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Genome-wide identification and analysis of long noncoding RNAs in longissimus muscle tissue from Kazakh cattle and Xinjiang brown cattle  

Yan, Xiang-Min (College of Animal Sciences, Jilin University)
Zhang, Zhe (College of Animal Sciences, Jilin University)
Liu, Jian-Bo (College of Animal Sciences, Jilin University)
Li, Na (Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry)
Yang, Guang-Wei (Yili State Animal Husbandry General Station)
Luo, Dan (College of Animal Sciences, Jilin University)
Zhang, Yang (Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry)
Yuan, Bao (College of Animal Sciences, Jilin University)
Jiang, Hao (College of Animal Sciences, Jilin University)
Zhang, Jia-Bao (College of Animal Sciences, Jilin University)
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Animal Bioscience / v.34, no.11, 2021 , pp. 1739-1748 More about this Journal
Objective: In recent years, long noncoding RNAs (lncRNAs) have been identified in many species, and some of them have been shown to play important roles in muscle development and myogenesis. However, the differences in lncRNAs between Kazakh cattle and Xinjiang brown cattle remain undefined; therefore, we aimed to confirm whether lncRNAs are differentially expressed in the longissimus dorsi between these two types of cattle and whether differentially expressed lncRNAs regulate muscle differentiation. Methods: We used RNA-seq technology to identify lncRNAs in longissimus muscles from these cattle. The expression of lncRNAs were analyzed using StringTie (1.3.1) in terms of the fragments per kilobase of transcript per million mapped reads values of the encoding genes. The differential expression of the transcripts in the two samples were analyzed using the DESeq R software package. The resulting false discovery rate was controlled by the Benjamini and Hochberg's approach. KOBAS software was utilized to measure the expression of different genes in Kyoto encyclopedia of genes and genomes pathways. We randomly selected eight lncRNA genes and validated them by quantitative reverse transcription polymerase chain reaction (RT-qPCR). Results: We found that 182 lncRNA transcripts, including 102 upregulated and 80 downregulated transcripts, were differentially expressed between Kazakh cattle and Xinjiang brown cattle. The results of RT-qPCR were consistent with the sequencing results. Enrichment analysis and functional annotation of the target genes revealed that the differentially expressed lncRNAs were associated with the mitogen-activated protein kinase, Ras, and phosphatidylinositol 3-kinase (PI3k)/Akt signaling pathways. We also constructed a lncRNA/mRNA coexpression network for the PI3k/Akt signaling pathway. Conclusion: Our study provides insights into cattle muscle-associated lncRNAs and will contribute to a more thorough understanding of the molecular mechanism underlying muscle growth and development in cattle.
Kazakh Cattle; LncRNA; Longissimus Muscle; Xinjiang Brown Cattle;
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1 Scollan N, Hocquette JF, Nuernberg K, Dannenberger D, Richardson I, Moloney A. Innovations in beef production systems that enhance the nutritional and health value of beef lipids and their relationship with meat quality. Meat Sci 2006;74:17-33.   DOI
2 Fan YY, Fu GW, Fu CZ, Zan LS, Tian WQ. A missense mutant of the PPAR-γ gene associated with carcass and meat quality traits in Chinese cattle breeds. Genet Mol Res 2012;11:37818.   DOI
3 Santos MD, Castro R, Delgadillo I, Saraiva JA. Improvement of the refrigerated preservation technology by hyperbaric storage for raw fresh meat. J Sci Food Agric 2020;100:96977.   DOI
4 Li N, Zhang Y, Li HP, et al. Differential expression of mRNA-miRNAs related to intramuscular fat content in the longissimus dorsi in Xinjiang brown cattle. PLoS One 2018;13:e0206757.   DOI
5 Ladeira MM, Schoonmaker JP, Gionbelli MP, et al. Nutrigenomics and beef quality: a review about lipogenesis. Int J Mol Sci 2016;17:918.   DOI
6 Yan XM, Zhang Z, Meng Y, et al. Genome-wide identification and analysis of circular RNAs differentially expressed in the longissimus dorsi between Kazakh cattle and Xinjiang brown cattle. Peer J 2020;8:e8646.   DOI
7 Yu J, Wu X, Huang K, et al. Bioinformatics identification of lncRNA biomarkers associated with the progression of esophageal squamous cell carcinoma. Mol Med Rep 2019;19: 5309-20.   DOI
