3个时期牛肌肉组织中长链非编码RNA表达谱的生物信息学分析

doi:10.16431/j.cnki.1671-7236.2019.01.001

Abstract

Abstract:

This study was aimed to analyze the expression profiles of long non-coding RNA (lncRNAs) in bovine muscle tissue from different periods and screen out lncRNAs which might involve in muscle development.The bovine muscle tissue RNA samples from 3-month-old embryos,6-month-old embryos and 9-month-old calf were collected for high-throughput sequencing.The identified lncRNAs were analyzed and filtered with bioinformatics methods,Veen analysis was performed on lncRNAs target gene and three periods differential mRNAs,Go and KEGG enrichment analysis were performed on Veen results to select lncRNAs and target mRNAs which related to muscle development.The results showed that 212 851 novel unannotated lncRNAs were identified by high-throughput sequencing,of which 9 913 were differentially expressed in different periods.These lncRNAs distributed on each chromosome and belonged to four types,which included intergenic,sense strand,antisense strand and bidirectional,and the sense strand lncRNAs had the largest number and the widest distribution range on each chromosome.The structural features analysis revealed that these lncRNAs had the characteristics of short open reading frame,low expression level,weak coding ability,wide distribution and the huge numbers.55 muscle myogenesis related differentially expressed lncRNAs among 3-month-old embryos,6-month-old embryos and 9-month-old calf were screened out by GO and KEGG enrichment analysis,and 38 candidate target mRNAs were also filtered.This study presented the expression pattern of lncRNAs in bovine muscle tissue from three periods by predicting the interaction between lncRNAs and mRNA,and greatly reduced the research range of bovine muscle development related lncRNAs.The study also provided a critical target for revealing the function of bovine muscle development.

Key words: bovine muscle tissue; RNA sequencing; bioinformatics analysis; lncRNAs

CLC Number:

ZHANG Xiaojuan, CHEN Mingming, XIN Xiangbo, LIU Xinfeng, ZHANG Linlin, DING Xiangbin, GUO Hong, LI Xin. Bioinformatics Analysis of Long Non-coding RNA Expression Profiles in Bovine Muscle Tissues from Three Periods[J]. , 2019, 46(1): 1-9.

