大白猪和莱芜猪肌内脂肪组织circRNAs的鉴定与分析

doi:10.11843/j.issn.0366-6964.2018.07.003

Abstract

Abstract:

The purpose of this study was to explore circRNAs potential role in adipose tissue, which would lay a basis for further understanding the regulation role of circRNA in fat deposition and lipid metabolism. In this study, we explored the expression profile of circRNAs in intramuscular adipose tissue from Large White and Laiwu pigs using RNA-seq and bioinformatics. The target genes to the differentially expressed circRNAs were predicted by miRanda and Targetscan. The enrichment analysis of target genes was performed by GO and KEGG. The results showed that 181 differentially expressed circRNAs were identified. Among them, 102 were up-regulated expression in intramuscular adipose tissue of Laiwu pigs, and 79 were down-regulated. GO and KEGG enrichment analysis of target genes of ssc_circ_0002807 and ssc_circ_0009352 with more miRNA binding sites were peformed. The target genes were found to be enriched in the biological process involved in lipid metabolism such as phospholipid homeostasis, cholesterol homeostasis, etc. And ssc_circ_0002807, ssc_circ_0005382, ssc_circ_0009172 and ssc_circ_0004824 were also confirmed by qRT-PCR. It is infered that ssc_circ_0002807 and ssc_circ_0009352 may regulate fat deposition and metabolism.

Key words: circRNA, intramuscular fat, fat deposition, lipid metabolism, pig

CLC Number:

S828.2

LI Ai, ZHANG Xiu-xiu, HUANG Wan-long, XIE Ling-li, MIAO Xiang-yang. Identification and Analysis of circRNAs in Intramuscular Adipose Tissues between Large White and Laiwu Pigs[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2018, 49(7): 1343-1353.

