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Special Issue:
动物科学合辑Animal Science
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| Identification and functional prediction of long intergenic noncoding RNAs in fetal porcine longissimus dorsi muscle |
| LI Cen-cen, YU Shu-long, REN Hai-feng, WU Wei, WANG Ya-ling, HAN Qiu, XU Hai-xia, XU Yong-jie, ZHANG Peng-peng |
| College of Life Sciences, Xinyang Normal University, Xinyang 464000, P.R.China |
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摘要
猪是全球重要的家养动物，以骨骼肌的形式为人类重提供蛋白质。为了研究长链基因间非编码RNA（LincRNA）在猪骨骼肌发育中的功能，我们收集猪胚胎发育期间背最长肌（LDM）的RNA-seq数据，并坚定了739条lincRNA转录本，这些转录本分布在除Y染色体外的所有染色体上。然后我们对鉴定的lincRNA的分子特征进行分析，相比于蛋白编码基因，lincRNA具有较短的转录本长度、较长的外显子长度、较少的外显子数目及较高的组织特异性。除此之外，我们还对lincRNA在5个胚胎发育时期的表达丰度进行分析，鉴定了45个差异表达的lincRNA，其中有3个差异表达的lincRNA在不同的胚胎发育期均差异表达。最后我们对lincRNa的潜在靶基因进行预测，共鉴定了1537个顺式作用的靶基因及8571个反式作用的靶基因。结合上述结果我们鉴定了两个参与骨骼肌发育的关键候选lincRNA：XLOC_024652和XLOC_001832。本研究在全基因组水平鉴定猪胚胎期骨骼肌发育过程中可能涉及的lincRNA，为进一步研究lincRNa的功能及猪的遗传育种提供有价值的素材。
Abstract Pigs are globally farmed animals which provide protein for human consumption in the form of skeletal muscle. To better understand the function of long intergenic noncoding RNAs (lincRNAs) in porcine skeletal muscle growth and development, we collected RNA-seq data from porcine longissimus dorsi muscle (LDM) during embryonic development. We identified a total of 739 lincRNA transcripts, which were distributed on all chromosomes except the chromosome Y, and analyzed their molecular characteristics. Compared to protein-coding genes, lincRNAs showed shorter transcripts, longer exons, fewer exons and higher tissue specificity. In addition, the abundance of lincRNAs in five embryonic development stages were analyzed and 45 differentially expressed lincRNAs were screened, three of which were highly expressed in LDM during porcine embryonic development. Finally, we predicted the potential target genes and functions of the lincRNAs, and identified 1 537 cis-target genes and 8 571 trans-target genes. Furthermore, we identified two key candidate lincRNAs involved in muscle development, XLOC_024652 and XLOC_001832, for post-trial validation. Our results provide a genome-wide resource of lincRNAs which are potentially involved in porcine embryonic skeletal muscle development and lay a foundation for the further study of their functions.
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Received: 16 January 2020
Accepted:
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| Fund: This work was financially supported by the National Natural Science Foundation of China (31601167, 31972537 and U1204326), the Natural Science Foundation of Henan Province, China (182300410027), the Central Plains Technological Innovation Leading Talents Project of Henan Province, China (194200510022), and the Nanhu Scholars Program of Xinyang Normal University, China. |
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Corresponding Authors:
Correspondence ZHANG Peng-peng, Tel: +86-376-6391380, E-mail: ppzhang15 @163.com; XU Yong-jie, E-mail: yongjx81@126.com
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| About author: LI Cen-cen, E-mail: licencen@xynu.edu.cn; |
Cite this article:
LI Cen-cen, YU Shu-long, REN Hai-feng, WU Wei, WANG Ya-ling, HAN Qiu, XU Hai-xia, XU Yong-jie, ZHANG Peng-peng.
2021.
Identification and functional prediction of long intergenic noncoding RNAs in fetal porcine longissimus dorsi muscle. Journal of Integrative Agriculture, 20(1): 201-211.
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Anders S, Pyl P T, Huber W. 2015. HTSeq - a Python framework to work with high-throughput sequencing data. Bioinformatics, 31, 166–169.
Bakhtiarizadeh M R, Salami S A. 2019. Identification and expression analysis of long noncoding RNAs in fat-tail of sheep breeds. G3: Genes, Genomes, Genetics, 9, 1263–1276.
Bolger A M, Lohse M, Usadel B. 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114–2120.
