Table 1. Differentially methylated and expressed genes.
| Symbol | Gene name |
Methylation |
Expression |
||||||
|---|---|---|---|---|---|---|---|---|---|
| Chr | Start | End | FC | in/de | FC | Change | Affy ID | ||
| A) Genotype (G) | |||||||||
| Bbx | Bobby sox homolog (Drosophila) | 16 | 50435836 | 50436363 | 1.58 | ↑ | 1.26 | ↑ | 1430820_a_at |
| Ldlrad3 | Low density lipoprotein receptor class A domain containing 3 | 2 | 102029692 | 102029893 | 1.28 | ↑ | 1.12 | ↓ | 1438666_at |
| Bcl2l11 // Acoxl | BCL2-like 11 (apoptosis facilitator) // acyl-Coenzyme A oxidase-like | 2 | 127946767 | 127947010 | 1.26 | ↑ | 1.11 | ↓ | 1456005_a_at |
| Bcl2l11 // Acoxl | BCL2-like 11 (apoptosis facilitator) // acyl-Coenzyme A oxidase-like | 2 | 127946767 | 127947010 | 1.26 | ↑ | 1.35 | ↑ | 1456006_at |
| Kif13a | Kinesin family member 13A | 13 | 47028519 | 47029667 | 1.23 | ↓ | 1.12 | ↓ | 1451890_at |
| Spsb1 | splA/ryaNodine receptor domain and SOCS box containing 1 | 4 | 149331144 | 149332126 | 1.23 | ↑ | 1.19 | ↓ | 1428472_at |
| Fank1 // Dhx32 | Fibronectin type 3 and ankyrin repeat domains 1 // DEAH(Asp-Glu-Ala-His) box polypeptide 32 | 7 | 140975216 | 140978199 | 1.19 | ↓ | 1.17 | ↓ | 1447495_at |
| Dhx32 // Fank | DEAH (Asp-Glu-Ala-His) box polypeptide 32 // fibronectin type 3 and ankyrin repeat domains 1 | 7 | 140975216 | 140978199 | 1.19 | ↓ | 1.19 | ↓ | 1420427_a_at |
| Fgfr4 | Fibroblast growth factor receptor 4 | 13 | 55249814 | 55250054 | 1.17 | ↑ | 1.15 | ↓ | 1427845_at |
| Fgfr4 | Fibroblast growth factor receptor 4 | 13 | 55249814 | 55250054 | 1.17 | ↑ | 1.26 | ↓ | 1427776_a_at |
| E2f3 | E2F transcription factor 3 | 13 | 30080878 | 30081078 | 1.17 | ↓ | 1.14 | ↑ | 1427462_at |
| Ttn | Titin | 2 | 76823368 | 76823897 | 1.17 | ↓ | 1.21 | ↑ | 1427446_s_at |
| Nr5a1 | Nuclear receptor subfamily 5, group A, member 1 | 2 | 38568797 | 38569145 | 1.15 | ↓ | 1.17 | ↓ | 1421730_at |
| BC030307 | cDNA sequence BC030307 | 10 | 86175833 | 86176109 | 1.14 | ↑ | 1.15 | ↑ | 1441409_at |
| Bmpr1b | Bone morphogenetic protein receptor, type 1B | 3 | 141593558 | 141593900 | 1.14 | ↑ | 1.19 | ↓ | 1422872_at |
| C030046E11Rik | RIKEN cDNA C030046E11 gene | 19 | 29654132 | 29654407 | 1.14 | ↓ | 1.14 | ↑ | 1431023_at |
| Cybrd1 | Cytochrome b reductase 1 | 2 | 70957388 | 70957814 | 1.12 | ↓ | 1.13 | ↑ | 1425040_at |
| Fabp6 | Fatty acid binding protein 6, ileal (gastrotropin) | 11 | 43418691 | 43419752 | 1.10 | ↑ | 1.27 | ↓ | 1450682_at |
| Akap6 // n-R5s58 | A kinase (PRKA) anchor protein 6 // nuclearencoded rRNA 5S 58 | 12 | 53980545 | 53980725 | 1.09 | ↓ | 1.14 | ↑ | 1440859_at |
| Krt23 | Keratin 23 | 11 | 99352405 | 99352894 | 1.07 | ↓ | 1.21 | ↓ | 1418213_at |
| Nr5a1 | Nuclear receptor subfamily 5, group A, member 1 | 2 | 38569234 | 38569481 | 1.07 | ↓ | 1.17 | ↓ | 1421730_at |
