*Result*: Construction of a competitive endogenous RNA regulatory network for intramuscular fat content in Laiwu pig based on whole transcriptome analysis.
Title:
Construction of a competitive endogenous RNA regulatory network for intramuscular fat content in Laiwu pig based on whole transcriptome analysis.
Authors:
Tian Z; College of Animal Science and Technology, Shandong Engineering Research Center for Protection of Livestock and Poultry Genetic Resources and Biological Breeding, Qingdao Agricultural University, Qingdao, China.; College of Life Sciences, Qingdao Agricultural University, Qingdao, China., Li W; College of Animal Science and Technology, Shandong Engineering Research Center for Protection of Livestock and Poultry Genetic Resources and Biological Breeding, Qingdao Agricultural University, Qingdao, China.; College of Life Sciences, Qingdao Agricultural University, Qingdao, China., Yu M; College of Animal Science and Technology, Shandong Engineering Research Center for Protection of Livestock and Poultry Genetic Resources and Biological Breeding, Qingdao Agricultural University, Qingdao, China., Wang T; College of Animal Science and Technology, Shandong Engineering Research Center for Protection of Livestock and Poultry Genetic Resources and Biological Breeding, Qingdao Agricultural University, Qingdao, China.; College of Life Sciences, Qingdao Agricultural University, Qingdao, China., Ruan G; Qingdao Academy of Agricultural Sciences, Qingdao, China., Li A; College of Animal Science and Technology, Shandong Engineering Research Center for Protection of Livestock and Poultry Genetic Resources and Biological Breeding, Qingdao Agricultural University, Qingdao, China.; College of Life Sciences, Qingdao Agricultural University, Qingdao, China., Zhang S; General Station of Animal Husbandry of Shandong Province, Jinan, China., Zhang M; General Station of Animal Husbandry of Shandong Province, Jinan, China., Zhai X; General Station of Animal Husbandry of Shandong Province, Jinan, China., Cheng S; College of Animal Science and Technology, Shandong Engineering Research Center for Protection of Livestock and Poultry Genetic Resources and Biological Breeding, Qingdao Agricultural University, Qingdao, China., Shen W; College of Animal Science and Technology, Shandong Engineering Research Center for Protection of Livestock and Poultry Genetic Resources and Biological Breeding, Qingdao Agricultural University, Qingdao, China., Wang J; College of Animal Science and Technology, Shandong Engineering Research Center for Protection of Livestock and Poultry Genetic Resources and Biological Breeding, Qingdao Agricultural University, Qingdao, China.
Source:
Animal genetics [Anim Genet] 2026 Feb; Vol. 57 (1), pp. e70070.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: Wiley-Blackwell Country of Publication: England NLM ID: 8605704 Publication Model: Print Cited Medium: Internet ISSN: 1365-2052 (Electronic) Linking ISSN: 02689146 NLM ISO Abbreviation: Anim Genet Subsets: MEDLINE
Imprint Name(s):
Publication: Oxford, England : Wiley-Blackwell
Original Publication: Oxford, England : Published by Blackwell Scientific Publications for the International Society for Animal Blood Group Research, c1986-
Original Publication: Oxford, England : Published by Blackwell Scientific Publications for the International Society for Animal Blood Group Research, c1986-
MeSH Terms:
References:
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Chen, J.N., Jiang, Y.Z., Cen, W.M., Xing, S.H., Zhu, L., Tang, G.Q. et al. (2014) Distribution of H‐FABP and ACSL4 gene polymorphisms and their associations with intramuscular fat content and backfat thickness in different pig populations. Genetics and Molecular Research, 13, 6759–6772.
Chen, S., Zhou, Y., Chen, Y. & Gu, J. (2018) Fastp: an ultra‐fast all‐in‐one FASTQ preprocessor. Bioinformatics, 34, i884–i890.
de Sena Brandine, G. & Smith, A.D. (2019) Falco: high‐speed FastQC emulation for quality control of sequencing data. F1000Research, 8, 1874.
Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S. et al. (2013) STAR: ultrafast universal RNA‐seq aligner. Bioinformatics, 29, 15–21.
Duo, T., Liu, X., Mo, D., Bian, Y., Cai, S., Wang, M. et al. (2023) Single‐base editing in IGF2 improves meat production and intramuscular fat deposition in Liang Guang small spotted pigs. Journal of Animal Science and Biotechnology, 14, 141.