Chen M, Li X, Zhang X, Li Y, Zhang J, Liu M, Zhang L, Ding X, Liu X, Guo H. 2019. A novel long non-coding RNA, lncKBTBD10, involved in bovine skeletal muscle myogenesis. In Vitro Cellular & Developmental Biology-Animal, 55, 25–35.
Feng J, Meyer C A, Wang Q, Liu J S, Shirley Liu X, Zhang Y. 2012. GFOLD: A generalized fold change for ranking differentially expressed genes from RNA-seq data. Bioinformatics, 28, 2782–2788.
da Huang W, Sherman B T, Zheng X, Yang J, Imamichi T, Stephens R, Lempicki R A. 2009. Extracting biological meaning from large gene lists with DAVID. Current Protocols in Bioinformatics, 27, doi: 10.1002/0471250953.bi1311s27.
Hwang J Y, Sun Y, Carroll C R, Usherwood E J. 2019. Neuropilin-1 regulates the secondary cd8 t cell response to virus infection. mSphere, 4, doi: 10.1128/mSphere.00221-19.
Jandura A, Krause H M. 2017. The new RNA world: Growing evidence for long noncoding RNA functionality. Trends in Genetics, 33, 665–676.
Kong L, Zhang Y, Ye Z Q, Liu X Q, Zhao S Q, Wei L, Gao G. 2007. CPC: Assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Research, 35, W345–W349.
Legnini I, Di Timoteo G, Rossi F, Morlando M, Briganti F, Sthandier O, Fatica A, Santini T, Andronache A, Wade M, Laneve P, Rajewsky N, Bozzoni I. 2017. Circ-ZNF609 is a circular RNA that can be translated and functions in myogenesis. Molecular Cell, 66, 22–37, e9.
Li C, Zou C, Cui Y, Fu Y, Fang C, Li Y, Li J, Wang W, Xiang H, Li C. 2018. Genome-wide epigenetic landscape of pig lincRNAs and their evolution during porcine domestication. Epigenomics, 10, 1603–1618.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078–2079.
Li H, Zhao J, Liu B, Luo J, Li Z, Qin X, Wei Y. 2019. MicroRNA-320 targeting neuropilin 1 inhibits proliferation and migration of vascular smooth muscle cells and neointimal formation. International Journal of Medical Sciences, 16, 106–114.
Li J, Gao Z, Wang X, Liu H, Zhang Y, Liu Z. 2016. Identification and functional analysis of long intergenic noncoding RNA genes in porcine pre-implantation embryonic development. Scientific Reports, 6, 38333.
Li X, Tian G G, Zhao Y, Wu J. 2019. Genome-wide identification and characterization of long noncoding and circular RNAs in germline stem cells. Scientific Data, 6, 8.
Li Y, Zhang C, Qin L, Li D, Zhou G, Dang D, Chen S, Sun T, Zhang R, Wu W, Xi Y, Jin Y, Duan G. 2018. Characterization of critical functions of long non-coding RNAs and mRNAs in rhabdomyosarcoma cells and mouse skeletal muscle infected by enterovirus 71 using RNA-Seq. Viruses, 10, 556.
Liao B Y, Zhang J. 2006. Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution. Molecular Biology and Evolution, 23, 1119–1128.
Liu H, Xi Y, Liu G, Zhao Y, Li J, Lei M. 2018. Comparative transcriptomic analysis of skeletal muscle tissue during prenatal stages in Tongcheng and Yorkshire pig using RNA-seq. Functional & Integrative Genomics, 18, 195–209.
Lowe V, Wisniewski L, Sayers J, Evans I, Frankel P, Mercader-Huber N, Zachary I C , Pellet-Many C. 2019. Neuropilin 1 mediates epicardial activation and revascularization in the regenerating zebrafish heart. Development, 146, 17448.
Ma J, Yang J, Zhou L, Ren J, Liu X, Zhang H, Yang B, Zhang Z, Ma H, Xie X, Xing Y, Guo Y, Huang L. 2014. A splice mutation in the PHKG1 gene causes high glycogen content and low meat quality in pig skeletal muscle. PLoS Genetics, 10, e1004710.
Pauli A, Valen E, Lin M F, Garber M, Vastenhouw N L, Levin J Z, Fan L, Sandelin A, Rinn J L, Regev A, Schier A F. 2012. Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Research, 22, 577–591.
Pollier J, Rombauts S, Goossens A. 2013. Analysis of RNA-Seq data with TopHat and Cufflinks for genome-wide expression analysis of jasmonate-treated plants and plant cultures. Methods in Molecular Biology, 1011, 305–315.