| Lgr5 | Leucine rich repeat containing G protein coupled receptor 5 | 10 | 115028742 | 115029312 | 1.05 | ↑ | 1.13 | ↑ | 1444519_at |
| Mttp | Microsomal triglyceride transfer protein | 3 | 137796736 | 137797014 | 1.04 | ↑ | 1.25 | ↑ | 1419399_at |
| Tmem100 | Transmembrane protein 100 | 11 | 89896819 | 89897137 | 1.03 | ↓ | 1.22 | ↑ | 1446625_at |
| Pdlim4 | PDZ and LIM domain 4 | 11 | 53883752 | 53883994 | 1.02 | ↑ | 1.21 | ↓ | 1417928_at |
| Pla2g5 // Pla2g2a | Phospholipase A2, group V // phospholipase A2, group IIA (platelets, synovial fluid) | 4 | 138390529 | 138390886 | 1.02 | ↑ | 1.59 | ↓ | 1417814_at |
| Kcnj5 | Potassium inwardly-rectifying channel, subfamily J, member 5 | 9 | 32130003 | 32130278 | 1.01 | ↑ | 1.18 | ↑ | 1421762_at |
| 0610040J01Rik | RIKEN cDNA 0610040J01 gene | 5 | 64268747 | 64268986 | 1.01 | ↓ | 1.12 | ↓ | 1424404_at |
| B) Environment (E) | |||||||||
| Ddx46 | Dead (Asp-Glu-Ala-Asp) box polypeptide 46 | 13 | 55749228 | 55749440 | 1.33 | ↑ | 1.16 | ↓ | 1424569_at |
| Kcnh3 | Potassium voltage-gated channel, subfamily H (eag-related), member 3 | 15 | 99050982 | 99051487 | 1.31 | ↑ | 1.11 | ↓ | 1459107_at |
| Tlr12 | Toll-like receptor 12 | 4 | 128291909 | 128292687 | 1.31 | ↑ | 1.10 | ↓ | 1437931_at |
| Ropn1l // Gm6361 | Ropporin 1-like // predictedgene 6361 | 15 | 31378527 | 31378689 | 1.26 | ↑ | 1.15 | ↓ | 1423959_at |
| Tmtc1 | Transmembrane and tetratricopeptide repeat containing 2 // Smallnucleolar RNA SNORA17 | 10 | 104626225 | 104626657 | 1.25 | ↓ | 1.14 | ↑ | 1441033_at |
| Fjx1 | Four jointed box 1 (Drosophila | 2 | 102295770 | 102296667 | 1.23 | ↑ | 1.20 | ↓ | 1450728_at |
| Fjx1 | Four jointed box 1 (Drosophila) | 2 | 102295770 | 102296667 | 1.23 | ↑ | 1.17 | ↓ | 1422733_at |
| Cdc73 | Cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae) | 1 | 144990530 | 144990925 | 1.23 | ↓ | 1.15 | ↑ | 1427972_at |
| Sox6 | SRY-box containing gene 6 | 7 | 123171580 | 123171989 | 1.23 | ↓ | 1.14 | ↑ | 1427677_a_at |
| Bcl10 // Ddah1 | B cell leukemia/lymphoma 10 // dimethylarginine dimethylamiNohydrolase 1 | 3 | 145538088 | 145538612 | 1.21 | ↓ | 1.18 | ↑ | 1443524_x_at |
| Mettl7a1 | Methyltransferase like 7A1 | 15 | 100131133 | 100131965 | 1.21 | ↑ | 1.16 | ↑ | 1434151_at |
| Mettl7a1 | Methyltransferase like 7A1 | 15 | 100131133 | 100131965 | 1.21 | ↑ | 1.13 | ↑ | 1454858_x_at |
| Prkab1 // Cit | Protein kinase, AMP-activated, beta 1 Non-catalytic subunit // citron | 5 | 116457782 | 116458147 | 1.20 | ↑ | 1.13 | ↓ | 1424119_at |
| BC051628 // BC006779 | cDNA sequence BC051628 // cDNA sequence BC006779 | 2 | 180964456 | 180964941 | 1.19 | ↓ | 1.11 | ↑ | 1431758_at |
| Pnlip | Pancreatic lipase | 19 | 58744425 | 58744760 | 1.17 | ↑ | 1.25 | ↑ | 1433431_at |