Feng, H., Yousuf, S., Liu, T., Zhang, X., Huang, W., Li, A. et al. (2022) The comprehensive detection of miRNA and circRNA in the regulation of intramuscular and subcutaneous adipose tissue of Laiwu pig. Scientific Reports, 12, 16542.
Filshtein, T.J., Mackenzie, C.O., Dale, M.D., Dela‐Cruz, P.S., Ernst, D.M., Frankenberger, E.A. et al. (2012) OrbId: origin‐based identification of microRNA targets. Mobile Genetic Elements, 2, 184–192.
Gu, H., Zhou, Y., Yang, J. et al. (2021) Targeted overexpression of PPARgamma in skeletal muscle by random insertion and CRISPR/Cas9 transgenic pig cloning enhances oxidative fiber formation and intramuscular fat deposition. The FASEB Journal, 35, e21308.
Jin, Z., Gao, H., Fu, Y., Ren, R., Deng, X., Chen, Y. et al. (2024) Whole‐transcriptome analysis sheds light on the biological contexts of intramuscular fat deposition in Ningxiang pigs. Genes, 15, 642.
Joo, S.T., Kim, G.D., Hwang, Y.H. & Ryu, Y.C. (2013) Control of fresh meat quality through manipulation of muscle fiber characteristics. Meat Science, 95, 828–836.
Kozomara, A., Birgaoanu, M. & Griffiths‐Jones, S. (2019) miRBase: from microRNA sequences to function. Nucleic Acids Research, 47, D155–D162.
Li, X., Wang, J., Zhang, F., Yu, M., Zuo, N., Li, L. et al. (2023) Cyanidin‐3‐O‐glucoside rescues zearalenone‐induced apoptosis via the ITGA7‐PI3K‐AKT signaling pathway in porcine ovarian granulosa cells. International Journal of Molecular Sciences, 24, 4441.
Li, Z., Huang, C., Bao, C., Chen, L., Lin, M., Wang, X. et al. (2015) Exon‐intron circular RNAs regulate transcription in the nucleus. Nature Structural & Molecular Biology, 22, 256–264.
Liao, Y., Smyth, G.K. & Shi, W. (2014) featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30, 923–930.
Liu, H., Wei, W., Lin, W., Yu, W., Luo, W., Niu, Y. et al. (2021) miR‐32‐5p regulates lipid accumulation in intramuscular fat of Erhualian pigs by suppressing KLF3. Lipids, 56, 279–287.
Liu, L., Liu, X., Cui, H., Liu, R., Zhao, G. & Wen, J. (2019) Transcriptional insights into key genes and pathways controlling muscle lipid metabolism in broiler chickens. BMC Genomics, 20, 863.
Liu, X., Bai, Y., Cui, R., He, S., Zhao, X., Wu, K. et al. (2022) Sus_circPAPPA2 regulates fat deposition in castrated pigs through the miR‐2366/GK pathway. Biomolecules, 12, 753.
Liu, Y., Dou, Y., Qi, K., Li, C., Song, C., Li, X. et al. (2022) CircSETBP1 acts as a MiR‐149‐5p sponge to promote intramuscular fat deposition by regulating CRTCs. Journal of Agricultural and Food Chemistry, 70, 12841–12851.
Liufu, S., Lan, Q., Liu, X., Chen, B., Xu, X., Ai, N. et al. (2023) Transcriptome analysis reveals the age‐related developmental dynamics pattern of the longissimus dorsi muscle in Ningxiang pigs. Genes, 14, 1050.
Love, M.I., Huber, W. & Anders, S. (2014) Moderated estimation of fold change and dispersion for RNA‐seq data with DESeq2. Genome Biology, 15, 550.
Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A. et al. (2013) Circular RNAs are a large class of animal RNAs with regulatory potency. Nature, 495, 333–338.
Munoz, M., Garcia‐Casco, J.M., Caraballo, C., Fernández‐Barroso, M.Á., Sánchez‐Esquiliche, F., Gómez, F. et al. (2018) Identification of candidate genes and regulatory factors underlying intramuscular fat content through longissimus dorsi transcriptome analyses in heavy Iberian pigs. Frontiers in Genetics, 9, 608.
