Table 4.
Top 30 hypermethylated CpG sites (P < 1.19E–09) located within gene body regions in PNS cows at 5 years of age compared with 28 days of age
| BTAa | Mb | Differenceb | Genec |
Additional sitesd |
|
|---|---|---|---|---|---|
| Control | PNS | ||||
| 4 | 103.7 | 0.28 | ubinuclein 2 (UBN2) | 31 | 14 |
| 17 | 0.6 | 0.14 | Carboxypeptidase E (CPE) | 0 | 1 |
| 7 | 51.3 | 0.18 | GDNF family receptor alpha 3 (GFRA3) | 4 | 2 |
| 29 | 6.0 | 0.24 | Folate hydrolase 1B (FOLH1B) | 6 | 14 |
| 19 | 55.9 | 0.36 | Cytoglobin (CYGB) | 3 | 2 |
| 29 | 44.4 | 0.40 | Latent transforming growth factor beta binding protein 3 (LTBP3) | 7 | 11 |
| 4 | 7.6 | 0.29 | Uridine phosphorylase 1 (UPP1) | 1 | 3 |
| 3 | 44.8 | 0.24 | Sorting nexin 7 (SNX7) | 3 | 1 |
| 4 | 117.3 | 0.29 | Dipeptidyl peptidase like 6 (DPP6) | 3 | 2 |
| X | 83.2 | 0.15 | Phosphorylase kinase regulatory subunit alpha 1 (PHKA1) | 13 | 6 |
| 9 | 70.3 | 0.39 | A-kinase anchoring protein 7 (AKAP7) | 0 | 0 |
| 14 | 47.2 | 0.24 | MAL, T cell differentiation protein 2 (gene/pseudogene) (MAL2) | 2 | 0 |
| 5 | 54.1 | 0.19 | Solute carrier family 16 member 7 (SLC16A7) | 6 | 2 |
| 27 | 26.4 | 0.23 | WRN RecQ like helicase (WRN) | 8 | 9 |
| 3 | 24.2 | 0.27 | T-box 15 (TBX15) | 14 | 15 |
| X | 145.4 | 0.24 | Anosmin 1 (ANOS1) | 0 | 4 |
| 8 | 71.7 | 0.23 | NK2 homeobox 6 (NKX2-6) | 7 | 6 |
| 15 | 53.6 | 0.38 | Rho guanine nucleotide exchange factor 17 (ARHGEF17) | 0 | 0 |
| 13 | 24.5 | 0.21 | Pancreas associated transcription factor 1A (PTF1A) | 4 | 4 |
| 11 | 1.2 | 0.20 | BCL2 like 11 (BCL2L11) | 1 | 2 |
| 2 | 107.6 | 0.38 | WNT family member 10A (WNT10A) | 3 | 3 |
| 14 | 79.0 | 0.28 | ATPase H+ transporting V0 subunit D2 (ATP6V0D2) | 0 | 1 |
| 3 | 44.8 | 0.20 | Sorting nexin 7 (SNX7) | 3 | 1 |
| 5 | 26.2 | 0.40 | Homeobox C9 (HOXC9) | 0 | 1 |
| 3 | 121.1 | 0.34 | THAP domain containing 4 (THAP4) | 3 | 2 |
| 19 | 13.6 | 0.52 | LIM homeobox 1 (LHX1) | 0 | 6 |
| 8 | 30.0 | 0.53 | Nuclear factor I B (NFIB) | 0 | 1 |
| 17 | 71.7 | 0.60 | Pescadillo ribosomal biogenesis factor 1 (PES1) | 0 | 2 |
| 13 | 2.4 | 0.30 | Lysosomal associated membrane protein family member 5 (LAMP5) | 0 | 0 |
| 25 | 28.9 | 0.20 | Calneuron 1 (CALN1) | 1 | 3 |
aBTA: Bos taurus autosome. X indicates Bos taurus X chromosome. DNA methylation in bolded chromosomes was located within exons, otherwise within introns.
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 gene body in Control cows, and additional sites in the gene body of the same gene in PNS, respectively.