| Zfp64 | Zinc finger protein 64 | 2 | 168808365 | 168808848 | 1.16 | ↑ | 1.21 | ↑ | 1456431_at |
| Zfp64 | Zinc finger protein 64 | 2 | 168808365 | 168808848 | 1.16 | ↑ | 1.12 | ↓ | 1451696_at |
| Xpot | Exportin, tRNA (nuclear export receptor for tRNAs) | 10 | 121044448 | 121044882 | 1.16 | ↑ | 1.13 | ↑ | 1441681_at |
| Nr2c1 // Ndufa12 | Nuclear receptor subfamily 2, group C, member 1 // NADHdehydrogenase (ubiquinone) 1 alpha subcomplex, 12 | 10 | 93657585 | 93657974 | 1.14 | ↑ | 1.19 | ↓ | 1449157_at |
| Mast4 // Cd179 | Microtubule-associated serine/threonine kinase family member 4 // CD180antigen | 13 | 103564348 | 103564628 | 1.14 | ↓ | 1.14 | ↑ | 1459387_at |
| Clstn2 | Calsyntenin 2 | 9 | 97936180 | 97936420 | 1.12 | ↑ | 1.19 | ↓ | 1422158_at |
| Cldn18 | Claudin 18 | 9 | 99617339 | 99617897 | 1.12 | ↑ | 1.19 | ↑ | 1425445_a_at |
| Map3k1 | Mitogen-activated protein kinase kinase kinase 1 | 13 | 112601065 | 112601546 | 1.12 | ↑ | 1.24 | ↑ | 1443540_at |
| Akap13 | A kinase (PRKA) anchor protein 13 | 7 | 82870878 | 82871179 | 1.11 | ↑ | 1.10 | ↓ | 1433722_at |
| Kdm6b // Dnahc2 | KDM1 lysine (K)-specific demethylase 6B // dynein, axonemal, heavy chain 2 | 11 | 69290421 | 69290898 | 1.11 | ↑ | 1.26 | ↑ | 1440346_at |
| Kdm6b // Dnahc2 | KDM1 lysine (K)-specific demethylase 6B // dynein, axonemal, heavy chain 2 | 11 | 69290421 | 69290898 | 1.11 | ↑ | 1.14 | ↑ | 1456610_at |
| Kat2a // Dhx58 | K(lysine) acetyltransferase 2A //DEXH(Asp-Glu-X-His) box polypeptide 58 | 11 | 100566819 | 100567318 | 1.10 | ↑ | 1.15 | ↓ | 1422972_s_at |
| Prok2 | Prokineticin 2 | 6 | 99674161 | 99674602 | 1.10 | ↑ | 1.15 | ↑ | 1451952_at |
| Ptpn21 | Protein tyrosine phosphatase, Non-receptor type 21 | 12 | 99923550 | 99923778 | 1.09 | ↑ | 1.15 | ↑ | 1419055_a_at |
| Rad9b | RAD9 homolog B (S. cerevisiae) | 5 | 122803144 | 122803311 | 1.09 | ↑ | 1.18 | ↓ | 1425800_at |
| Mcm3 | Minichromosome maintenance deficient 3 (S. cerevisiae) | 1 | 20807895 | 20808068 | 1.09 | ↑ | 1.17 | ↑ | 1420029_at |
| Msi1 | Musashi homolog 1(Drosophila) | 5 | 115873837 | 115874905 | 1.08 | ↑ | 1.24 | ↑ | 1444306_at |
| Stt3b | STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae) | 9 | 115162948 | 115163232 | 1.08 | ↑ | 1.22 | ↑ | 1431541_at |
| Dna2 // Slc25a16 | DNA replication helicase 2 homolog (yeast) // solute carrier family 25 (mitochondrial carrier, Graves disease autoantigen), member 16 | 10 | 62407000 | 62407211 | 1.08 | ↑ | 1.25 | ↑ | 1457909_at |
| Slc30a1 // 1700034H15Rik | Solute carrier family 30 (zinc transporter), member 1 // RIKEN cDNA 1700034H15 gene | 1 | 193732789 | 193733167 | 1.08 | ↑ | 1.15 | ↓ | 1436164_at |
| Nos1 | Nitric oxide synthase 1, neuronal | 5 | 118312626 | 118312968 | 1.07 | ↑ | 1.20 | ↓ | 1438483_at |
