Table 2.
Top 30 hypermethylated CpG sites (P < 7.02E–09) located within promoter regions of genes in PNS cows at 5 years of age compared with 28 days of age
| |
|
|
|
Additional sitesd |
|
|---|---|---|---|---|---|
| BTAa | Mb | Differenceb | Genec | Control | PNS |
| 3 | 85.2 | 0.62 | Nuclear factor I A (NFIA) | 2 | 8 |
| 29 | 6.0 | 0.24 | Folate hydrolase 1B (FOLH1B) | 5 | 13 |
| 4 | 7.6 | 0.29 | Uridine phosphorylase 1 (UPP1) | 0 | 3 |
| 8 | 77.3 | 0.51 | Ciliary neurotrophic factor receptor (CNTFR) | 1 | 0 |
| 3 | 44.8 | 0.24 | Sorting nexin 7 (SNX7) | 3 | 2 |
| 2 | 20.9 | 0.27 | Homeobox D13 (HOXD13) | 16 | 2 |
| 17 | 45.2 | 0.38 | Zinc finger protein 891 (ZNF891) | 0 | 2 |
| 1 | 40.6 | 0.43 | EPH receptor A6 (EPHA6) | 19 | 20 |
| X | 145.4 | 0.25 | Anosmin 1 (ANOS1) | 0 | 3 |
| 10 | 57.7 | 0.21 | One cut homeobox 1 (ONECUT1) | 1 | 1 |
| 11 | 1.2 | 0.20 | BCL2 like 11 (BCL2L11) | 2 | 1 |
| 8 | 75.1 | 0.25 | PNMA family member 2 (PNMA2) | 0 | 1 |
| 14 | 79.0 | 0.28 | ATPase H+ transporting V0 subunit D2 (ATP6V0D2) | 0 | 1 |
| 3 | 44.8 | 0.20 | Sorting nexin 7 (SNX7) | 3 | 2 |
| 25 | 38.1 | 0.24 | Neuronal pentraxin 2 (NPTX2) | 5 | 0 |
| 2 | 41.5 | 0.33 | Potassium voltage-gated channel subfamily J member 3 (KCNJ3) | 2 | 3 |
| 12 | 90.0 | 0.26 | SRY-box 1 (SOX1) | 4 | 3 |
| 7 | 59.5 | 0.18 | POU class 4 homeobox 3 (POU4F3) | 2 | 0 |
| 3 | 85.2 | 0.48 | Nuclear factor I A (NFIA) | 2 | 8 |
| 5 | 1.9 | 0.30 | Thyrotropin releasing hormone degrading enzyme (TRHDE) | 2 | 8 |
| 18 | 13.2 | 0.21 | Junctophilin 3 (JPH3) | 0 | 1 |
| 8 | 5.8 | 0.39 | Heart and neural crest derivatives expressed 2 (HAND2) | 3 | 8 |
| 13 | 55.1 | 0.27 | Neurotensin receptor 1 (NTSR1) | 1 | 1 |
| 1 | 40.6 | 0.38 | EPH receptor A6 (EPHA6) | 19 | 20 |
| 21 | 66.3 | 0.13 | HHIP like 1 (HHIPL1) | 0 | 2 |
| 10 | 59.1 | 0.25 | Gliomedin (GLDN) | 0 | 1 |
| 10 | 21.4 | 0.37 | BCL2 like 2 (BCL2L2) | 4 | 0 |
| 8 | 101.8 | 0.19 | Sushi, von willebrand factor type A, EGF and pentraxin domain containing 1 (SVEP1) | 0 | 8 |
| 15 | 35.3 | 0.23 | Potassium voltage-gated channel subfamily C member 1 (KCNC1) | 0 | 7 |
| 4 | 120.5 | 0.24 | Vasoactive intestinal peptide receptor 2 (VIPR2) | 4 | 0 |
aBTA: Bos taurus autosome. X indicates Bos taurus X chromosome.
bMethylation difference was calculated by subtracting the mean methylation ratio in PNS at 28 days of age from the mean methylation ratio in PNS at 5 years of age.
cGenes in bold have the same CpG site differentially hypermethylated in Control (P < 0.01) as in PNS.
dTotal number of CpG sites differentially hypermethylated (P < 0.01; methylation ratio difference > 0.1) in the same gene’s promoter in Control cows, and additional sites in the promoter of the same gene in PNS, respectively.