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.
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.
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.
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.
Iram SHAFIQ, Sajad HUSSAIN, Muhammad Ali RAZA, Nasir IQBAL, Muhammad Ahsan ASGHAR, Ali RAZA, FAN Yuan-fang, Maryam MUMTAZ, Muhammad SHOAIB, Muhammad ANSAR, Abdul MANAF, YANG Wen-yu, YANG Feng. Crop photosynthetic response to light quality and light intensity[J]. >Journal of Integrative Agriculture, 2021, 20(1): 4-23.
