Dissection of Myogenic Differentiation Signatures in Chickens by RNA-Seq Analysis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Chicken Primary Myoblast Isolation and Culture
2.3. Immunofluorescence
2.4. RNA Isolation, Library Preparation, and Sequencing
2.5. Quality Control
2.6. Sequencing Data Analysis and Transcriptome Assembly
2.7. Identification of lncRNAs
2.8. lncRNAs Targets Prediction and Annotation
2.9. Screening and Clustering Analysis of Differentially Expressed lncRNAs and mRNAs
2.10. Gene Ontology and KEGG Enrichment Analysis
2.11. Validation of Gene Expression by Quantitative Real-Time Polymerase Chain Reaction Analysis
3. Results
3.1. Proliferation and Differentiation of Embryonic Primary Myoblasts
3.2. Overview of RNA-Sequencing
3.3. Identification and Characterization of lncRNAs in Chicken Myoblasts
3.4. Functional Enrichment Analysis: GO and KEGG
3.5. Differentially-Expressed lncRNAs and mRNAs during Primary Myoblast Differentiation
3.6. Verification of Gene Expression Profiles Using qPCR
4. Discussion
5. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Cluster (# of genes) | Example genes | Enriched GO terms | # of gens | p-value |
---|---|---|---|---|
K1 (1,436) | YY1, TGFβ1, SOX8, SIX1, SIX2, PAX3, PAX7, MYF5, MYF6, ID1, ID2, E2F7, E2F3, E2F1, E2F2, CDC7, CDC6, CDC45, CDC20, CDK1, CDK2, CDK6, CDK7 | Cell cycle process | 138 | 3.81 × 10−22 |
DNA metabolic process | 123 | 5.17 × 10−22 | ||
Cell cycle | 156 | 9.67 × 10−22 | ||
Chromosome organization | 132 | 4.51 × 10−21 | ||
DNA replication | 59 | 2.94 × 10−20 | ||
Mitotic cell cycle process | 92 | 1.86 × 10−17 | ||
Nuclear division | 73 | 5.56 × 10−17 | ||
DNA repair | 76 | 8.60 × 10−17 | ||
Mitotic cell cycle | 98 | 3.19 × 10−16 | ||
Chromosome segregation | 54 | 2.18 × 10−15 | ||
K2 (440) | MYOC, IGF2, MYO1D, FGF7, FGF18, FABP4, ECM2, DCX, FAP, FAT4, KLF15, LBP, SHOX, TF | Extracellular structure organization | 18 | 5.03 × 10−7 |
Extracellular matrix organization | 18 | 5.03 × 10−7 | ||
Chemotaxis | 24 | 1.0 6 ×10−5 | ||
Taxis | 24 | 1.13 × 10−5 | ||
Cellular response to chemical stimulus | 59 | 2.49 × 10−5 | ||
Response to external stimulus | 52 | 3.50 × 10−5 | ||
Regulation of cell migration | 27 | 6.87 × 10−5 | ||
Cellular response to organic substance | 49 | 7.19 × 10−5 | ||
Cell adhesion | 41 | 9.90 × 10−5 | ||
Biological adhesion | 41 | 1.09 × 10−4 | ||
K3 (1,762) | FLI1, KLF4, WNT9A, CTR, WNT5A, EGFR, BMP5, FAK, FGF14, FGF9, RAC2, MYH6, MYH10, MYCN, MXD4, IGFBP2, IGFBP4, IGFBP5 | Locomotion | 139 | 6.05 × 10−8 |
Movement of cell or subcellular component | 148 | 1.79 × 10−6 | ||
Enzyme linked receptor protein signaling pathway | 86 | 3.16 × 10−6 | ||
Transmembrane receptor protein tyrosine kinase signal | 61 | 7.29 × 10−6 | ||
Organ morphogenesis | 93 | 7.34 × 10−6 | ||
Biological adhesion | 118 | 9.30 × 10−6 | ||
Skeletal system development | 59 | 1.04 × 10−5 | ||
Cell adhesion | 117 | 1.25 × 10−5 | ||
Skeletal system morphogenesis | 36 | 1.42 × 10−5 | ||
Neurogenesis | 127 | 1.59 × 10−5 | ||
K4 (784) | TNNT3, SRF, RGS2, Myosin, MYOG, TMEM8C, DLL1 NOTCH1, MYOD, MEF2C, GDF8, MEF2D, MAPK13, DIK2, BMP4, β-FGF, ACTC1, MTOR, SMYD1 | Muscle structure development | 61 | 3.24 × 10−20 |
Muscle system process | 41 | 6.97 × 10−18 | ||
Muscle contraction | 37 | 3.07 × 10−17 | ||
Striated muscle cell differentiation | 35 | 2.35 × 10−15 | ||
System process | 87 | 5.03 × 10−14 | ||
Muscle cell differentiation | 41 | 1.18 × 10−13 | ||
Muscle tissue development | 41 | 2.72 × 10−13 | ||
Muscle organ development | 36 | 1.40 × 10−12 | ||
Striated muscle tissue development | 38 | 1.51 × 10−12 | ||
Muscle cell development | 26 | 3.83 × 10−12 |
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Li, T.; Zhang, G.; Wu, P.; Duan, L.; Li, G.; Liu, Q.; Wang, J. Dissection of Myogenic Differentiation Signatures in Chickens by RNA-Seq Analysis. Genes 2018, 9, 34. https://doi.org/10.3390/genes9010034
Li T, Zhang G, Wu P, Duan L, Li G, Liu Q, Wang J. Dissection of Myogenic Differentiation Signatures in Chickens by RNA-Seq Analysis. Genes. 2018; 9(1):34. https://doi.org/10.3390/genes9010034
Chicago/Turabian StyleLi, Tingting, Genxi Zhang, Pengfei Wu, Lian Duan, Guohui Li, Qiuhong Liu, and Jinyu Wang. 2018. "Dissection of Myogenic Differentiation Signatures in Chickens by RNA-Seq Analysis" Genes 9, no. 1: 34. https://doi.org/10.3390/genes9010034
APA StyleLi, T., Zhang, G., Wu, P., Duan, L., Li, G., Liu, Q., & Wang, J. (2018). Dissection of Myogenic Differentiation Signatures in Chickens by RNA-Seq Analysis. Genes, 9(1), 34. https://doi.org/10.3390/genes9010034