The Integration of Genome-Wide DNA Methylation and Transcriptomics Identifies the Potential Genes That Regulate the Development of Skeletal Muscles in Ducks
Abstract
:1. Introduction
2. Results
2.1. DNA Methylation Pattern in Duck Skeletal Muscle
2.2. Identification of Differentially Methylated Regions (DMRs)
2.3. Functional Enrichment of Genes with Methylation
2.4. Association Analysis of DNA Methylation and Gene Expression
2.5. The Key Pathways Enriched the DMGs Negatively Associated with DEGs
2.6. Identification of Genes Implicated in the Development of Skeletal Muscles
2.7. Prediction of the CpG Islands on the Promoters
3. Discussion
4. Materials and Methods
4.1. Tissue Sampling
4.2. DNA and RNA Extraction
4.3. RNA-Seq
4.4. Genome-Wide DNA Methylation Profiling
4.5. Gene Functional Enrichment Analysis
4.6. Verification of Critical Gene Expression Level
4.7. CpG Island Prediction of Key Genes
4.8. Statistical Analysis
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene Name | Log2 Fold Change | Diff.Methy | C Context | Region |
---|---|---|---|---|
Klhl38 | 6.341923585 | −0.161196584 | CG | promoter |
Mylk2 | 3.680553968 | −0.353681294 | CG | promoter |
Got1 | 2.956657678 | −0.209114374 | CG | promoter |
Klf2 | 1.683077721 | −0.291024055 | CG | promoter |
Erbin | 1.483720868 | −0.310759514 | CG | promoter |
Idh3a | 3.115334047 | −0.126427439 | CG | exon |
Bcl2 | 1.555105211 | −0.228206336 | CG | exon |
E2f1 | −2.0475711 | 0.125491948 | CG | exon |
Fn1 | −2.834137149 | 0.353384159 | CG | exon |
Wfikkn1 | −3.111804698 | 0.161546317 | CG | exon |
Dnmt3b | −3.684262185 | 0.269994984 | CG | exon |
Col22a1 | −4.123660418 | 0.35941219 | CG | exon |
Rprm | −5.226699842 | 0.122454333 | CG | exon |
Gene Name | Primer Sequences | Product Length | Gene Accession Number |
---|---|---|---|
Bcl2 | F: 5′-TGTGCGTGGAGAGCGTCAAC-3′ | 79 | XM_027451680.2 |
R: 5′-CGGTTCAGGTACTCGGTCATCC-3′ | |||
Klf2 | F: 5′-GCCTGCCCTTACAACCCTCTG-3′ | 172 | XM_027472014.2 |
R: 5′-TGCGAACTCTTGGTGTAGGTCTTC-3′ | |||
Fn1 | F: 5′-GGAGGTAGTCACAGTTGGCAATAC-3′ | 71 | XM_038182473.1 |
R: 5′-TGTCGTAGCAGGTGTCGTCAG-3′ | |||
Klhl38 | F: 5′-TCCAGGCAAGACAAGGCTACATC-3′ | 122 | XM_038174946.1 |
R: 5′-GCAAGTGGGTGAAGACTGAACAAG-3′ | |||
Erbin | F: 5′-AGCAATATTCAGCCGGAAGC-3′ | 153 | XM_038169994.1 |
R: 5′-AACAAGTGCAGCCATCTGTG-3′ | |||
Mylk2 | F: 5′-AACGACACCGAGACGCTGAAC-3′ | 173 | XM_038166457.1 |
R: 5′-AGGTTGTTGAGCCAGGGATGC-3′ | |||
Dnmt3b | F: 5′-TCTGGGGAAAGATCAAAGGTT-3′ | 191 | XM_038166400.1 |
R: 5′-AAACGTGGCAGAATTGAAATG-3′ | |||
Wfikkn1 | F: 5′-GGCTCTGACTGCGACATCTGG-3′ | 128 | XM_027468956.2 |
R: 5′-TCGGCGTCCATGTAGCACTTG-3′ | |||
Got1 | F: 5′-TTGCCGAGTGGAAGGACAACG-3′ | 138 | XM_027460734.2 |
R: 5′-AGCTGAACATGCCGATCTGGTC-3′ | |||
Idh3a | F: 5′-TGCTGGATTGATTGGGGGTC-3′ | 146 | XM_027465914.2 |
R: 5′-CAGCACTCAGAAGAAGGGCA-3′ | |||
Col22a1 | F: 5′-ATTGACAAGTACGGCATACCACAG-3′ | 106 | XM_038175073.1 |
R: 5′-AAACCACTCTCACGGCATCTTTG-3′ | |||
Rprm | F: 5′-TGGTGCAGATCGCCGTCATG-3′ | 73 | XM_038182513.1 |
R: 5′-AGGTTGCAGCCGAGGAAGAAG-3′ | |||
E2f1 | F: 5′-CTCGCTGAACCTCACCACCAAG-3′ | 113 | XM_038166109.1 |
R: 5′-AGATTCGCCTCTTCTGCACCTTC-3′ | |||
β-actin | F: 5′-TGCGTGACATCAAGGAGAAG-3′ | 300 | NM_001310421.1 |
R: 5′-TGCCCGGGTACATTGTGGTA-3′ |
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Lu, Y.; Zhou, J.; Li, F.; Cao, H.; Zhang, X.; Yu, D.; He, Z.; Ji, H.; Lv, K.; Wu, G.; et al. The Integration of Genome-Wide DNA Methylation and Transcriptomics Identifies the Potential Genes That Regulate the Development of Skeletal Muscles in Ducks. Int. J. Mol. Sci. 2023, 24, 15476. https://doi.org/10.3390/ijms242015476
Lu Y, Zhou J, Li F, Cao H, Zhang X, Yu D, He Z, Ji H, Lv K, Wu G, et al. The Integration of Genome-Wide DNA Methylation and Transcriptomics Identifies the Potential Genes That Regulate the Development of Skeletal Muscles in Ducks. International Journal of Molecular Sciences. 2023; 24(20):15476. https://doi.org/10.3390/ijms242015476
Chicago/Turabian StyleLu, Yinglin, Jing Zhou, Fan Li, Heng Cao, Xingyu Zhang, Debing Yu, Zongliang He, Hongjie Ji, Kunpeng Lv, Guansuo Wu, and et al. 2023. "The Integration of Genome-Wide DNA Methylation and Transcriptomics Identifies the Potential Genes That Regulate the Development of Skeletal Muscles in Ducks" International Journal of Molecular Sciences 24, no. 20: 15476. https://doi.org/10.3390/ijms242015476