References

[1] JIN C F,LI Y,DING X B,et al.lnc133b,a novel,long non-coding RNA,regulates bovine skeletal muscle satellite cell proliferation and differentiation by mediating miR-133b[J].Gene,2017,30(630):35-43.
[2] YUE Y,JIN C,CHEN M,et al.A lncRNA promotes myoblast proliferation by up-regulating GH1[J].In Vitro Cellular & Developmental Biology-Animal,2017,53(8):699-705.
[3] ZHOU L,SUN K,ZHAO Y,et al.Linc-YY1 promotes myogenic differentiation and muscle regeneration through an interaction with the transcription factor YY1[J].Nature Communications,2015,6:10026.
[4] WANG L,ZHAO Y,BAO X,et al.lncRNA Dum interacts with Dnmts to regulate Dppa2 expressionduring myogenic differentiation and muscle regeneration[J].Cell Research, 2015,25(3):335-350.
[5] YU X,ZHANG Y,LI T,et al.Long non-coding RNA Linc-RAM enhances myogenic differentiation by interacting with MyoD[J]. Nature Communications, 2017,8:14016.
[6] GUO Y,WANG J,ZHU M,et al.Identification of MyoD-responsive transcripts reveals a novel long non-coding RNA (lncRNA-AK143003) that negatively regulates myoblast differentiation[J].Scientific Reports,2017,7(1):2828.
[7] BILLEREY C,BOUSSAHA M,ESQUERRÉ D,et al.Identification of large intergenic non-codingRNAs in bovine muscle using next-generation transcriptomic sequencing[J].BMC Genomics,2014,15(1):499.
[8] SUN X,LI M,SUN Y,et al.The developmental transcriptome sequencing of bovine skeletal muscle reveals a long noncoding RNA,lncMD,promotes muscle differentiation by sponging miR-125b[J].BBA-Molecular Cell Research,2016,1863(11):2835-2845.
[9] LU L,SUN K,CHEN X,et al.Genome-wide surveyby ChIP-seq reveals YY1 regulation of lincRNAs in skeletalmyogenesis[J].EMBO Journal,2013,32(19):2575-2588.
[10] WANG K C,CHANG H Y.Molecular mechanisms of long noncoding RNAs[J].Molecular Cell,2011,43(6):904-914.
[11] LV J,CUI W,LIU H,ET A L.Identification and characterization of long non-coding RNAs related to mouse embryonic brain development from available transcriptomic data[J].PLoS One,2013,8(8):e71152.
[12] KORNIENKO A E,GUENZL P M,BARLOW D P,et al.Gene regulation by the act of long non-codingRNA transcription[J].BMC Biology,2013,11(1):59.
[13] LI L,EICHTEN S R,SHIMIZU R,et al.Genome-wide discovery and characterization of maize long non-coding RNAs[J].Genome Biology,2014,15(2):R40.
[14] LIU X F,DING X B,LI X,et al.An atlas and analysis of bovine skeletal muscle long noncoding RNAs[J].Animal Genetics,2017,48(3):278-286.
[15] WANG T Z,LIU M,ZHAO M G,et al.Identification and characterization of long non-coding RNAs involved in osmotic and salt stress in Medicago truncatulausing genome-wide high-throughput sequencing[J].BMC Plant Biology,2015,15(1):131.
[16] SUN L,ZHANG Z,BAILEY T L,et al.Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study[J].BMC Bioinformatics,2012,13:331.
[17] WEIKARD R,HADLICH F,KUEHN C.Identification of novel transcripts and noncoding RNAs in bovine skin by deep next generation sequencing[J].BMC Genomics,2013,14:789.
[18] GONG C,LI Z,RAMANUJAN K,et al.A long non-coding RNA,lncMyoD,regulates skeletal muscle differentiation by blocking IMP2-mediated mRNA translation[J].Developmental Cell,2015,34(2):181-191.
[19] HENTY-RIDILLA J L,JUANES M A,GOODE B L,et al.Profilin directly promotes microtubule growth through residues mutated in amyotrophic lateral sclerosis[J].Current Biology, 2017,27(22):3535-3543.
[20] MÉTAIS A,LAMSOUL I,MELET A,et al.Asb2α-filamin A axis is essential for actin cytoskeleton remodeling during heart development[J].Circulation Research,2018,122(6):e34-e48.
[21] KIBE K,NAKATOMI M,KATAOKA S,et al.Hey1 and Hey2 are differently expressed during mouse tooth development[J]. Gene Expression Patterns,2017,27(8):99-105.
[22] DOUCET C,GUTIERREZ G J,LINDON C,et al.Multiple phosphorylation events control mitotic degradation of the muscle transcription factor Myf5[J]. BMC Biochemistry,2005,6:27.
[23] ARNOLD H H,WINTER B.Muscle differentiation:More complexity tothe network of myogenic regulators[J].Current Opinion in Genetics & Development,1998,8(5):539-544.
[24] KABLAR B,RUDNICKI M A.Development in the absence of skeletal muscle results in the sequential ablation of motor neurons from the spinal cord to the brain[J].Developmental Biology,1999,208(1):93-105.
[25] 李东晓.利用CRISPRi干扰研究MyoD和Myf6基因对牛骨骼肌卫星细胞分化的影响[D].哈尔滨:东北农业大学,2016. LI D X.Determine the effects of MyoG and Myf6 genes on differentiation of bovine skeletal muscle satellite cells using CRISPRi[D].Harbin:Northeast Agricultural University,2016.(in Chinese)

Bioinformatics Analysis of Long Non-coding RNA Expression Profiles in Bovine Muscle Tissues from Three Periods