Nonneman, D.J., Shackelford, S.D., King, D.A. et al. (2013) Genome‐wide association of meat quality traits and tenderness in swine. Journal of Animal Science, 91, 4043–4050.
Pan, S., Zheng, Y., Zhao, R. & Yang, X. (2013) miRNA‐374 regulates dexamethasone‐induced differentiation of primary cultures of porcine adipocytes. Hormone and Metabolic Research, 45, 518–525.
Rosen, E.D. (2005) The transcriptional basis of adipocyte development. Prostaglandins, Leukotrienes, and Essential Fatty Acids, 73, 31–34.
Shan, B., Yan, M., Yang, K., Lin, W., Yan, J., Wei, S. et al. (2022) MiR‐218‐5p affects subcutaneous adipogenesis by targeting ACSL1, a novel candidate for pig fat deposition. Genes, 13, 260.
Sharma, D., Sehgal, P., Hariprakash, J., Sivasubbu, S. & Scaria, V. (2019) Methods for annotation and validation of circular RNAs from RNAseq data. Methods in Molecular Biology, 1912, 55–76.
Shi, C., Huang, F., Gu, X., Zhang, M., Wen, J., Wang, X. et al. (2016) Adipogenic miRNA and meta‐signature miRNAs involved in human adipocyte differentiation and obesity. Oncotarget, 7, 40830–40845.
Tang, D., Chen, M., Huang, X., Zhang, G., Zeng, L., Wu, S. et al. (2023) SRplot: a free online platform for data visualization and graphing. PLoS One, 18, e0294236.
Wang, J., Ren, Q., Hua, L., Chen, J., Zhang, J., Bai, H. et al. (2019) Comprehensive analysis of differentially expressed mRNA, lncRNA and circRNA and their ceRNA networks in the longissimus dorsi muscle of two different pig breeds. International Journal of Molecular Sciences, 20, 1107.
Wang, L., Liang, W., Wang, S., Wang, Z., Bai, H., Jiang, Y. et al. (2020) Circular RNA expression profiling reveals that circ‐PLXNA1 functions in duck adipocyte differentiation. PLoS One, 15, e0236069.
Wang, T., Tian, Z., Yu, M., Zhang, S., Zhang, M., Zhai, X. et al. (2024) Whole‐transcriptome analysis reveals the regulatory network of immune response in Dapulian pig. Animals, 14, 3546.
Wei, X., Shu, Z., Wang, L., Zhang, T., Zhang, L., Hou, X. et al. (2022) Copy number variations contribute to intramuscular fat content differences by affecting the expression of PELP1 alternative splices in pigs. Animals, 12, 1382.
Wu, W., Zhang, Z., Chao, Z., Li, B., Li, R., Jiang, A. et al. (2021) Transcriptome analysis reveals the genetic basis of skeletal muscle glycolytic potential based on a pig model. Gene, 766, 145157.
Xu, Z., Wu, J., Zhou, J., Zhang, Y., Qiao, M., Sun, H. et al. (2022) Integration of ATAC‐seq and RNA‐seq analysis identifies key genes affecting intramuscular fat content in pigs. Frontiers in Nutrition, 9, 1016956.
Yang, X., Li, F., Ma, J., Liu, Y., Wang, X., Wang, R. et al. (2021) Study on the relationship between the miRNA‐centered ceRNA regulatory network and fatigue. Journal of Molecular Neuroscience, 71, 1967–1974.
Yu, H., Yu, S., Guo, J., Wang, J., Mei, C., Abbas Raza, S.H. et al. (2024) Comprehensive analysis of transcriptome and metabolome reveals regulatory mechanism of intramuscular fat content in beef cattle. Journal of Agricultural and Food Chemistry, 72, 2911–2924.
Yu, M., Feng, Y., Yan, J., Zhang, X., Tian, Z., Wang, T. et al. (2024) Transcriptomic regulatory analysis of skeletal muscle development in landrace pigs. Gene, 915, 148407.
Yu, M., Zhang, X., Yan, J., Guo, J., Zhang, F., Zhu, K. et al. (2022) Transcriptional specificity analysis of testis and epididymis tissues in donkey. Genes, 13, 2339.
Zebisch, K., Voigt, V., Wabitsch, M. & Brandsch, M. (2012) Protocol for effective differentiation of 3T3‐L1 cells to adipocytes. Analytical Biochemistry, 425, 88–90.
