References
- Abdalla, B. A., J. Chen, Q. Nie, and X. Zhang. 2018. “Genomic Insights into the Multiple Factors Controlling Abdominal Fat Deposition in a Chicken Model.” Frontiers in Genetics 9: 262. doi:https://doi.org/10.3389/fgene.2018.00262.
- Agarwal, V., G. W. Bell, J.-W. Nam, and D. P. Bartel. 2015. “Predicting Effective microRNA Target Sites in Mammalian mRNAs.” eLife 4: e05005. doi:https://doi.org/10.7554/eLife.05005.
- Bastian, M., S. Heymann, and M. Jacomy. 2009. “Gephi: An Open Source Software for Exploring and Manipulating Networks.” International AAAI Conference on Weblogs and Social Media 8: 361–362. doi:https://doi.org/10.13140/2.1.1341.1520.
- Bushati, N., and S. M. Cohen. 2007. “microRNA Functions.” Annual Review of Cell and Developmental Biology 23: 175–205. doi:https://doi.org/10.1146/annurev.cellbio.23.090506.123406.
- Chao, X., L. Guo, Q. Wang, W. Huang, M. Liu, K. Luan, J. Jiang, et al. 2020. “miR-429-3p/LPIN1 Axis Promotes Chicken Abdominal Fat Deposition via PPARγ Pathway.” Frontiers in Cell and Developmental Biology 8: 595637. doi:https://doi.org/10.3389/fcell.2020.595637.
- Chen, C., B. Deng, M. Qiao, R. Zheng, J. Chai, Y. Ding, J. Peng, and S. Jiang. 2012. “Solexa Sequencing Identification of Conserved and Novel microRNAs in Backfat of Large White and Chinese Meishan Pigs.” PLoS One 7: e31426. doi:https://doi.org/10.1371/journal.pone.0031426.
- Chen, K. H., X. H. Xu, Y. Liu, Y. Hu, M. W. Jin, and G. R. Li. 2014. “TRPM7 Channels Regulate Proliferation and Adipogenesis in 3T3-L1 Preadipocytes.” Journal of Cellular Physiology 229: 60–67. doi:https://doi.org/10.1002/jcp.24417.
- Chen, S., Y. Zhou, Y. Chen, and G. Jia. 2018. “Fastp: An Ultra-fast All-in-one FASTQ Preprocessor.” Bioinformatics 34: i884–i890. doi:https://doi.org/10.1093/bioinformatics/bty560.
- Claire D’Andre, H., W. Paul, X. Shen, X. Jia, R. Zhang, L. Sun, and X. Zhang. 2013. “Identification and Characterization of Genes that Control Fat Deposition in Chickens.” Journal of Animal Science and Biotechnology 4: 43. doi:https://doi.org/10.1186/2049-1891-4-43.
- Espinoza, J. L., V. H. Nguyen, T. T. Hiroshi Ichimura, T. Pham, C. H. Nguyen, T. V. Pham, M. I. Elbadry, et al. 2016. “A Functional Polymorphism in the NKG2D Gene Modulates NK-cell Cytotoxicity and Is Associated with Susceptibility to Human Papilloma Virus-related Cancers.” Scientific Reports 6: 39231. doi:https://doi.org/10.1038/srep39231.
- Friedländer, M. R., S. D. Mackowiak, L. Na, W. Chen, and N. Rajewsky. 2012. “miRDeep2 Accurately Identifies Known and Hundreds of Novel microRNA Genes in Seven Animal Clades.” Nucleic Acids Research 40: 37–52. doi:https://doi.org/10.1093/nar/gkr688.
- Fu, S., Y. Zhao, Y. Li, G. Li, Y. Chen, Z. Li, G. Sun, H. Li, X. Kang, and F. Yan. 2018. “Characterization of miRNA Transcriptome Profiles Related to Breast Muscle Development and Intramuscular Fat Deposition in Chickens.” Journal of Cellullar Biochemistry 119: 7063–7079. doi:https://doi.org/10.1002/jcb.27024.
- Gao, S., Z. Wu, X. Feng, S. Kajigaya, X. Wang, and N. S. Young. 2020. “Comprehensive Network Modeling from Single Cell RNA Sequencing of Human and Mouse Reveals Well Conserved Transcription Regulation of Hematopoiesis.” BMC Genomics 21: 849. doi:https://doi.org/10.1186/s12864-020-07241-2.