References

[1] 王蜀金,郭春华.全球猪肉市场纵览:附加生产力刺激世界猪肉产量[J].猪业科学,2014(12):24-25.
WANG S J,GUO C H.Global pork market overview:additional productivity stimulates world pork production[J].Swine Industry Science,2014(12):24-25. (in Chinese)
[2] DODSON M V,JIANG Z H,CHEN J,et al.Allied industry approaches to alter intramuscular fat content and composition in beef animals[J].J Food Sci,2010,75(1):R1-R8.
[3] LISTRAT A,LEBRET B,LOUVEAU I,et al.How muscle structure and composition influence meat and flesh quality[J].Sci World J,2016,2016:3182746.
[4] 尹靖东,李德发.猪肉质形成的分子机制与营养调控[J].动物营养学报,2014,26(10):2979-2985.
YIN J D,LI D F.Molecular mechanism underlying meat quality formation and its nutritional regulation in pigs[J].Chinese Journal of Animal Nutrition,2014,26(10):2979-2985. (in Chinese)
[5] LUKIW W J.Circular RNA (circRNA) in Alzheimer's disease (AD)[J]. Front Genet,2013,4:307.
[6] BACHMAYR-HEYDA A,REINER A T,AUER K,et al.Correlation of circular RNA abundance with proliferation-exemplified with colorectal and ovarian cancer,idiopathic lung fibrosis,and normal human tissues[J].Sci Rep,2015,5:8057.
[7] QIN M L,LIU G,HUO X S,et al.Hsa_circ_0001649:A circular RNA and potential novel biomarker for hepatocellular carcinoma[J].Cancer Biomark,2016,16(1):161-169.
[8] 姜隽,杨悠,姜睿,等.环状RNA对基因的调控作用及其与心血管疾病的关系[J].中华心血管病杂志,2016,44(4):364-366.
JIANG J,YANG Y,JIANG R,et al.Regulating mechanisms of circRNA and their relationship with cardiovascular diseases[J].Chinese Journal of Cardiology,2016,44(4):364-366. (in Chinese)
[9] LU D,XU A D.Mini review:circular RNAs as potential clinical biomarkers for disorders in the central nervous system[J].Front Genet,2016,7:53.
[10] XIE H J,REN X L,XIN S N,et al.Emerging roles of circRNA_001569 targeting miR-145 in the proliferation and invasion of colorectal cancer[J].Oncotarget,2016,7(18):26680-26691.
[11] DANG Y J,YAN L Y,HU B Q,et al.Tracing the expression of circular RNAs in human pre-implantation embryos[J].Genome Biol,2016,17:130.
[12] HANSEN T B,JENSEN T I,CLAUSEN B H,et al.Natural RNA circles function as efficient microRNA sponges[J].Nature,2013,495(7441):384-388.
[13] HANSEN T B,KJEMS J,DAMGAARD C K.Circular RNA and miR-7 in cancer[J].Cancer Res,2013,73(18):5609-5612.
[14] 李美航,仇杨,刘帅,等.过表达miR-103促进猪前体脂肪细胞分化[J].生物工程学报,2012,28(8):927-936.
LI M H,QIU Y,LIU S,et al.Over-expressed miR-103 promotes porcine adipocyte differentiation[J].Chinese Journal of Biotechnology,2012,28(8):927-936. (in Chinese)
[15] LI H X,ZHANG Z,ZHOU X,et al.Effects of microRNA-143 in the differentiation and proliferation of bovine intramuscular preadipocytes[J].Mol Biol Rep,2010,38(7):4273-4280.
[16] MIGDAL L,KOZIOL K,PALKA S,et al.Mutations in leptin (LEP) gene are associated with carcass and meat quality traits in crossbreed rabbits[J].Anim Biotechnol,2017,29(2):153-159.
[17] SERāO N V,VERONEZE R,RIBEIRO A M,et al.Candidate gene expression and intramuscular fat content in pigs[J].J Anim Breed Genet,2011,128(1):28-34.
[18] WON S,JUNG J,PARK E,et al.Identification of genes related to intramuscular fat content of pigs using genome-wide association study[J].Asian-Australas J Anim Sci,2018,31(2):157-162.
[19] 曾勇庆,王根林,魏述东,等.含不同比例莱芜猪血缘杂交猪胴体品质及肉质特性的研究[J].遗传,2005,27(1):65-69.
ZENG Q Y,WANG G L,WEI S D,et al.Studies on carcass and meat quality performance of crossbred pigs with graded proportions of Laiwu Black genes[J].Hereditas,2005,27(1):65-69. (in Chinese)
[20] 于永生,张志彬,李娜,等.不同日龄东北民猪与大白猪背最长肌游离水和肌内脂肪含量的测定[J].养猪,2015(1):47-48.
YU Y S,ZHANG Z B,LI N,et al.Determination of the maximum muscle free water and intramuscular fat content of Northeast China pigs and big white pigs with different age[J].Swine Production,2015(1):47-48. (in Chinese)
