptic plasticity and inhibitory synapse development and abnormal social communication and startle response[J].J Neurosci,2018,38(26):5872-5887.
[38]	林嘉颖,袁源,刘新光.磷酸烯醇式丙酮酸羧激酶1(PCK1)的研究进展[J].生命的化学,2019,39(4):637-642.LIN J Y,YUAN Y,LIU X G.The research progress of PCK1[J].Chemistry of Life,2019,39(4):637-642.(in Chinese)
[39]	瞿秋红,夏琴,崔悦悦,等.巴马香猪和杜长大猪的PDK4基因的克隆及组织表达分析[J].基因组学与应用生物学,2020, 39(3):1013-1019.QU Q H,XIA Q,CUI Y Y,et al.Cloning and tissue expression analysis of PDK4 genes in Bama Xiang pig and DLY pig[J]. Genomics and Applied Biology,2020,39(3):1013-1019.(in Chinese)
[40]	ZHAN S Y,DONG Y,ZHAO W,et al.Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat[J]. BMC Genomics,2016,17(1):666.

Screening and Analysis of Differentially Expressed lncRNA in Min Pig Back Fat after Cold Stress

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References 40

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	ZHANG De'an, YANG Ruozhu, LIU Jie, LIU Dewu, DENG Ming, LIU Guangbin, SUN Baoli, GUO Yongqing, LI Yaokun. Expression Analysis of Transcriptome in the Liver of Chuanzhong Black Goats Fed with Silage Neolamarckia Cadamba Substitute for Silage Corn [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(1): 232-244.
[2]	CHEN Xin, QIN Tong. mRNA Vaccine and Its Research Prospect in Zoonotic Diseases [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2732-2742.
[3]	CHEN Songbiao, SHANG Ke, DU Fuxi, YU Zuhua, LI Jing, JIA Yanyan, LIAO Chengshui, ZHANG Chunjie, DING Ke, CHENG Xiangchao. Research Process of Assembly, Structural Features, and Secretion Regulatory Networks of Type VI Secretion System in Salmonella [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2252-2263.
[4]	YANG Chuang, WU Longfei, LIU Guangbin, LI Yaokun, LIU Dewu, SUN Baoli. Expression Profile and Bioinformatics Analysis of lncRNA and Its Associated ceRNA Networks in Longissimus Dorsi from Lufeng Cattle and Leiqiong Cattle [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(5): 1951-1963.
[5]	QIN Xue, SHA Yiwen, YANG Menghao, CAI Rui, PANG Weijun. Advances in Regulation of Non-coding RNA on Mammalian Endometrial Receptivity and Decidualization [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(4): 1347-1358.
[6]	JIA Hongru, YANG Chaoqun, WANG Meng, WU Zhangqing, ZAN Linsen, YANG Wucai. LRTN4RL1-AS Mediates Milk Fat Synthesis in Bovine Mammary Epithelial Cells through miR-27a-3p Targeting PPARγ [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(4): 1465-1477.
[7]	JIN Meilin, LI Taotao, SUN Dongxiao, WEI Caihong. Research Progress of Epigenetic Regulation in Fat Deposition Mechanism of Livestock and Poultry [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(3): 855-867.
[8]	YE Junning, DENG Ming, XUE Huiwen, LIU Guangbin, ZOU Xian, SUN Baoli, GUO Yongqing, LIU Dewu, LI Yaokun. Identification and Analysis of mRNA and lncRNA Affecting Goat Fetal Muscle Development [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(3): 989-1002.
[9]	YANG Guang, XU Jing, LI Xin, HU Debao, GUO Yiwen, DING Xiangbin, GUO Hong, ZHANG Linlin. Effect of Interfering lncbMD on Proliferation and Differentiation of Bovine Skeletal Muscle Satellite Cells [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(3): 1015-1025.
[10]	MENG Zhaoyi, WANG Yunlu, XU Yefen, NIU Jiaqiang, SUOLANG Sizhu, GUO Min, XI Guangyin. Construction of Yak lncRNA ENSBGRT00000000387.1 Lentivirus Vector and Its Effect on Apoptosis of Yak Follicular Granulosa Cells [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(3): 1058-1070.
[11]	YU Zhirui, ZHANG Xu, NIU Shasha, DENG Guangcun, WU Xiaoling. LncRNA NR_003508 Regulates BCG-infected Mouse Macrophages Necrosis by the Sponge Adsorption of miR-483-3p and Targeting MLKL [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(9): 3149-3159.
[12]	ZHANG Dongjie, WANG Liang, MA Hong, LI Zhongqiu, WANG Wentao, LIU Di. Analysis of Transcriptional Regulation in Min Pig Skeletal Muscle under Low Temperature Stress [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(8): 2524-2536.
[13]	LIU Lihua, ZHONG Zhenyu, ZHENG Yujie, WANG Xin. lncRNA EPB41L4A-AS Inhibits the Proliferation of Bovine Mammary Epithelial Cells by Regulating the Expression of ErbB3 Gene [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(7): 2152-2159.
[14]	JIAO Peng, WANG Xingping, WANG Shuzhe, WANG Jinpeng, LUORENG Zhuoma, JIA Li, WEI Dawei, MA Yun. Effect of Differentially Expressed lncRNA BCL2 in Dairy Cow with Mastitis on the Expression of Inflammation and Apoptosis Related mRNA [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(7): 2160-2171.
[15]	ZHANG Hui, PAN Yangyang, WANG Jinglei, ZHANG Rui, HUANG Jiaxin, YU Sijiu, CUI Yan. RBM3 Gene Cloning and Its Expression, Localization in Ovary, Fallopian Tube and Uterus at Different Reproductive Stages of Yak (Bos grunniens) [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(7): 2202-2214.