- Gu, D., B. Yu, C. Zhao, W. Ye, Q. Lv, Z. Hua, J. Ma, and Y. Zhang. 2007. “The Effect of Pleiotrophin Signaling on Adipogenesis.” FEBS Letters 581: 382–388. doi:https://doi.org/10.1016/j.febslet.2006.12.043.
- Guo, J., W. Fang, L. Sun, Y. Lu, L. Dou, X. Huang, W. Tang, L. Yu, and J. Li. 2018. “Ultraconserved Element Uc.372 Drives Hepatic Lipid Accumulation by Suppressing miR-195/miR4668 Maturation.” Nature Communications 9: 612. doi:https://doi.org/10.1038/s41467-018-03072-8.
- Jeon, Y., S. Song, H. Kim, and Y. P. Cheon. 2013. “Diphlorethohydroxycarmalol of Ishige Okamurae and Caffeine Modified the Expression of Extracellular Fibrillars during Adipogenesis of Mouse Subcutaneous Adipose Derived Stem Cell.” Development & Reproduction 17: 275–287. doi:https://doi.org/10.12717/dr.2013.17.3.275.
- Jeong, B. C., I. H. Kang, Y. C. Hwang, S. H. Kim, and J. T. Koh. 2014. “MicroRNA-194 Reciprocally Stimulates Osteogenesis and Inhibits Adipogenesis via Regulating COUP-TFII Expression.” Cell Death & Disease 5: e1532–e1532. doi:https://doi.org/10.1038/cddis.2014.485.
- Jiang, M., W. L. Fan, S. Y. Xing, J. Wang, P. Li, R. R. Liu, Q. H. Li, et al. 2017. “Effects of Balanced Selection for Intramuscular Fat and Abdominal Fat Percentage and Estimates of Genetic Parameters.” Poultry Science 96: 282–287. doi:https://doi.org/10.3382/ps/pew334.
- Keller, M., L. Hopp, X. Liu, T. Wohland, K. Rohde, R. Cancello, M. Klös, et al. 2017. “Genome-wide DNA Promoter Methylation and Transcriptome Analysis in Human Adipose Tissue Unravels Novel Candidate Genes for Obesity.” Molecular Metabolism 6: 86–100. doi:https://doi.org/10.1016/j.molmet.2016.11.003.
- Kim, D., J. M. Paggi, C. Park, C. Bennett, and S. L. Salzberg. 2019. “Graph-based Genome Alignment and Genotyping with HISAT2 and HISAT-genotype.” Nature Biotechnology 37: 907–915. doi:https://doi.org/10.1038/s41587-019-0201-4.
- Krüger, J., and M. Rehmsmeier. 2006. “RNAhybrid: MicroRNA Target Prediction Easy, Fast and Flexible.” Nucleic Acids Research 34: W451–W454. doi:https://doi.org/10.1093/nar/gkl243.
- Langmead, B., and S. L. Salzberg. 2012. “Fast Gapped-read Alignment with Bowtie 2.” Nature Methods 9: 357–359. doi:https://doi.org/10.1038/nmeth.1923.
- Lee, E. K., M. J. Lee, K. Abdelmohsen, W. Kim, M. M. Kim, S. Srikantan, J. L. Martindale, et al. 2011. “miR-130 Suppresses Adipogenesis by Inhibiting Peroxisome Proliferator-activated Receptor Gamma Expression.” Molecular and Cellular Biology 31: 626–638. doi:https://doi.org/10.1128/mcb.00894-10.
- Lee, R. C., and V. Ambros. 2001. “An Extensive Class of Small RNAs in Caenorhabditis Elegans.” Science 294: 862–864. doi:https://doi.org/10.1126/science.1065329.
- Li, F., L. Donghua, M. Zhang, J. Sun, L. Wenting, R. Jiang, R. Han, et al. 2019. “miRNA-223 Targets the GPAM Gene and Regulates the Differentiation of Intramuscular Adipocytes.” Gene 685: 106–113. doi:https://doi.org/10.1016/j.gene.2018.10.054.
- Li, G., Y. Chen, W. Jin, B. Zhai, Y. Li, G. Sun, H. Li, X. Kang, and Y. Tian. 2021. “Effects of miR-125b-5p on Preadipocyte Proliferation and Differentiation in Chicken.” Molecular Biology Reports 48: 491–502. doi:https://doi.org/10.1007/s11033-020-06080-4.
- Livak, K. J., and T. D. Schmittgen. 2001. “Analysis of Relative Gene Expression Data Using Real-time Quantitative PCR and the 2(T)(-Delta Delta C) Method.” Methods 25: 402–408. doi:https://doi.org/10.1006/meth.2001.1262.