[21] SUN W X,WANG H H,JIANG B C,et al.Global comparison of gene expression between subcutaneous and intramuscular adipose tissue of mature Erhualian pig[J].Genet Mol Res,2013,12(4):5085-5101.
[22] GARDON A,HANNON G J.FASTX-TOOLKIT.FASTQ/A short-reads pre-processing tools[EB/OL].(2010).http://hannonlab.cshl.edu/fastx_toolkit.
[23] LI H.Aligning sequence reads,clone sequences and assembly contigs with BWA-MEM[C].arXiv preprint arXiv:1303.3997,2013.
[24] GAO Y,WANG J F,ZHAO F Q.CIRI:an efficient and unbiased algorithm for de novo circular RNA identification[J].Genome Biol,2015,16:4.
[25] LOVE M I,HUBER W,ANDERS S.Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2[J].Genome Biol,2014,15(12):550.
[26] ENRIGHT A J,JOHN B,GAUL U,et al.microRNA targets in Drosophila[J].Genome Biol,2003,5(1):R1.
[27] PASQUINELLI A E.microRNAs and their targets:recognition,regulation and an emerging reciprocal relationship[J].Nat Rev Genet,2012,13(4):271-282.
[28] REHMSMEIER M,STEFFEN P,HÖECHSMANN M,et al.Fast and effective prediction of microRNA/target duplexes[J].RNA,2004,10(10):1507-1517.
[29] KERTESZ M,IOVINO N,UNNERSTALL U,et al.The role of site accessibility in microRNA target recognition[J].Nat Genet,2007,39(10):1278-1284.
[30] 黄万龙.两品种猪不同脂肪组织中长链非编码RNA的鉴定及其功能分析[D].北京:中国农业科学院,2017.
HUANG W L.Identification and functional analysis of long non-coding RNA in distinct adipose tissues from two pig breeds[D].Beijing:Chinese Academy of Agricultural Sciences, 2017. (in Chinese)
[31] SMOOT M E,ONO K,RUSCHEINSKI J,et al.Cytoscape 2.8:new features for data integration and network visualization[J].Bioinformatics,2011,27(3):431-432.
[32] BINDEA G,MLECNIK B,HACKL H,et al.ClueGO:a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks[J].Bioinformatics,2009,25(8):1091-1093.
[33] KANEHISA M,ARAKI M,GOTO S,et al.KEGG for linking genomes to life and the environment[J].Nucleic Acids Res,2008,36(Database issue):D480-D484.
[34] JECK W R,SORRENTINO J A,WANG K,et al.Circular RNAs are abundant,conserved,and associated with ALU repeats[J].RNA,2013,19(2):141-157.
[35] CORTÉS-LÓPEZ M,MIURA P.Emerging functions of circular RNAs[J].Yale J Biol Med,2016,89(4):527-537.
[36] WANG N D,FINEGOLD M J,BRADLEY A,et al.Impaired energy homeostasis in C/EBPα knockout mice[J].Science,1995,269(5227):1108-1112.
[37] LOBO S,WICZER B M,BERNLOHR D A.Functional analysis of long-chain acyl-CoA synthetase 1 in 3T3-L1 adipocytes[J].J Biol Chem,2009,284(27):18347-18356.
[38] RUBINOW K B,WALL V Z,NELSON J,et al.Acyl-CoA synthetase 1 is induced by gram-negative bacteria and lipopolysaccharide and is required for phospholipid turnover in stimulated macrophages[J].J Biol Chem,2013,288(14):9957-9970.
[39] ZHAO X M,BAI X Y,GUAN L Y,et al.microRNA-4331 promotes TGEV-induced mitochondrial damage via targeting RB1,up-regulating IL1RAP,and activating p38 MAPK pathway in vitro[J].Mol Cell Proteomics,2018,17(2):190-204.
[40] ZHAO Q,LU Y Z,YU H Y,et al.Low magnitude high frequency vibration promotes adipogenic differentiation of bone marrow stem cells via P38 MAPK signal[J].PLoS One,2017,12(3):e0172954.
[41] SQUILLACE N,BRESCIANI E,TORSELLO A,et al.Changes in subcutaneous adipose tissue microRNA expression in HIV-infected patients[J].J Antimicrob Chemother,2014,69(11):3067-3075.
[42] CHEN Y H,LI C,TAN C L,et al.Circular RNAs:a new frontier in the study of human diseases[J].J Med Genet,2016,53(6):359-365.
[43] WANG S X,SONG K X,SRIVASTAVA R,et al.Nonalcoholic fatty liver disease induced by noncanonical Wnt and its rescue by Wnt3a[J].FASEB J,2015,29(8):3436-3445.
[44] KLÖTING N,BLVHER M.Adipocyte dysfunction,inflammation and metabolic syndrome[J].Rev Endocr Metab Disord,2014,15(4):277-287.