Zhang, F.L., Feng, Y.Q., Wang, J.Y., Zhu, K.‐X., Wang, L., Yan, J.‐M. et al. (2023) Single cell epigenomic and transcriptomic analysis uncovers potential transcription factors regulating mitotic/meiotic switch. Cell Death & Disease, 14, 134.
Zhang, J., Wang, J., Ma, C., Wang, W., Wang, H. & Jiang, Y. (2022) Comparative transcriptomic analysis of mRNAs, miRNAs and lncRNAs in the longissimus dorsi muscles between fat‐type and lean‐type pigs. Biomolecules, 12, 1294.
Zhang, X., Huang, W., Guo, Y. & Miao, X. (2022) Integrative analysis of miRNAs involved in fat deposition in different pig breeds. Genes, 14, 94.
Zhang, Y., Zhang, J., Gong, H., Cui, L., Zhang, W., Ma, J. et al. (2019) Genetic correlation of fatty acid composition with growth, carcass, fat deposition and meat quality traits based on GWAS data in six pig populations. Meat Science, 150, 47–55.
Zhang, Z., Wang, W., Liu, J.B., Liu, J.‐.B., Wang, Y., Hao, J.‐.D. et al. (2020) Ssc‐miR‐204 regulates porcine preadipocyte differentiation and apoptosis by targeting TGFBR1 and TGFBR2. Journal of Cellular Biochemistry, 121, 609–620.
Zhang, Z., Zhang, Z., Oyelami, F.O., Sun, H., xu, Z., Ma, P. et al. (2021) Identification of genes related to intramuscular fat independent of backfat thickness in duroc pigs using single‐step genome‐wide association. Animal Genetics, 52, 108–113.
Zhou, J., Wu, J., Yang, T., Zhang, X., Qiao, M., Xu, Z. et al. (2024) Integration of ATAC‐seq and RNA‐seq reveals VDR‐SELENBP1 Axis promotes adipogenesis of porcine intramuscular preadipocytes. International Journal of Molecular Sciences, 25, 12528.
Zhuang, Z., Ding, R., Qiu, Y., Wu, J., Zhou, S., Quan, J. et al. (2021) A large‐scale genome‐wide association analysis reveals QTL and candidate genes for intramuscular fat content in duroc pigs. Animal Genetics, 52, 518–522.
Chen, J.N., Jiang, Y.Z., Cen, W.M., Xing, S.H., Zhu, L., Tang, G.Q. et al. (2014) Distribution of H‐FABP and ACSL4 gene polymorphisms and their associations with intramuscular fat content and backfat thickness in different pig populations. Genetics and Molecular Research, 13, 6759–6772.
Chen, S., Zhou, Y., Chen, Y. & Gu, J. (2018) Fastp: an ultra‐fast all‐in‐one FASTQ preprocessor. Bioinformatics, 34, i884–i890.
de Sena Brandine, G. & Smith, A.D. (2019) Falco: high‐speed FastQC emulation for quality control of sequencing data. F1000Research, 8, 1874.
Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S. et al. (2013) STAR: ultrafast universal RNA‐seq aligner. Bioinformatics, 29, 15–21.
Duo, T., Liu, X., Mo, D., Bian, Y., Cai, S., Wang, M. et al. (2023) Single‐base editing in IGF2 improves meat production and intramuscular fat deposition in Liang Guang small spotted pigs. Journal of Animal Science and Biotechnology, 14, 141.
Feng, H., Yousuf, S., Liu, T., Zhang, X., Huang, W., Li, A. et al. (2022) The comprehensive detection of miRNA and circRNA in the regulation of intramuscular and subcutaneous adipose tissue of Laiwu pig. Scientific Reports, 12, 16542.
Filshtein, T.J., Mackenzie, C.O., Dale, M.D., Dela‐Cruz, P.S., Ernst, D.M., Frankenberger, E.A. et al. (2012) OrbId: origin‐based identification of microRNA targets. Mobile Genetic Elements, 2, 184–192.
Gu, H., Zhou, Y., Yang, J. et al. (2021) Targeted overexpression of PPARgamma in skeletal muscle by random insertion and CRISPR/Cas9 transgenic pig cloning enhances oxidative fiber formation and intramuscular fat deposition. The FASEB Journal, 35, e21308.
