Ferdowsi University of Mashhad

Document Type : Research Articles


1 Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Iran

2 Chief of Agricultural Engineers, Ministry of Agriculture, Baghdad, Iraq

3 Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran


Long non-coding RNAs (lncRNAs) compose a plentiful category of transcripts that have gained increasing importance because of their roles in different biological processes. Although the function of most lncRNAs remains unclear. They are implicated in epigenetic regulation of gene expression, including muscle development and differentiation. We aimed to identify the effect of novel lncRNAs (Alternatively spliced) and their target genes on two stages of sheep skeletal muscle growth and development. FastQC files have been used to examine the quality control and the Trimmomatic program for trimming low-quality reads from twelve longissimus dorsal muscle tissue samples (including six young and six old from Texel sheep). Hisat2, Cufflink, Cuffmerge, and Cuffdiff investigated the expression levels. Novel lncRNAs (Alternative spliced) were distinguished using NONCODE databases and Cuffcompare software. In addition, the lncRNA–mRNA interactions and regulatory network visualization were identified via RIsearch and Cytoscape software, respectively. Those 139 novel lncRNA (Alternative spliced) transcripts had been recognized, probably 65 lncRNAs interacted with their target genes and regulated sheep skeletal muscle growth and development. Three novel lncRNA transcripts (TCONS_00041386, TCONS_00050059, and TCONS_00056428) showed a strong association and five transcripts (TCONS_00055761, TCONS_00055762, TCONS_00055763, TCONS_00055764, and TCONS_00055770) had made complex network correlations with mRNAs. Our research provided more knowledge of the associated mechanisms with novel lncRNAs, which could play a role in regulating sheep skeletal muscle tissue development and growth.


