Table 3.
Top 30 hypomethylated CpG sites (P < 1.76E–04) 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 |
| 10 | 41.9 | −0.24 | Melanoma-associated antigen 10-like (LOC618806) | 11 | 4 |
| 10 | 41.9 | −0.30 | Melanoma-associated antigen 10-like (LOC618806) | 11 | 4 |
| 3 | 68.1 | −0.46 | ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5 (ST6GALNAC5) | 1 | 0 |
| 2 | 133.4 | −0.34 | Phospholipase A2 group IIE (PLA2G2E) | 0 | 0 |
| 12 | 90.7 | −0.26 | Transcription factor Dp-1 (TFDP1) | 0 | 1 |
| 19 | 12.8 | −0.27 | Chromosome 19 C17ORF64 homolog (C19H17ORF64) | 0 | 0 |
| X | 14.1 | −0.26 | Zinc finger protein 280 C (ZNF280C) | 2 | 0 |
| 3 | 92.3 | −0.43 | acyl-CoA thioesterase 11 (ACOT11) | 0 | 0 |
| 25 | 41.4 | −0.18 | Kinesin-like protein (F1N4G9) | 0 | 0 |
| 7 | 45.5 | −0.18 | polo like kinase 5 (PLK5) | 0 | 0 |
| 19 | 39.2 | −0.40 | Proline rich 15 like (PRR15L) | 0 | 0 |
| 18 | 14.3 | −0.39 | acyl-CoA synthetase family member 3 (ACSF3) | 0 | 0 |
| 11 | 101.6 | −0.43 | Proline rich coiled-coil 2B (PRRC2B) | 0 | 0 |
| 5 | 91.8 | −0.32 | Phospholipase C zeta 1 (PLCZ1) | 0 | 0 |
| 5 | 91.8 | −0.32 | Capping actin protein of muscle Z-line subunit alpha 3 (CAPZA3) | 0 | 0 |
| 11 | 38.2 | −0.42 | Protein phosphatase 4 regulatory subunit 3B (PPP4R3B) | 1 | 0 |
| 1 | 143.6 | −0.30 | PR/SET domain 15 (PRDM15) | 0 | 1 |
| 13 | 30.2 | −0.29 | Non-coding RNA: RF00026 | 0 | 0 |
| 6 | 5.5 | −0.12 | Mitotic arrest deficient 2 like 1 (MAD2L1) | 1 | 0 |
| 26 | 22.9 | −0.11 | Nuclear factor kappa B subunit 2 (NFKB2) | 0 | 0 |
| 18 | 46.2 | −0.22 | Myelin-associated glycoprotein (MAG) | 2 | 0 |
| 13 | 79.4 | −0.29 | RIPOR family member 3 (RIPOR3) | 0 | 0 |
| 12 | 90.7 | −0.38 | Transcription factor Dp-1 (TFDP1) | 0 | 1 |
| 29 | 50.3 | −0.36 | Troponin I2, fast skeletal type (TNNI2) | 0 | 0 |
| 7 | 18.3 | −0.29 | Zinc finger protein 414 (ZNF414) | 0 | 0 |
| 16 | 49.7 | −0.25 | Leiomodin 1 (LMOD1) | 0 | 0 |
| 16 | 77.5 | −0.22 | CD46 molecule (CD46) | 0 | 0 |
| 1 | 147.4 | −0.35 | Collagen type VI alpha 1 chain (COL6A1) | 0 | 1 |
| 3 | 20.2 | −0.38 | Extracellular matrix protein 1 (ECM1) | 0 | 1 |
| 13 | 75.4 | −0.25 | Zinc finger SWIM-type containing 3 (ZSWIM3) | 0 | 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 hypomethylated in Control (P < 0.01) as in PNS.
dTotal number of CpG sites differentially hypomethylated (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.