Jin, Z., Gao, H., Fu, Y., Ren, R., Deng, X., Chen, Y. et al. (2024) Whole‐transcriptome analysis sheds light on the biological contexts of intramuscular fat deposition in Ningxiang pigs. Genes, 15, 642.
Joo, S.T., Kim, G.D., Hwang, Y.H. & Ryu, Y.C. (2013) Control of fresh meat quality through manipulation of muscle fiber characteristics. Meat Science, 95, 828–836.
Kozomara, A., Birgaoanu, M. & Griffiths‐Jones, S. (2019) miRBase: from microRNA sequences to function. Nucleic Acids Research, 47, D155–D162.
Li, X., Wang, J., Zhang, F., Yu, M., Zuo, N., Li, L. et al. (2023) Cyanidin‐3‐O‐glucoside rescues zearalenone‐induced apoptosis via the ITGA7‐PI3K‐AKT signaling pathway in porcine ovarian granulosa cells. International Journal of Molecular Sciences, 24, 4441.
Li, Z., Huang, C., Bao, C., Chen, L., Lin, M., Wang, X. et al. (2015) Exon‐intron circular RNAs regulate transcription in the nucleus. Nature Structural & Molecular Biology, 22, 256–264.
Liao, Y., Smyth, G.K. & Shi, W. (2014) featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30, 923–930.
Liu, H., Wei, W., Lin, W., Yu, W., Luo, W., Niu, Y. et al. (2021) miR‐32‐5p regulates lipid accumulation in intramuscular fat of Erhualian pigs by suppressing KLF3. Lipids, 56, 279–287.
Liu, L., Liu, X., Cui, H., Liu, R., Zhao, G. & Wen, J. (2019) Transcriptional insights into key genes and pathways controlling muscle lipid metabolism in broiler chickens. BMC Genomics, 20, 863.
Liu, X., Bai, Y., Cui, R., He, S., Zhao, X., Wu, K. et al. (2022) Sus_circPAPPA2 regulates fat deposition in castrated pigs through the miR‐2366/GK pathway. Biomolecules, 12, 753.
Liu, Y., Dou, Y., Qi, K., Li, C., Song, C., Li, X. et al. (2022) CircSETBP1 acts as a MiR‐149‐5p sponge to promote intramuscular fat deposition by regulating CRTCs. Journal of Agricultural and Food Chemistry, 70, 12841–12851.
Liufu, S., Lan, Q., Liu, X., Chen, B., Xu, X., Ai, N. et al. (2023) Transcriptome analysis reveals the age‐related developmental dynamics pattern of the longissimus dorsi muscle in Ningxiang pigs. Genes, 14, 1050.
Love, M.I., Huber, W. & Anders, S. (2014) Moderated estimation of fold change and dispersion for RNA‐seq data with DESeq2. Genome Biology, 15, 550.
Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A. et al. (2013) Circular RNAs are a large class of animal RNAs with regulatory potency. Nature, 495, 333–338.
Munoz, M., Garcia‐Casco, J.M., Caraballo, C., Fernández‐Barroso, M.Á., Sánchez‐Esquiliche, F., Gómez, F. et al. (2018) Identification of candidate genes and regulatory factors underlying intramuscular fat content through longissimus dorsi transcriptome analyses in heavy Iberian pigs. Frontiers in Genetics, 9, 608.
Nonneman, D.J., Shackelford, S.D., King, D.A. et al. (2013) Genome‐wide association of meat quality traits and tenderness in swine. Journal of Animal Science, 91, 4043–4050.
Pan, S., Zheng, Y., Zhao, R. & Yang, X. (2013) miRNA‐374 regulates dexamethasone‐induced differentiation of primary cultures of porcine adipocytes. Hormone and Metabolic Research, 45, 518–525.
Rosen, E.D. (2005) The transcriptional basis of adipocyte development. Prostaglandins, Leukotrienes, and Essential Fatty Acids, 73, 31–34.
Shan, B., Yan, M., Yang, K., Lin, W., Yan, J., Wei, S. et al. (2022) MiR‐218‐5p affects subcutaneous adipogenesis by targeting ACSL1, a novel candidate for pig fat deposition. Genes, 13, 260.
