Table 2.
Differentially methylated genes in PBC-discordant MZ twins.
| Gene | Chr/base pair (bp)a | Description/function | Localizationb |
|---|---|---|---|
| ABCD1 | chrX:152989993–152991024 | ATP-binding cassette, sub-family D (ALD), member 1 | PM |
| ATP12A | chr13:25254828–25254890 | ATPase, H+/K+ transporting, non-gastric, alpha polypeptide | PM |
| ATP5A1 | chr18:43678161–43678731 | ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle | C |
| BCAP31 | chrX:152989493–152990063 | B cell receptor-associated protein 31 | C |
| BGN | chrX:152760629–152761596 | Biglycan | E |
| BRCC3 | chrX:154299261–154299925 | BRCA1/BRCA2-containing complex, subunit 3 | N |
| CFP | chrX:47483418–47483642 | Complement factor properdin | E |
| CHST7 | chrX:46434647–46434858 | Carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 7 | C |
| CTAG1A, CTAG1B | chrX:153813591–153814161 | Cancer/testis antigen 1A, B | C |
| DDX41 | chr5:176943911–176944481 | DEAD (Asp–Glu–Ala–Asp) box polypeptide 41 | N |
| FAM104B | chrX:55187570–55188140 | Family with sequence similarity 104, member B | U |
| FGD1 | chrX:54521696–54522266 | FYVE, RhoGEF, and PH domain containing 1 | C |
| FUNDC2 | chrX:154255133–154255703 | FUN14 domain containing 2 | C |
| GAGE12B, 12I, 2A, 5, 7, 8 | chrX:49315376–49315946 | G antigen 1, 5, 7 | U |
| GTPBP6 | chrX:230686–231256 | GTP-binding protein 6 (putative) | U |
| HCCS | chrX:11129525–11129638 | Holocytochrome c synthase | C |
| HOXD4 | chr2:177016716–177017157 | Homeobox D4 | N |
| IDH3G | chrX:153059742–153059944 | Isocitrate dehydrogenase 3 (NAD+) gamma | C |
| IDS | chrX:148586616–148587185 | Iduronate 2-sulfatase | C |
| IRAK1 | chrX:153285317–153285887 | Interleukin-1 receptor-associated kinase 1 | PM |
| KBTBD6 | chr13:41706829–41707399 | Kelch repeat and BTB (POZ) domain containing 6 | U |
| MAGEA3 | chrX:151938154–151938356 | Melanoma antigen family A, 3 | U |
| MAGEA6 | chrX:151867135–151867705 | Melanoma antigen family A, 6 | U |
| MAGEA9 | chrX:148793401–148793568 | Melanoma antigen family A, 9 | U |
| MAGED4B | chrX:51928209–51929228 | Melanoma antigen family D, 4B | U |
| MTCP1 | chrX:154299410–154299612 | Mature T cell proliferation 1 | C |
| MTM1 | chrX:149737348–149737918 | Myotubularin 1 | C |
| MTMR8 | chrX:63614954–63615524 | Myotubularin-related protein 8 | U |
| NHS | chrX:17393481–17393959 | Nance–Horan syndrome (congenital cataracts and dental anomalies) | N |
| ORC1L | chr1:52869831–52870401 | Origin recognition complex, subunit 1 | N |
| CDK16 | chrX:47078470–47079428 | Cyclin-dependent kinase 16 | C |
| PDZD4 | chrX:153095693–153096406 | PDZ domain containing 4 | C |
| PHF16 | chrX:46772444–46773014 | PHD finger protein 16 | N |
| PRKX | chrX:3631431–3632001 | Protein kinase, X-linked | C |
| PRPF38A | chr1:52869831–52870401 | PRP38 pre-mRNA processing factor 38 (yeast) domain containing A | N |
| RIBC1 | chrX:53449681–53450600 | RIB43A domain with coiled-coils 1 | U |
| RNF128 | chrX:105970276–105970478 | Ring finger protein 128 | C |
| SCLY | chr2:238969783–238970252 | Selenocysteine lyase | C |
| SHROOM4 | chrX:50557007–50557209 | Shroom family member 4 | PM |
| SLC10A3 | chrX:153718280–153718749 | Solute carrier family 10 (sodium/bile acid cotransporter family), member 3 | PM |
| SLC9A6 | chrX:135067977–135068547 | Solute carrier family 9 (sodium/hydrogen exchanger), member 6 | PM |
| SLITRK2 | chrX:144903417–144903908 | SLIT and NTRK-like family, member 2 | U |
| SLITRK4 | chrX:142722571–142723141 | SLIT and NTRK-like family, member 4 | U |
| SMARCA1 | chrX:128657308–128657936 | SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, sub-family A, member 1 | N |
| SSR4 | chrX:153060191–153060761 | Signal sequence receptor, delta (translocon-associated protein delta) | C |
| TAF9B | chrX:77394695–77395265 | TAF9B RNA polymerase II, TATA box-binding protein-associated factor, 31 kDa | N |
| TCEAL6 | chrX:101397122–101397692 | Transcription elongation factor A (SII)-like 6 | U |
| TUSC3 | chr8:15397909–15398479 | Tumor suppressor candidate 3 | PM |
| UBL4A | chrX:153714886–153715456 | Ubiquitin-like 4° | U |
| VCX2, VCX3A | chrX:6451316–6452154 | Variable charge, X-linked 2, X-linked 3A | U, N |
| YIPF6 | chrX:67718891–67718965 | Yip1 domain family, member 6 | C |
| ZIC3 | chrX:136649002–136649910 | Zic family member 3 (odd-paired homolog, Drosophila) | N |
| ZNF182 | chrX:47862911–47863428 | Zinc finger protein 182 | N |
Of note, all regions were hypermethylated in the PBC proband and only SMARCA1 was differentially expressed in RT-PCR.
aPositions of each gene based on GRCh37/hg19.
bFor each gene product the localization is specified as nuclear (N), cytoplasmic (C), plasma membrane (PM), extracellular (E), unknown (U).