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	LIU Jialong, ZHANG Yiwen, ZHANG Yueran, SUN Qijuan, CHEN Jian, HE Lei, JIA Yanyan, DING Ke, YU Zuhua. Cloning,Prokaryotic Expression and Bioinformatics Analysis of ELAVL1 Gene in Chicken [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(5): 1807-1817.
[2]	ZHUO Na, ZHU Zhongwu, LI Jing, HU Shixiang, WANG Jianchang, LIN Hua, CHEN Chaolin, HAN Diangang, AI Jun, CHEN Peifu. Bioinformatics Analysis and Eukaryotic Expression of ORF2 Protein of Swine Hepatitis E Virus [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(5): 1959-1970.
[3]	FAN Bingfeng, LI Wen, LIU Lixiang, ZHAO Xiangyuan, SHAO Jing, LIN Lefeng, SUN Huimin, ZHANG Xulin, XU Baozeng. Cloning and Bioinformatics Analysis of AANAT Gene in Mink [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(4): 1307-1318.
[4]	JIA Xinyue, MA Jing, ZHANG Yanyan, MA Xun, WANG Zhengrong, BO Xinwen. Bioinformatics Analysis and Prokaryotic Expression of EGR-07243 and EGR-07243 Genes of Echinococcus granulosus [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(3): 847-858.
[5]	WEI Yirong, ZHENG Zihua, ZHANG Sanbao, SONG Ying, JIANG Haiyu, SUN Wenyue, CHENG Pengfei, LIU Yufan, ZOU Jianwei, HUANG Yanna, PAN Yan, JIANG Qinyang. Cloning,Bioinformatics Analysis and Tissue Expression of UCP1 Gene in Nubian Goats [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(2): 440-450.
[6]	ZHANG Jiupan, MA Qing, WANG Jin, MA Lina, WEI Dawei, LIANG Xiaojun. Single-cell RNA Sequencing Technology and Its Application in the Study of Intramuscular Adipocytes [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(2): 479-489.
[7]	TANG Jingyu, DU Hanyu, MENG Chunchun, LIU Guangqing. Cloning,Bioinformatics Analysis and Subcellular Localization of Interferon-stimulated Gene 15 in Goats [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(8): 2843-2854.
[8]	FU Yongzhi, MA Xiaojun, WANG Maohan, LI Zhe, CHEN Zhiyuan, QUAN Wei, ZHAO Han, SU Yongmei, WU Jianhua, ZHU Wenjin. Bioinformatics Analysis and Tissue Expression of MSTN Gene in Yangyuan Donkeys [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(8): 2910-2919.
[9]	ZOU Jianwei, ZOU Juhong, SHEN Yujian, WEI Yi, ZHANG Sanbao, LIAN Zitong, XU Jianjian, SONG Ying, HUANG Yanna, WEI Yingming, JIANG Qinyang, ZHENG Zihua. Bioinformatics Analysis, Construction of Eukaryotic Expression Vector and Expression of LMCD1 Gene in Nubian Goats [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(6): 2033-2042.
[10]	ZHANG Limeng, LIU Aiju, LI Runting, LI Yuhua, LI Lin, NIE Xiaoning, WANG Linqing, CHEN Longxin. Cloning,Bioinformatics and Tissue Expression Analysis of CREBRF Gene in Ovis aries [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(5): 1599-1609.
[11]	LEI Xing, LI Tianfeng, LI Jiahao, MAN Xin, BAI Suying. Bioinformatics Analysis and Expression of Elovl1 Gene in Muskrat Scent Gland [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(4): 1201-1212.
[12]	SHEN Xiang, CHEN Linghui, YAO Jingjie, WANG Sanhu, BAI Yueyu, ZHANG Xiaojian. Cloning,Bioinformatics and Expression Analysis of Bovine CCR7 Gene [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(4): 1244-1252.
[13]	ZHANG Mingliang, GENG Yachun, LIAN Kaiqi, MA Lei, CHANG Ying, WANG Shuangshan, ZHANG Fuliang. Cloning,Bioinformatics Analysis and Truncated Fragment Expression for Truncated M Gene of Porcine Epidemic Diarrhea Virus [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(4): 1479-1487.
[14]	SHI Yuzhu, LUO Rutang, CHEN Chao, WU Xu, LI Ang. Cloning, Bioinformatics and Tissue Expression Analysis of GDF9 Genes in Muscovy Duck [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(3): 817-829.
[15]	HOU Jinxing, WANG Zhanhang, ZHU Junru, JIANG Yue, LIU Shujuan, AN Xiaopeng. Cloning, Bioinformatics and Tissue Expression Profile Analysis of CSN1S1 Gene in Guanzhong Dairy Goats [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(3): 857-865.