Sharma, D., Sehgal, P., Hariprakash, J., Sivasubbu, S. & Scaria, V. (2019) Methods for annotation and validation of circular RNAs from RNAseq data. Methods in Molecular Biology, 1912, 55–76.
Shi, C., Huang, F., Gu, X., Zhang, M., Wen, J., Wang, X. et al. (2016) Adipogenic miRNA and meta‐signature miRNAs involved in human adipocyte differentiation and obesity. Oncotarget, 7, 40830–40845.
Tang, D., Chen, M., Huang, X., Zhang, G., Zeng, L., Wu, S. et al. (2023) SRplot: a free online platform for data visualization and graphing. PLoS One, 18, e0294236.
Wang, J., Ren, Q., Hua, L., Chen, J., Zhang, J., Bai, H. et al. (2019) Comprehensive analysis of differentially expressed mRNA, lncRNA and circRNA and their ceRNA networks in the longissimus dorsi muscle of two different pig breeds. International Journal of Molecular Sciences, 20, 1107.
Wang, L., Liang, W., Wang, S., Wang, Z., Bai, H., Jiang, Y. et al. (2020) Circular RNA expression profiling reveals that circ‐PLXNA1 functions in duck adipocyte differentiation. PLoS One, 15, e0236069.
Wang, T., Tian, Z., Yu, M., Zhang, S., Zhang, M., Zhai, X. et al. (2024) Whole‐transcriptome analysis reveals the regulatory network of immune response in Dapulian pig. Animals, 14, 3546.
Wei, X., Shu, Z., Wang, L., Zhang, T., Zhang, L., Hou, X. et al. (2022) Copy number variations contribute to intramuscular fat content differences by affecting the expression of PELP1 alternative splices in pigs. Animals, 12, 1382.
Wu, W., Zhang, Z., Chao, Z., Li, B., Li, R., Jiang, A. et al. (2021) Transcriptome analysis reveals the genetic basis of skeletal muscle glycolytic potential based on a pig model. Gene, 766, 145157.
Xu, Z., Wu, J., Zhou, J., Zhang, Y., Qiao, M., Sun, H. et al. (2022) Integration of ATAC‐seq and RNA‐seq analysis identifies key genes affecting intramuscular fat content in pigs. Frontiers in Nutrition, 9, 1016956.
Yang, X., Li, F., Ma, J., Liu, Y., Wang, X., Wang, R. et al. (2021) Study on the relationship between the miRNA‐centered ceRNA regulatory network and fatigue. Journal of Molecular Neuroscience, 71, 1967–1974.
Yu, H., Yu, S., Guo, J., Wang, J., Mei, C., Abbas Raza, S.H. et al. (2024) Comprehensive analysis of transcriptome and metabolome reveals regulatory mechanism of intramuscular fat content in beef cattle. Journal of Agricultural and Food Chemistry, 72, 2911–2924.
Yu, M., Feng, Y., Yan, J., Zhang, X., Tian, Z., Wang, T. et al. (2024) Transcriptomic regulatory analysis of skeletal muscle development in landrace pigs. Gene, 915, 148407.
Yu, M., Zhang, X., Yan, J., Guo, J., Zhang, F., Zhu, K. et al. (2022) Transcriptional specificity analysis of testis and epididymis tissues in donkey. Genes, 13, 2339.
Zebisch, K., Voigt, V., Wabitsch, M. & Brandsch, M. (2012) Protocol for effective differentiation of 3T3‐L1 cells to adipocytes. Analytical Biochemistry, 425, 88–90.
Zhang, F.L., Feng, Y.Q., Wang, J.Y., Zhu, K.‐X., Wang, L., Yan, J.‐M. et al. (2023) Single cell epigenomic and transcriptomic analysis uncovers potential transcription factors regulating mitotic/meiotic switch. Cell Death & Disease, 14, 134.
Zhang, J., Wang, J., Ma, C., Wang, W., Wang, H. & Jiang, Y. (2022) Comparative transcriptomic analysis of mRNAs, miRNAs and lncRNAs in the longissimus dorsi muscles between fat‐type and lean‐type pigs. Biomolecules, 12, 1294.
Zhang, X., Huang, W., Guo, Y. & Miao, X. (2022) Integrative analysis of miRNAs involved in fat deposition in different pig breeds. Genes, 14, 94.