- Love, M. I., W. Huber, and S. Anders. 2014. “Moderated Estimation of Fold Change and Dispersion for RNA-seq Data with DESeq2.” Genome Biology 15: 550. doi:https://doi.org/10.1186/s13059-014-0550-8.
- Maharjan, B. R., S. V. McLennan, S. M. Twigg, and P. F. Williams. 2020. “The Effect of TGFβ1 on Thermogenic Markers Is Dependent on the Degree of Adipocyte Differentiation.” Bioscience Reports 40 (BSR20194262). doi:https://doi.org/10.1042/bsr20194262.
- Milićević, D., D. Vranić, Z. Mašić, N. Parunović, D. Trbović, J. Nedeljković-Trailović, and Z. Petrović. 2014. “The Role of Total Fats, Saturated/unsaturated Fatty Acids and Cholesterol Content in Chicken Meat as Cardiovascular Risk Factors.” Lipids in Health and Disease 13: 42. doi:https://doi.org/10.1186/1476-511x-13-42.
- Nematbakhsh, S., C. Pei Pei, J. Selamat, N. Nordin, L. H. Idris, and A. F. Abdull Razis. 2021. “Molecular Regulation of Lipogenesis, Adipogenesis and Fat Deposition in Chicken.” Genes (Basel) 12: 414. doi:https://doi.org/10.3390/genes12030414.
- Pertea, M., G. M. Pertea, C. M. Antonescu, T.-C. Chang, J. T. Mendell, and S. L. Salzberg. 2015. “StringTie Enables Improved Reconstruction of a Transcriptome from RNA-seq Reads.” Nature Biotechnology 33: 290–295. doi:https://doi.org/10.1038/nbt.3122.
- Robinson, M. D., D. J. McCarthy, and G. K. Smyth. 2010. “edgeR: A Bioconductor Package for Differential Expression Analysis of Digital Gene Expression Data.” Bioinformatics 26: 139–140. doi:https://doi.org/10.1093/bioinformatics/btp616.
- Soukas, A., N. D. Socci, B. D. Saatkamp, S. Novelli, and J. M. Friedman. 2001. “Distinct Transcriptional Profiles of Adipogenesis in Vivo and in Vitro.” Journal of Biological Chemistry 276: 34167–34174. doi:https://doi.org/10.1074/jbc.M104421200.
- Sun, G., F. Li, X. Ma, J. Sun, R. Jiang, Y. Tian, R. Han, et al. 2019. “gga-miRNA-18b-3p Inhibits Intramuscular Adipocytes Differentiation in Chicken by Targeting the ACOT13 Gene.” Cells 8: 556. doi:https://doi.org/10.3390/cells8060556.
- Tang, Q. Q., and M. D. Lane. 2012. “Adipogenesis: From Stem Cell to Adipocyte.” Annual Review of Biochemistry 81: 715–736. doi:https://doi.org/10.1146/annurev-biochem-052110-115718.
- Tao, C., H. Ren, P. Xu, J. Cheng, S. Huang, R. Zhou, Y. Mu, et al. 2016. “Adipocyte miR-200b/a/429 Ablation in Mice Leads to High-fat-diet-induced Obesity.” Oncotarget 7: 67796–67807. doi:https://doi.org/10.18632/oncotarget.12080.
- Tontonoz, P., and B. M. Spiegelman. 2008. “Fat and Beyond: The Diverse Biology of PPARgamma.” Annual Review of Biochemistry 77: 289–312. doi:https://doi.org/10.1146/annurev.biochem.77.061307.091829.
- Ullah, M., M. Sittinger, and J. Ringe. 2013. “Extracellular Matrix of Adipogenically Differentiated Mesenchymal Stem Cells Reveals a Network of Collagen Filaments, Mostly Interwoven by Hexagonal Structural Units.” Matrix Biology 32: 452–465. doi:https://doi.org/10.1016/j.matbio.2013.07.001.
- Wang, J. M., Y. Qiu, Z. Yang, H. Kim, Q. Qian, Q. Sun, C. Zhang, et al. 2018. “IRE1α Prevents Hepatic Steatosis by Processing and Promoting the Degradation of Select microRNAs.” Science Signaling 11 (eaao4617). doi:https://doi.org/10.1126/scisignal.aao4617.