8 He H, Liu X. Characterization of transcriptional complexity during longissimus muscle development in bovines using high-throughput sequencing. PLoS One 2013;8:e64356.   DOI
9 Trovero MF, Rodriguez-Casuriaga R, Romeo C, et al. Revealing stage-specific expression patterns of long noncoding RNAs along mouse spermatogenesis. RNA Biol 2020;17:350-65.   DOI
10 Liu B, Ma T, Li Q, et al. Identification of a lncRNA-associated competing endogenous RNA-regulated network in clear cell renal cell carcinoma. Mol Med Rep 2019;20:485-94.   DOI
11 Wang J, Xi C, Yang X, et al. LncRNA WT1-AS inhibits triple-negative breast cancer cell migration and invasion by down-regulating transforming growth factor β1. Cancer Biother Radiopharm 2019;34:671-5.   DOI
12 Li N, Yu QL, Yan XM, Li HB, Zhang Y. Sequencing and characterization of miRNAs and mRNAs from the longissimus dorsi of Xinjiang brown cattle and Kazakh cattle. Gene 2020;741:144537.   DOI
13 Lim KS, Lee KT, Park JE, et al. Identification of differentially expressed genes in longissimus muscle of pigs with high and low intramuscular fat content using RNA sequencing. Anim Genet 2017;48:166-74.   DOI
14 Bodine SC, Stitt TN, Gonzalez M, et al. Akt/mTOR pathway is a crucial regulator of skeletal muscle hypertrophy and can prevent muscle atrophy in vivo. Nat Cell Biol 2001;3:1014-9.   DOI
15 McCarthy SN, Henchion M, White A, Brandon K, Allen P. Evaluation of beef eating quality by Irish consumers. Meat Sci 2017;132:118-24.   DOI
16 Farmer LJ, Farrell DT. Review: beef-eating quality: a European journey. Animal 2018;12:2424-33.   DOI
17 Esteller M. Non-coding RNAs in human disease. Nat Rev Genet 2011;12:861-74.   DOI
18 Berry DP, Conroy S, Pabiou T, Cromie AR. Animal breeding strategies can improve meat quality attributes within entire populations. Meat Sci 2017;132:6-18.   DOI
19 Duricki DA, Soleman S, Moon LD. Analysis of longitudinal data from animals with missing values using SPSS. Nat Protoc 2016;11:1112-29.   DOI
20 Adnan S, Ullah R. Top-cited articles in regenerative endodontics: a bibliometric analysis. J Endod 2018;44:1650-64.   DOI
21 Boisgontier MP, Cheval B. The anova to mixed model transition. Neurosci Biobehav Rev 2016;68:1004-5.   DOI
22 Romao JM, He ML, McAllister TA, Guan LL. Effect of age on bovine subcutaneous fat proteome: molecular mechanisms of physiological variations during beef cattle growth. J Anim Sci 2014;92:3316-27.   DOI
23 Li N, Li HB, Yan XM, et al. Correlation between four metabolism-related genes in different adipose tissues and adipocyte morphology in Xinjiang brown cattle. Int J Clin Exp Med 2016;9:5912-21.
24 Alexander RP, Fang G, Rozowsky J, Snyder M, Gerstein MB. Annotating non-coding regions of the genome. Nat Rev Genet 2010;11:559-71.   DOI
25 Wang KC, Chang HY. Molecular mechanisms of long non-coding RNAs. Mol Cell 2011;43:904-14.   DOI
26 Sun L, Bai M, Xiang L, Zhang G, Ma W, Jiang H. Comparative transcriptome profiling of longissimus muscle tissues from Qianhua Mutton Merino and Small Tail Han sheep. Sci Rep 2016;6:33586.   DOI
27 O'Neill BT, Lauritzen HPMM, Hirshman MF, Smyth G, Goodyear LJ, Kahn CR. Differential role of insulin/IGF-1 receptor signaling in muscle growth and glucose homeostasis. Cell Rep 2015;11:1220-35.   DOI
28 Zanou N, Gailly P. Skeletal muscle hypertrophy and regeneration: interplay between the myogenic regulatory factors (MRFs) and insulin-like growth factors (IGFs) pathways. Cell Mol Life Sci 2013;70:4117-30.   DOI
29 Schiaffino S, Mammucari C. Regulation of skeletal muscle growth by the IGF1-Akt/PKB pathway: insights from genetic models. Skelet Muscle 2011;1:4.   DOI
30 Taniguchi CM, Emanuelli B, Kahn R. Critical nodes in signalling pathways: insights into insulin action. Nat Rev Mol Cell Biol 2006;7:85-96.   DOI
31 Yue B, Li H, Liu M, et al. Characterization of lncRNA-miRNAmRNA network to reveal potential functional ceRNAs in bovine skeletal muscle. Front Genet 2019;10:91.   DOI
32 Liu M, Li B, Peng W, et al. LncRNA-MEG3 promotes bovine myoblast differentiation by sponging miR-135. J Cell Physiol 2019;234:18361-70.   DOI
33 Cai R, Tang G, Zhang Q, et al. A novel lnc-RNA, named lnc-ORA, is identified by RNA-Seq analysis, and its knockdown inhibits adipogenesis by regulating the PI3K/AKT/mTOR signaling pathway. Cells 2019;8:477.   DOI
34 Xie C, Mao X, Huang J, et al. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res 2011;39(Suppl 2):W316-22.   DOI