Zhang, Y., Zhang, J., Gong, H., Cui, L., Zhang, W., Ma, J. et al. (2019) Genetic correlation of fatty acid composition with growth, carcass, fat deposition and meat quality traits based on GWAS data in six pig populations. Meat Science, 150, 47–55.
Zhang, Z., Wang, W., Liu, J.B., Liu, J.‐.B., Wang, Y., Hao, J.‐.D. et al. (2020) Ssc‐miR‐204 regulates porcine preadipocyte differentiation and apoptosis by targeting TGFBR1 and TGFBR2. Journal of Cellular Biochemistry, 121, 609–620.
Zhang, Z., Zhang, Z., Oyelami, F.O., Sun, H., xu, Z., Ma, P. et al. (2021) Identification of genes related to intramuscular fat independent of backfat thickness in duroc pigs using single‐step genome‐wide association. Animal Genetics, 52, 108–113.
Zhou, J., Wu, J., Yang, T., Zhang, X., Qiao, M., Xu, Z. et al. (2024) Integration of ATAC‐seq and RNA‐seq reveals VDR‐SELENBP1 Axis promotes adipogenesis of porcine intramuscular preadipocytes. International Journal of Molecular Sciences, 25, 12528.
Zhuang, Z., Ding, R., Qiu, Y., Wu, J., Zhou, S., Quan, J. et al. (2021) A large‐scale genome‐wide association analysis reveals QTL and candidate genes for intramuscular fat content in duroc pigs. Animal Genetics, 52, 518–522.
Grant Information:
23-1-3-3-zyyd-nsh The Science & Technology Fund Planning Projects of Qingdao City; 2024LZGC002 Key Technology Research and Development Program of Shandong Province; 2024LZGC017 Key Technology Research and Development Program of Shandong Province; ZR2021QC041 Natural Science Foundation of Shandong Province; 6651122011 Start-Up Fund for High-Level Talents of Qingdao Agricultural University; SDAIT-08 Shandong Provincial Modern Agricultural Industry and Technology System
Contributed Indexing:
Keywords: SCML4; ceRNAs; intramuscular fat; pig; transcriptome
Substance Nomenclature:
0 (MicroRNAs)
0 (RNA, Circular)
0 (RNA, Messenger)
0 (RNA, Competitive Endogenous)
0 (RNA, Circular)
0 (RNA, Messenger)
0 (RNA, Competitive Endogenous)
Entry Date(s):
Date Created: 20260125 Date Completed: 20260125 Latest Revision: 20260125
Update Code:
20260130
DOI:
10.1002/age.70070
PMID:
41581928
Database:
MEDLINE
*Further Information*
*Intramuscular fat (IMF) content is an important factor for meat quality evaluation, which varies between species, and mainly involves the number and size of intramuscular adipocytes. However, the potential mechanism has not been well elucidated. In this study, the whole transcriptomic data of longissimus dorsi muscle from Laiwu pigs (LW, fatty type) and Duroc×Landrace×Yorkshire pigs (DLY, lean type) were collected and an in-depth analysis was conducted. Through differentially expressed analysis between species, 1899 mRNAs, 10 microRNAs (miRNAs), and 247 circular RNAs were identified. An integrated analysis of differentially expressed mRNAs and miRNAs generated two network modules that potentially regulate IMF formation in LW pigs, one consisted of 13 mRNAs (such as ESR1 and COQ3) and one miRNA gene (ssc-miR-874), and another included 31 mRNAs (such as SCML4 and PDE7B) and three miRNAs (ssc-miR-125a, ssc-miR-1343, and ssc-miR-204). In addition, a competitive endogenous RNA network including 13 circular RNAs, three miRNAs, and 31 genes was also delineated, which is probably involved in differential regulatory patterns of IMF deposition between LW and DLY pigs. The function of the SCML4 gene was verified with the 3T3-L1 cell line in vitro, and, when SCML4 was decreased, the expression of key proteins associated with fat formation (PPARγ and FABP4) was significantly inhibited. In summary, the study provided the novel insight of a competitive endogenous RNA regulatory network for IMF content in pig, and our results indicated that SCML4 is likely to be a regulatory gene promoting IMF formation.
(© 2026 Stichting International Foundation for Animal Genetics.)*