TABLE 1.
Differentially Methylated Promoter CpG Islands in Degenerating Human Neurons
| Gene | Entrez Gene | Chromo-some | Aliases/Name | UniProtKB ID | Methylation Change | Significance p Value | Functions |
|---|---|---|---|---|---|---|---|
| FOXRED1 | 55572 | 11 | FAD-dependent oxidoreductase domain-containing protein 1; H17 | Q96CU9 | Hyper | 6.8×10−8 | Mitochondrial chaperone protein for complex I |
| UBE2V2 | 7336 | 8 | Ubiquitin-conjugating enzyme E2 variant 2; MMS2 | Q15819 | Hypo | 1.3×10−7 | Catalyzes noncanonical poly-ubiquitination to mediate transcriptional activation; DDR |
| GTPBP4 | 23560 | 10 | GTP binding protein 4; nucleolar GTP-binding protein 1 (NGB) | Q9BZE4 | Hypo | 7.9×10−6 | Signal transduction; 60S ribosomal subunit biogenesis |
| RHOU | 58480 | 1 | Ras homolog family member U/WRCH-1 | Q7L0Q8 | Hypo | 1.3×10−5 | Rho family GTPase; regulation of cell morphology and cytoskeletal organization |
| CPS1 | 1373 | 2 | Carbamoyl-phosphate synthase 1, mitochondrial | P31327 | Hypo | 1.4×10−8 | Urea cycle enzyme; core mitochondrial nucleoid protein; antiapoptotic |
| ENC1 | 8507 | 5 | Ectodermal-neural cortex; Nuclear matrix protein NRP/B | O14682 | Hypo | 5.9×10−5 | p53-induced gene 10; oxidative stress response and regulation of Nrf2; neuron-specific |
| SIM2 | 6493 | 21 | Single-minded family BHLH transcription factor 2 | Q14190 | Hypo | 1.3×10−7 | Major gene in CNS development in cooperation with Arnt; ubiquitination target of parkin; related to Down syndrome phenotypes |
| MAGEE1 | 57692 | X | Melanoma-associated antigen (MAGE) family member E1; DAMAGE (dystrobrevin associated MAGE protein) | 57692 | Hypo | 2.5×10−6 | Nuclear protein that enhances ubiquitin ligase activity of RING-type zinc finger-containing protein ligases; links to mental retardation |
| TEAD2 | 8463 | 19 | TEA domain transcriptional enhancer factor 4 | 8463 | Hypo | 1.5×10−4 | Involved in gene regulation of neuronal development; mediates expression of YAP1 |
| SORCS3 | 22986 | 10 | Sortilin-related VPS10 domain containing receptor 3 | Q9UPU3 | Hypo | 2.6×10−7 | Vacuolar protein sorting (VPS); variants associated with Alzheimer’s disease |
| ZEB2 | 9839 | 2 | Zinc finger E-box binding homeobox 2; ZFHX1B; SMAD interacting protein 1(SIP1) | O60315 | Hypo | 6.8×10−6 | Nuclear protein that functions as a DNA-binding transcriptional repressor; interacts with activated SMADS; protects against DNA damage-induced apoptosis |
| SIL1 | 64374 | 5 | SIL1 nucleotide exchange factor; NiP-associated protein; SIL1-like protein ER chaperone | Q9H173 | Hypo | 1.5×10−6 | ER resident protein; function in UPR |
| SMURF2 | 64750 | 17 | SMAD specific E3 ubiquitin protein ligase 2 | Q9HAU4 | Hypo | 1.1×10−6 | Accepts ubiquitin from E2 and transfers it to target protein; interacts with SMAD1 and SMAD7 to trigger their degradation; SMURF2 is neuroprotective in stroke |
| TOP2B | 7155 | 3 | DNA topoisomerase IIβ | Q02880 | Hypo | 2.8×10−5 | Nuclear enzyme controlling topological stated of DNA |