Quinlan A R, Hall I M. 2010. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841–842.
Rossi F, Legnini I, Megiorni F, Colantoni A, Santini T, Morlando M, Di Timoteo G, Dattilo D, Dominici C, Bozzoni I. 2019. Circ-ZNF609 regulates G1-S progression in rhabdomyosarcoma. Oncogene, 38, 3843–3854.
Sayers E W, Barrett T, Benson D A, Bolton E, Bryant S H, Canese K, Chetvernin V, Church D M, Dicuccio M, Federhen S, Feolo M, Fingerman I M, Geer L Y, Helmberg W, Kapustin Y, Krasnov S, Landsman D, Lipman D J, Lu Z, Madden T L, et al. 2012. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 40, D13–D25.
Schachtschneider K M, Madsen O, Park C, Rund L A, Groenen M A, Schook L B. 2015. Adult porcine genome-wide DNA methylation patterns support pigs as a biomedical model. BMC Genomics, 16, 743.
Stachowiak M, Flisikowski K. 2019. Analysis of allele-specific expression of seven candidate genes involved in lipid metabolism in pig skeletal muscle and fat tissues reveals allelic imbalance of ACACA, LEP, SCD, and TNF. Journal of Applied Genetics, 60, 97–101.
Talyan S, Andrade-Navarro M A, Muro E M. 2018. Identification of transcribed protein coding sequence remnants within lincRNAs. Nucleic Acids Research, 46, 8720–8729.
Tang Z, Li Y, Wan P, Li X, Zhao S, Liu B, Fan B, Zhu M, Yu M, Li K. 2007. LongSAGE analysis of skeletal muscle at three prenatal stages in Tongcheng and Landrace pigs. Genome Biology, 8, R115.
Tang Z, Wu Y, Yang Y, Yang Y T, Wang Z, Yuan J, Yang Y, Hua C, Fan X, Niu G, Zhang Y, Lu Z J, Li K. 2017. Comprehensive analysis of long non-coding RNAs highlights their spatio-temporal expression patterns and evolutional conservation in Sus scrofa. Scientific Reports, 7, 43166.
Trapnell C, Williams B A, Pertea G, Mortazavi A, Kwan G, van Baren M J, Salzberg S L, Wold B J, Pachter L. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology, 28, 511–515.
Voellenkle C, Perfetti A, Carrara M, Fuschi P, Renna L V, Longo M, Sain S B, Cardani R, Valaperta R, Silvestri G, Legnini I, Bozzoni I, Furling D, Gaetano C, Falcone G, Meola G. Martelli F. 2019. Dysregulation of circular RNAs in myotonic dystrophy type 1. International Journal of Molecular Science, 20, 1938.
Wang L, Feng Z, Wang X, Wang X. Zhang X. 2010. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics, 26, 136–138.
Weikard R, Demasius W, Kuehn C. 2017. Mining long noncoding RNA in livestock. Animal Genetics, 48, 3–18.
Wigmore P M, Stickland N C. 1983. Muscle development in large and small pig fetuses. Journal of Anatomy, 137(Pt 2),
235–245.
Xiang H, Zhu J, Chen Q, Dai F, Li X, Li M, Zhang H, Zhang G, Li D, Dong Y, Zhao L, Lin Y, Cheng D, Yu J, Sun J, Zhou X, Ma K, He Y, Zhao Y, Guo S, et al. 2010. Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nature Biotechnology, 28, 516–520.
Xiong Q, Chai J, Zhang P P, Wu J, Jiang S W, Zheng R, Deng C Y. 2011. MyoD control of SKIP expression during pig skeletal muscle development. Molecular Biology Reports, 38, 267–274.
Yanai I, Benjamin H, Shmoish M, Chalifa-Caspi V, Shklar M, Ophir R, Bar-Even A, Horn-Saban S, Safran M, Domany E, Lancet D, Shmueli O. 2005. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics, 21, 650–659.
Zhao Y, Li J, Liu H, Xi Y, Xue M, Liu W, Zhuang Z, Lei M. 2015. Dynamic transcriptome profiles of skeletal muscle tissue across 11 developmental stages for both Tongcheng and Yorkshire pigs. BMC Genomics, 16, 377.
Zou C, Li L, Cheng X, Li C, Fu Y, Fang C, Li C. 2018. Identification and functional analysis of long intergenic non-coding RNAs underlying intramuscular fat content in pigs. Frontiers in Genetics, 9, 102.
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