Identification of Susceptibility Genes Underlying Bovine Respiratory Disease in Xinjiang Brown Cattle Based on DNA Methylation
Abstract
:1. Introduction
2. Results
2.1. Genome-Wide DNA Methylation Profile Analyses
2.2. DMR Profiling
2.3. GO/KEGG Enrichment Analysis for DMGs
2.4. Screening of Possibly Valuable DMGs Linked to Immune Function
2.5. Differential Gene Methylation Regulating Influence upon the Immunology of Cattle
3. Discussion
4. Materials and Methods
4.1. Animal Experiments
4.2. Library Construction
4.3. Whole-Genome Bisulfite Sequencing (WGBS) and Differentially Methylated Region (DMR) Determination
4.4. Functional Enrichment Analysis
4.5. Quantitative Reverse Transcription-PCR
4.6. RNA-Seq Data Analysis
4.7. Correlation 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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Group | Samples | Clean Bases (Gb) | Clean Reads | GC (%) | Q 30 (%) | Mapping Rate (%) | Bs Conversion Rate (%) | mC Percent (%) |
---|---|---|---|---|---|---|---|---|
Cases | Case1 | 76.94 | 280,373,522 | 23.22 | 91.9 | 72.05 | 99.742 | 3.13 |
Case2 | 78.94 | 287,142,601 | 22.86 | 92.59 | 72.12 | 99.717 | 3.21 | |
Case3 | 78.90 | 287,493,079 | 22.81 | 91.37 | 72.05 | 99.703 | 3.19 | |
Controls | Control1 | 75.60 | 277,034,171 | 22.77 | 89.35 | 70.79 | 99.702 | 3.05 |
Control2 | 74.03 | 272,716,162 | 22.73 | 88.91 | 70.42 | 99.673 | 3.07 | |
Control3 | 76.73 | 279,618,157 | 23.05 | 91.34 | 73.19 | 99.707 | 3.39 |
RNA-Seq | WGBS-Seq | |||
---|---|---|---|---|
Gene | Regulation | Meth Chr | Annotation | Stat |
LTA | Underexpressed | 23 | exon, utr5, TSS, promoter, | hyper |
IRAK1 | Underexpressed | X | exon, intron, utr5, TSS promoter | hyper |
CSK | Underexpressed | 21 | intron, exon, utr5 | hyper |
STAT3 | Overexpressed | 19 | intron | hypo |
IKBKG | Overexpressed | X | TSS, exon, utr5, intron, promoter | hypo |
NOD2 | Overexpressed | 18 | exon | hypo |
TLR2 | Overexpressed | 17 | exon | hypo |
TNFRSF1A | Overexpressed | 5 | promoter, intron, exon, utr3 | hypo |
IKBKB | Underexpressed | 27 | intron | hypo |
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Cao, H.; Fang, C.; Liu, L.-L.; Farnir, F.; Liu, W.-J. Identification of Susceptibility Genes Underlying Bovine Respiratory Disease in Xinjiang Brown Cattle Based on DNA Methylation. Int. J. Mol. Sci. 2024, 25, 4928. https://doi.org/10.3390/ijms25094928
Cao H, Fang C, Liu L-L, Farnir F, Liu W-J. Identification of Susceptibility Genes Underlying Bovine Respiratory Disease in Xinjiang Brown Cattle Based on DNA Methylation. International Journal of Molecular Sciences. 2024; 25(9):4928. https://doi.org/10.3390/ijms25094928
Chicago/Turabian StyleCao, Hang, Chao Fang, Ling-Ling Liu, Frederic Farnir, and Wu-Jun Liu. 2024. "Identification of Susceptibility Genes Underlying Bovine Respiratory Disease in Xinjiang Brown Cattle Based on DNA Methylation" International Journal of Molecular Sciences 25, no. 9: 4928. https://doi.org/10.3390/ijms25094928
APA StyleCao, H., Fang, C., Liu, L. -L., Farnir, F., & Liu, W. -J. (2024). Identification of Susceptibility Genes Underlying Bovine Respiratory Disease in Xinjiang Brown Cattle Based on DNA Methylation. International Journal of Molecular Sciences, 25(9), 4928. https://doi.org/10.3390/ijms25094928