Genome-Wide DNA Methylation Profile Indicates Potential Epigenetic Regulation of Aging in the Rhesus Macaque Thymus
Abstract
:1. Introduction
2. Results
2.1. WGBS Data Processing and Alignment
2.2. DNA Methylation Profiles of the Thymus in Rhesus Macaques
2.3. DMGs and ASMs from the Thymus between the Two Age Groups
2.4. DEGs of the Thymus between the Two Age Groups in Macaques
2.5. Associations of Methylation and Expression
2.6. Promoter Methylation
2.7. Comparisons of the Age-Related Methylated Genes in Four Mammals
3. Discussion
3.1. DNA Methylation Profiles of the Thymus in the Rhesus Macaque
3.2. Age-Related Alterations of DNA Methylation and Gene Expression
3.3. Changes in Immune Function of the Thymus with Age
3.4. Comparisons of Age-Related Methylated Genes in Four Mammals
4. Materials and Methods
4.1. Sample Collection
4.2. Whole-Genome Bisulfite Library and RNA Library Preparation and Sequencing
4.3. Data Quality Control and Alignment
4.4. Differentially Methylated Regions Analysis and Annotation
4.5. Promoter Methylation Analysis
4.6. Associations of Methylation and Expression
4.7. Protein–Protein Interaction Network Analysis
4.8. Gene Annotation and Multi-Species Synteny
4.9. Identification of ASM Sites and aDMRs
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Pathway and Term | Pathway and Term ID | Gene Name | Ensembl ID | DNA Methylation Difference | Expression Change |
---|---|---|---|---|---|
Complement and coagulation cascades | KEGG:04610 | C3 | ENSMMUG00000008693 | − | + |
Complement and coagulation cascades | KEGG:04610 | F13A1 | ENSMMUG00000001248 | − | + |
Complement and coagulation cascades | KEGG:04610 | CPB2 | ENSMMUG00000017029 | − | − |
Complement and coagulation cascades; immune system process | KEGG:04610; GO:0002376 | C7 | ENSMMUG00000014171 | + | + |
Immune system process | GO:0002376 | C5AR2 | ENSMMUG00000009277 | − | + |
Immune system process | GO:0002376 | CLEC4D | ENSMMUG00000013703 | − | + |
Immune system process | GO:0002376 | CLEC4E | ENSMMUG00000013706 | − | + |
Immune system process | GO:0002376 | DNASE1L3 | ENSMMUG00000011235 | − | − |
Immune system process | GO:0002376 | FCN3 | ENSMMUG00000018322 | − | + |
Immune system process | GO:0002376 | HELLS | ENSMMUG00000017255 | + | − |
Immune system process | GO:0002376 | LCK | ENSMMUG00000040694 | + | − |
Immune system process; system development | GO:0002376; GO:0048733 | FANCD2 | ENSMMUG00000008966 | − | − |
Immune system process; system development | GO:0002376; GO:0048732 | LILRB4 | ENSMMUG00000047009 | + | − |
Immune system process; system development | GO:0002376; GO:0048734 | PDGFRA | ENSMMUG00000017395 | − | + |
Immune system process; system development | GO:0002376; GO:0048731 | RARA | ENSMMUG00000012486 | − | + |
System development | GO:0048731 | ADGRG3 | ENSMMUG00000015690 | − | + |
System development | GO:0048731 | CD3G | ENSMMUG00000017600 | − | − |
System development | GO:0048731 | NOX4 | ENSMMUG00000011116 | − | + |
System development | GO:0048731 | PROX1 | ENSMMUG00000011914 | − | + |
Carboxy-lyase activity | GO:0016831 | GAD2 | ENSMMUG00000012233 | − | − |
Cation binding | GO:0043169 | TRAIP | ENSMMUG00000016476 | + | − |
Cell division | GO:0051301 | MIS18BP1 | ENSMMUG00000016515 | + | − |
Cell–cell junction | GO:0005911 | CLDN11 | ENSMMUG00000009274 | − | + |
Cellular response to stress | GO:0033554 | UBE2T | ENSMMUG00000013795 | − | − |
Cytokinesis | GO:0000910 | KIF23 | ENSMMUG00000014887 | + | − |
DNA polymerase binding | GO:0070182 | FANCI | ENSMMUG00000011155 | − | − |
Hydrolase activity, hydrolyzing N-glycosyl compounds | GO:0016799 | NEIL3 | ENSMMUG00000007394 | + | − |
Hydrolase activity, hydrolyzing O-glycosyl compounds | GO:0004553 | MGAM | ENSMMUG00000016273 | − | + |
Immune response | GO:0006955 | CTSV | ENSMMUG00000022971 | − | − |
Intrinsic component of membrane | GO:0031224 | TMPO | ENSMMUG00000023719 | − | − |
Metallopeptidase activity | GO:0008237 | ADAMDEC1 | ENSMMUG00000005318 | − | − |
Metallopeptidase activity | GO:0008237 | ADAM28 | ENSMMUG00000005317 | − | − |
Microfilament motor activity | GO:0000146 | MYH8 | ENSMMUG00000009763 | − | − |
Molecular function | GO:0003674 | DLEU7 | ENSMMUG00000021744 | − | − |
Nucleic acid metabolic process | GO:0090304 | MCM4 | ENSMMUG00000015360 | + | − |
Nucleobase-containing compound metabolic process | GO:0006139 | POLE2 | ENSMMUG00000003913 | − | − |
Phosphoric ester hydrolase activity | GO:0042578 | PTPN7 | ENSMMUG00000013789 | − | − |
Plus-end-directed microtubule motor activity | GO:0008574 | KIF11 | ENSMMUG00000023266 | + | − |
Positive regulation of epithelial cell proliferation | GO:0050679 | FGF7 | ENSMMUG00000009842 | − | + |
Protein catabolic process | GO:0030163 | LRR1 | ENSMMUG00000037526 | + | − |
Protein catabolic process | GO:0030163 | LNX1 | ENSMMUG00000041981 | − | + |
Protein modification process | GO:0036211 | FBXO32 | ENSMMUG00000023778 | − | + |
Protein-containing complex | GO:0032991 | POLE | ENSMMUG00000015463 | − | − |
Regulation of gene expression | GO:0010468 | FGF2 | ENSMMUG00000007419 | − | + |
Response to stress | GO:0006950 | RAD51AP1 | ENSMMUG00000015189 | − | − |
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Qiu, H.; Li, H.; Fan, R.; Song, Y.; Pan, X.; Zhang, C.; Li, J. Genome-Wide DNA Methylation Profile Indicates Potential Epigenetic Regulation of Aging in the Rhesus Macaque Thymus. Int. J. Mol. Sci. 2022, 23, 14984. https://doi.org/10.3390/ijms232314984
Qiu H, Li H, Fan R, Song Y, Pan X, Zhang C, Li J. Genome-Wide DNA Methylation Profile Indicates Potential Epigenetic Regulation of Aging in the Rhesus Macaque Thymus. International Journal of Molecular Sciences. 2022; 23(23):14984. https://doi.org/10.3390/ijms232314984
Chicago/Turabian StyleQiu, Hong, Haobo Li, Ruiwen Fan, Yang Song, Xuan Pan, Chunhui Zhang, and Jing Li. 2022. "Genome-Wide DNA Methylation Profile Indicates Potential Epigenetic Regulation of Aging in the Rhesus Macaque Thymus" International Journal of Molecular Sciences 23, no. 23: 14984. https://doi.org/10.3390/ijms232314984