Andrews S. (2010) FastQC: a quality control tool for high throughput sequence data. Available online. Retrieved May, 17: www.bioinformatics.babraham.ac.uk/projects/fastqc/.
Ballarino M., Cazzella V., D'Andrea D., Grassi L., Bisceglie L., Cipriano A., et al. (2015) Novel long noncoding RNAs (lncRNAs) in myogenesis: a miR-31 overlapping lncRNA transcript controls myoblast differentiation. Molecular and Cellular Biology, 35(4), 728-736.‏
Badday Betti S., Tahmoorespur M., Javadmanesh A. (2022) Identification of lncRNAs expression and their regulatory networks associated with development and growth of skeletal muscle in sheep using RNA-Seq. Agriculture and Natural Resources, 56(2): 161-174.
Bolger A. M., Lohse M. and Usadel B. (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics (Oxford,England), 30(15),2114–2120.
Chao T., Ji Z., Hou L., Wang J., Zhang C., Wang G., et al. (2018) Sheep skeletal muscle transcriptome analysis reveals muscle growth regulatory lncRNAs. PeerJ, 6: e4619.
Chao T., Wang G., Wang J., Liu Z., Ji Z., Hou L., et al. (2016) Identification and classification of new transcripts in dorper and small-tailed han sheep skeletal muscle transcriptomes. PLoS One, 11(7), e0159638.‏
Clark E. L., Bush S. J., McCulloch M. E., Farquhar I. L., Young R., Lefèvre L., et al. (2018) A High Resolution Atlas of Gene Expression in the Domestic Sheep. In Plant and Animal Genome XXVI Conference (January 13-17, 2018). PAG.‏
Derrien T., Johnson R., Bussotti G., Tanzer A., Djebali S., Tilgner H., et al. (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Research, 22(9), 1775-1789.‏
Fang S., Zhang L., Guo J., Niu Y., Wu Y., Li H., et al. (2018) NONCODEV5: a comprehensive annotation database for long noncoding RNAs. Nucleic Acids Research, 46(D1), D308-D314.‏
Gabory A., Jammes H. and Dandolo L. (2010) The H19 locus: role of an imprinted noncoding RNA in growth and development. Bioessays, 32(6), 473-480.‏
Gabory A., Ripoche M. A., Le Digarcher A., Watrin F., Ziyyat A., Forné T., et al. (2009) H19 acts as a trans regulator of the imprinted gene network controlling growth in mice. Development, 136(20), 3413-3421.‏
Ghanipoor-Samami M., Javadmanesh A., Burns B. M., Thomsen D. A., Nattrass G. S., Estrella C., Kind K. L., et al. (2018) Atlas of tissue- and developmental stage specific gene expression for the bovine insulin-like growth factor (IGF) system. PloS one, 13(7), e0200466.
Kang Y. J., Yang D. C., Kong L., Hou M., Meng Y. Q., Wei L., et al. (2017) CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features. Nucleic Acids Research, 45(W1), W12-W16.‏
Kim D., Langmead B. and Salzberg S. L. (2015) HISAT: a fast spliced aligner with low memory requirements. Nature Methods, 12(4), 357-360.‏
Kinka D. and Young J. K. (2019) Evaluating domestic sheep survival with different breeds of livestock guardian dogs. Rangeland Ecology & Management, 72(6), 923-932.‏
Li A., Zhang J. and Zhou Z. (2014) PLEK: a tool for predicting long noncoding RNAs and messenger RNAs based on an improved k-mer scheme. BMC Bioinformatics, 15(1), 1-10.‏
Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25(16), 2078-2079.‏
Li Q., Liu R., Zhao H., Di R., Lu Z., Liu E., et al. (2018) Identification and Characterization of Long Noncoding RNAs in Ovine Skeletal Muscle. Animals, 8(7), 127.‏
Li Z., Zhao W., Wang M. and Zhou X. (2019) The role of long noncoding RNAs in gene expression regulation, Gene Expression Profiling in Cancer. BoD – Books on Demand, pp. 1-17.
Lobjois V., Liaubet L., SanCristobal M., Glénisson J., Feve K., Rallieres J., et al. (2008) A muscle transcriptome analysis identifies positional candidate genes for a complex trait in pig. Animal Genetics, 39(2), 147-162.‏
Neguembor M.V., Jothi M. and Gabellini D. (2014) Long noncoding RNAs, emerging players in muscle differentiation and disease. Skeletal Muscle, 4(1): 1-12.
Nihashi Y., Umezawa K., Shinji S., Hamaguchi Y., Kobayashi H., Kono T., et al. (2019) Distinct cell proliferation, myogenic differentiation, and gene expression in skeletal muscle myoblasts of layer and broiler chickens. Scientific Reports, 9(1), 1-15.‏
Noce A., Cardoso T. F., Manunza A., Martínez A., Cánovas A., Pons A., et al. (2018) Expression patterns and genetic variation of the ovine skeletal muscle transcriptome of sheep from five Spanish meat breeds. Scientific Reports, 8(1), 1-7.‏
Pertea G. and Pertea M. (2020). GFF utilities: GffRead and GffCompare. F1000Research, 9.‏   
Ramakrishnaiah Y., Kuhlmann L. and Tyagi S. (2020) Towards a comprehensive pipeline to identify and functionally annotate long noncoding RNA (lncRNA). Computers in Biology and Medicine: 104028.
Rashidian, Z., Dehdilani, N., Dehghani, H., Javadmanesh, A. (2020). Isolation and culturing myogenic satellite cells from ovine skeletal muscle. Iranian Journal of Veterinary Science and Technology, 12(2), 36-43.
Relaix F. and Zammit P. S. (2012) Satellite cells are essential for skeletal muscle regeneration: the cell on the edge returns centre stage. Development, 139(16), 2845-2856.‏
Saliani M., Mirzaiebadizi A., Javadmanesh A., Siavoshi A. and Ahmadian M.R. (2021) KRAS-related long noncoding RNAs in human cancers. Cancer Gene Therapy, 1-10.
Saliani M., Jalal R. and Javadmanesh A. 2022. Differential expression analysis of genes and long non-coding RNAs associated with KRAS mutation in colorectal cancer cells. Scientific Reports, Accepted.
Shannon P., Markiel A., Ozier O., Baliga N. S., Wang J. T., Ramage D., et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research, 13(11), 2498-2504.‏
Trapnell C., Roberts A., Goff L., Pertea G., Kim D., Kelley D. R., et al. (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols, 7(3), 562-578.‏
Trapnell C., Williams B. A., Pertea G., Mortazavi A., Kwan G., Van Baren M. J., et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology, 28(5), 511-515.‏
Wenzel A., Akbaşli E. and Gorodkin J. (2012) RIsearch: fast RNA–RNA interaction search using a simplified nearest-neighbor energy model. Bioinformatics, 28(21), 2738-2746.
Yuan C., Zhang K., Yue Y., Guo T., Liu J., Niu C., et al. (2020) Analysis of dynamic and widespread lncRNA and miRNA expression in fetal sheep skeletal muscle. PeerJ, 8, e9957.‏