Identification and Analysis of circRNAs in Intramuscular Adipose Tissues between Large White and Laiwu Pigs

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	WANG Jing, HUA Liushuai, CHEN Junfeng, ZHANG Jiaqing, REN Qiaoling, BAI Hongjie, GUO Hongxia, XU Zhaoxue, XING Baosong, BAI Xianxiao, CAO Hai. Effect of Castration on Gene Expression in Longissimus dorsi Muscle of Huainan Male Pig by Transcriptome Analysis [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(9): 1746-1758.
[2]	GUO Xiaohong, GUO Yulong, LIU Yadan, LIU Juan, SHI Wenqian, DONG Lei, CAI Chunbo, CAO Guoqing, LI Bugao, GAO Pengfei. Characteristics of Intestinal Microflora of Colon at Different Developmental Stages in Piglets [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(9): 1759-1774.
[3]	LIU Guoqing, ZHANG Liyang, MA Xuelian, WANG Liangzhi, LIU Dongyuan, XING Guanzhong, YANG Liu, LI Sufen, LIAO Xiudong, Lü Lin, LUO Xugang. A Survey on Distribution of Phosphorus Contents in Feedstuffs for Livestock and Poultry in China [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(9): 1841-1848.
[4]	WANG Changying, LU Hongyu, SUI Minmin, WANG Yanchao, LIU Gen, SUN Yi, JIANG Yunliang. Effect of SERPINC1 Gene on PCV2 Replication and Its Transcriptional Regulation [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(8): 1545-1553.
[5]	LI Zhiqiang, YAN Shuping, JI Xiaoxia, WANG Kai, ZHANG Yuanshu. Distribution and Expression of Angiotensin-Converting Enzyme 2 (ACE2) in the Jejunum of Piglets and Its Relationship with Substance Transport [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(8): 1676-1684.
[6]	WANG Changying, LU Hongyu, SUI Minmin, WANG Yanchao, LIU Gen, SUN Yi, JIANG Yunliang. Effect of SERPINC1 Gene on PCV2 Replication and Its Transcriptional Regulation [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(8): 1545-1553.
[7]	LI Zhiqiang, YAN Shuping, JI Xiaoxia, WANG Kai, ZHANG Yuanshu. Distribution and Expression of Angiotensin-Converting Enzyme 2 (ACE2) in the Jejunum of Piglets and Its Relationship with Substance Transport [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(8): 1676-1684.
[8]	LIU Zongli, CHEN Tao, YANG Dandan, CUI Jingxiang, LI Chuanhao, ZENG Yongqing, CHEN Wei. Molecular Cloning, Bioinformatics Analysis and Transcriptional Activity of Promoter of Nuclear Factor Erythroid 2-related Factor (Nrf2) Gene in Pig [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(7): 1328-1339.
[9]	GONG Jianfei, YUE Jingwei, ZHAO Lingling, LIU Yunpeng, WANG Lixian, LIU Xin, SUN Jinhai. Tissue Expression Profiles of HMGA1 Gene in Pigs and Its Association with Backfat Thickness [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(7): 1340-1346.
[10]	WANG Ya, ZHAO Feng, ZHANG Hu, DANG Fangkun, GAO Qingtao, YU Yao, DU Zhongyuan, SA Renna. Study on the Variation of Digestive Enzyme Activities Depending on Digestion Time in the Simulated Digestion for Pigs [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(7): 1412-1423.
[11]	WANG Ya, ZHAO Feng, ZHANG Hu, DANG Fangkun, GAO Qingtao, YU Yao, DU Zhongyuan, SA Renna. Study on the Variation of Digestive Enzyme Activities Depending on Digestion Time in the Simulated Digestion for Pigs [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(7): 1412-1423.
[12]	GONG Jianfei, YUE Jingwei, ZHAO Lingling, LIU Yunpeng, WANG Lixian, LIU Xin, SUN Jinhai. Tissue Expression Profiles of HMGA1 Gene in Pigs and Its Association with Backfat Thickness [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(7): 1340-1346.
[13]	LIU Zongli, CHEN Tao, YANG Dandan, CUI Jingxiang, LI Chuanhao, ZENG Yongqing, CHEN Wei. Molecular Cloning, Bioinformatics Analysis and Transcriptional Activity of Promoter of Nuclear Factor Erythroid 2-related Factor (Nrf2) Gene in Pig [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(7): 1328-1339.
[14]	REN Ling, HU Xin, XING Yishen, WANG Yahui, LI Junya, ZHANG Lupei. Effects of S100a10 on White and Brown Adipogenic Differentiation of Mice Preadipocytes [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(6): 1171-1178.
[15]	REN Ling, HU Xin, XING Yishen, WANG Yahui, LI Junya, ZHANG Lupei. Effects of S100a10 on White and Brown Adipogenic Differentiation of Mice Preadipocytes [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(6): 1171-1178.