Genome-wide identification and analysis of long noncoding RNAs in longissimus muscle tissue from Kazakh cattle and Xinjiang brown cattle
2
조회
0
다운로드
1
인용
0
참고문헌
키워드
초록
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.
Abstract
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.
참고문헌 (34)
- Scollan N, "Innovations in beef production systems that enhance the nutritional and health value of beef lipids and their relationship with meat quality", Meat Sci, 74, pp.17~33 (2006)[DOI]
- Fan YY, "A missense mutant of the PPAR-γ gene associated with carcass and meat quality traits in Chinese cattle breeds", Genet Mol Res, 11, pp.37818~ (2012)[DOI]
- Santos MD, "Improvement of the refrigerated preservation technology by hyperbaric storage for raw fresh meat", J Sci Food Agric, 100, pp.96977~ (2020)[DOI]
- Ladeira MM, "Nutrigenomics and beef quality : a review about lipogenesis", Int J Mol Sci, 17, pp.918~ (2016)[DOI]
- Berry DP, "Animal breeding strategies can improve meat quality attributes within entire populations", Meat Sci, 132, pp.6~18 (2017)[DOI]
- Li N, "Correlation between four metabolism-related genes in different adipose tissues and adipocyte morphology in Xinjiang brown cattle", Int J Clin Exp Med, 9, pp.5912~5921 (2016)
- Li N, "Differential expression of mRNAmiRNAs related to intramuscular fat content in the longissimus dorsi in Xinjiang brown cattle", PLoS One, 13, pp.e0206757~ (2018)[DOI]
- Yan XM, "Genome-wide identification and analysis of circular RNAs differentially expressed in the longissimus dorsi between Kazakh cattle and Xinjiang brown cattle", Peer J, 8, pp.e8646~ (2020)[DOI]
- Li N, "Sequencing and characterization of miRNAs and mRNAs from the longissimus dorsi of Xinjiang brown cattle and Kazakh cattle", Gene, 741, pp.144537~ (2020)[DOI]
- Alexander RP, "Annotating non-coding regions of the genome", Nat Rev Genet, 11, pp.559~571 (2010)[DOI]
- Wang KC, "Molecular mechanisms of long noncoding RNAs", Mol Cell, 43, pp.904~914 (2011)[DOI]
- Sun L, "Comparative transcriptome profiling of longissimus muscle tissues from Qianhua Mutton Merino and Small Tail Han sheep", Sci Rep, 6, pp.33586~ (2016)[DOI]
- Lim KS, "Identification of differentially expressed genes in longissimus muscle of pigs with high and low intramuscular fat content using RNA sequencing", Anim Genet, 48, pp.166~174 (2017)[DOI]
- He H, "Characterization of transcriptional complexity during longissimus muscle development in bovines using high-throughput sequencing", PLoS One, 8, pp.e64356~ (2013)[DOI]
- Trovero MF, "Revealing stage-specific expression patterns of long noncoding RNAs along mouse spermatogenesis", RNA Biol, 17, pp.350~365 (2020)[DOI]
- Liu B, "Identification of a lncRNA-associated competing endogenous RNA-regulated network in clear cell renal cell carcinoma", Mol Med Rep, 20, pp.485~494 (2019)[DOI]
- Yu J, "Bioinformatics identification of lncRNA biomarkers associated with the progression of esophageal squamous cell carcinoma", Mol Med Rep, 19, pp.5309~5320 (2019)[DOI]
- Xie C, "KOBAS 2. 0: a web server for annotation and identification of enriched pathways and diseases", Nucleic Acids Res, 39(Suppl 2), pp.W316~W322 (2011)[DOI]
- Duricki DA, "Analysis of longitudinal data from animals with missing values using SPSS", Nat Protoc, 11, pp.1112~1129 (2016)[DOI]
- Adnan S, "Top-cited articles in regenerative endodontics : a bibliometric analysis", J Endod, 44, pp.1650~1664 (2018)[DOI]
- Boisgontier MP, "The anova to mixed model transition", Neurosci Biobehav Rev, 68, pp.1004~1005 (2016)[DOI]
- Romao JM, "Effect of age on bovine subcutaneous fat proteome : molecular mechanisms of physiological variations during beef cattle growth", J Anim Sci, 92, pp.3316~3327 (2014)[DOI]
- McCarthy SN, "Evaluation of beef eating quality by Irish consumers", Meat Sci, 132, pp.118~124 (2017)[DOI]
- Farmer LJ, "Review : beef-eating quality : a European journey", Animal, 12, pp.2424~2433 (2018)[DOI]
- Esteller M, "Non-coding RNAs in human disease", Nat Rev Genet, 12, pp.861~874 (2011)[DOI]
- Zanou N, "Skeletal muscle hypertrophy and regeneration : interplay between the myogenic regulatory factors(MRFs)and insulin-like growth factors(IGFs)pathways", Cell Mol Life Sci, 70, pp.4117~4130 (2013)[DOI]
- Schiaffino S, "Regulation of skeletal muscle growth by the IGF1-Akt", PKB pathway : insights from genetic models, 2011, pp.1, 4~
- Taniguchi CM, "Critical nodes in signalling pathways : insights into insulin action", Nat Rev Mol Cell Biol, 7, pp.85~96 (2006)[DOI]
- Bodine SC, "Akt", mTOR pathway is a crucial regulator of skeletal muscle hypertrophy and can prevent muscle atrophy in vivo, 2001, pp.3, 1014~1019
- O'Neill BT, "Differential role of insulin", IGF-1receptor signaling in muscle growth and glucose homeostasis, 2015, pp.11, 1220~1235
- Yue B, "Characterization of lncRNA-miRNAmRNA network to reveal potential functional ceRNAs in bovine skeletal muscle", Front Genet, 10, pp.91~ (2019)[DOI]
- Liu M, "LncRNA-MEG3 promotes bovine myoblast differentiation by sponging miR-135", J Cell Physiol, 234, pp.18361~18370 (2019)[DOI]
- Wang J, "LncRNA WT1-AS inhibits triplenegative breast cancer cell migration and invasion by downregulating transforming growth factor β1", Cancer Biother Radiopharm, 34, pp.671~675 (2019)[DOI]
- Cai R, "A novel lnc-RNA, named lncORA, is identified by RNA-Seq analysis, and its knockdown inhibits adipogenesis by regulating the PI3K", AKT, Cells, pp.2019, 8[DOI]