- Wang, Y., H. Wang, W. Na, F. Qin, Z. Zhang, J. Dong, H. Li, and H. Zhang. 2019. “The Retinoblastoma 1 Gene (RB1) Modulates the Proliferation of Chicken Preadipocytes.” British Poultry Science 60: 323–329. doi:https://doi.org/10.1080/00071668.2019.1584792.
- Xu, S., Y. Chang, W. Guanxian, W. Zhang, and C. Man. 2020. “Potential Role of miR-155-5p in Fat Deposition and Skeletal Muscle Development of Chicken.” Bioscience Reports 40 (BSR20193796). doi:https://doi.org/10.1042/BSR20193796.
- Yang, M., X. Liu, F. Meng, Y. Zhang, M. Wang, Y. Chen, X. Guo, W. Chen, and W. Wang. 2020. “The rs7911488-T Allele Promotes the Growth and Metastasis of Colorectal Cancer through Modulating miR-1307/PRRX1.” Cell Death & Disease 11: 651. doi:https://doi.org/10.1038/s41419-020-02834-x.
- You, L., Y. Wang, Y. Gao, X. Wang, X. Cui, Y. Zhang, L. Pang, C. Ji, X. Guo, and X. Chi. 2020. “The Role of microRNA-23b-5p in Regulating Brown Adipogenesis and Thermogenic Program.” Endocrine Connections 9: 457–470. doi:https://doi.org/10.1530/ec-20-0124.
- Yu, Y., J. T. Dong, B. He, Y. F. Zou, X. S. Li, C. H. Xi, and Y. Yu. 2019. “LncRNA SNHG16 Induces the SREBP2 to Promote Lipogenesis and Enhance the Progression of Pancreatic Cancer.” Future Oncology 15: 3831–3844. doi:https://doi.org/10.2217/fon-2019-0321.
- Yun, U. J., N. J. Song, D. K. Yang, S. M. Kwon, K. Kim, S. Kim, D. G. Jo, W. J. Park, K. W. Park, and H. Kang. 2015. “miR-195a Inhibits Adipocyte Differentiation by Targeting the Preadipogenic Determinator Zfp423.” Journal of Cellular Biochemistry 116: 2589–2597. doi:https://doi.org/10.1002/jcb.25204.
- Zhang, M., D. H. Li, F. Li, J. W. Sun, R. R. Jiang, Z. J. Li, R. L. Han, et al. 2018. “Integrated Analysis of MiRNA and Genes Associated with Meat Quality Reveals that Gga-MiR-140-5p Affects Intramuscular Fat Deposition in Chickens.” Cellullar Physiology and Biochemistry 46: 2421–2433. doi:https://doi.org/10.1159/000489649.
- Zhang, M., F. Li, J. W. Sun, D. H. Li, W. T. Li, R. R. Jiang, Z. J. Li, et al. 2019b. “LncRNA IMFNCR Promotes Intramuscular Adipocyte Differentiation by Sponging miR-128-3p and miR-27b-3p.” Frontiers in Genetics 10: 42. doi:https://doi.org/10.3389/fgene.2019.00042.
- Zhang, M., F. Li, X. F. Ma, W. T. Li, R. R. Jiang, R. L. Han, G. X. Li, et al. 2019a. “Identification of Differentially Expressed Genes and Pathways between Intramuscular and Abdominal Fat-derived Preadipocyte Differentiation of Chickens in Vitro.” BMC Genomics 20: 743. doi:https://doi.org/10.1186/s12864-019-6116-0.
- Zhang, M., X. Ma, Y. Zhai, D. Zhang, L. Sui, W. Li, R. Jiang, et al. 2020. “Comprehensive Transcriptome Analysis of lncRNAs Reveals the Role of lncAD in Chicken Intramuscular and Abdominal Adipogenesis.” Journal of Agricultural and Food Chemistry 68: 3678–3688. doi:https://doi.org/10.1021/acs.jafc.9b07405.
- Zhang, T., X. Zhang, K. Han, G. Zhang, J. Wang, K. Xie, and Q. Xue. 2017. “Genome-Wide Analysis of lncRNA and mRNA Expression during Differentiation of Abdominal Preadipocytes in the Chicken.” G3 (Bethesda) 7 (953–966). doi:https://doi.org/10.1534/g3.116.037069.
- Zhou, H., T. Kaplan, Y. Li, I. Grubisic, Z. Zhang, P. J. Wang, M. B. Eisen, and R. Tjian. 2013. “Dual Functions of TAF7L in Adipocyte Differentiation.” Elife 2: e00170. doi:https://doi.org/10.7554/eLife.00170.