| Prss23 // 1700019G06Rik | Protease, serine, 23 // RIKEN cDNA 1700019G06 gene | 7 | 96658688 | 96659035 | 1.07 | ↓ | 1.17 | ↓ | 1446560_at |
| Chaf1b // Morc3 | Chromatin assembly factor 1, subunit B (p60) // microrchidia 3 | 16 | 93865780 | 93866055 | 1.07 | ↑ | 1.24 | ↑ | 1431275_at |
| Gja1 | Gap junction protein, alpha 1 | 10 | 56216896 | 56217111 | 1.04 | ↑ | 1.42 | ↓ | 1415801_at |
| C) G × E | |||||||||
| 2010001K21Rik | RIKEN cDNA 2010001K21 gene | 13 | 47102005 | 47102256 | — | — | — | — | 1447576_at |
| 5430421N21Rik | RIKEN cDNA 5430421N21 gene | 15 | 101325243 | 101325528 | — | — | — | — | 1427118_at |
| Ank3 | Ankyrin 3, epithelial | 10 | 68991227 | 68992000 | — | — | — | — | 1447259_at |
| Atp10b | ATPase, class V, type 10B | 11 | 42964973 | 42965240 | — | — | — | — | 1444911_at |
| Cabin1 | Calcineurin binding protein 1 | 10 | 75229253 | 75229611 | — | — | — | — | 1437794_at |
| Cage1 | Cancer antigen 1 | 13 | 38127687 | 38128016 | — | — | — | — | 1434810_a_at |
| Chrna9 | Cholinergic receptor, nicotinic, alpha polypeptide 9 | 5 | 66361850 | 66362047 | — | — | — | — | 1447214_at |
| Chrna9 | Cholinergic receptor, nicotinic, alpha polypeptide 9 | 5 | 66362494 | 66362774 | — | — | — | — | 1447214_at |
| Clpb // Phox2a | ClpB caseinolytic peptidase B homolog (E. coli) // paired-likehomeobox 2a | 7 | 108938653 | 108939395 | — | — | — | — | 1454168_a_at |
| Dppa3 | Developmental pluripotency-associated 3 | 6 | 122594236 | 122594653 | — | — | — | — | 1424295_at |
| F10 // Proz | Coagulation factor X // proteinZ, vitamin K-dependent plasma glycoprotein | 8 | 13055218 | 13055381 | — | — | — | — | 1449305_at |
| Fam135a // 1110058L19Rik | Family with sequence similarity 135, member A // RIKEN cDNA 1110058L19 gene | 1 | 24034551 | 24034832 | — | — | — | — | 1453122_at |
| Fam170a | Family with sequence similarity 170, member A | 18 | 50438458 | 50438693 | — | — | — | — | 1456560_at |
| Foxj1 // Rnf157 | Forkhead box J1 // ring finger protein 157 | 11 | 116218086 | 116218410 | — | — | — | — | 1425291_at |
| Glra1 | Glycine receptor, alpha 1 subunit | 11 | 55418779 | 55418960 | — | — | — | — | 1422277_at |
| Heatr1 // Lgals8 | Heat repeat containing 1 // lectin,galactose binding, soluble 8 | 13 | 12520880 | 12521218 | — | — | — | — | 1452419_at |
| Mbp // Rpl21-ps8 | Myelin basic protein // ribosomalprotein L21, pseudogene 8 | 18 | 82693616 | 82694069 | — | — | — | — | 1451961_a_at |
| Parp14 | Poly (ADP-ribose) polymerase family, member 14 | 16 | 35858088 | 35858439 | — | — | — | — | 1451564_at |
| Pim1 | Proviral integration site 1 | 17 | 29656335 | 29656796 | — | — | — | — | 1423006_at |
| Pla2g5 // Pla2g2a | Phospholipase A2, group V // phospholipase A2, group IIA (platelets, synovial fluid) | 4 | 138382101 | 138382425 | — | — | — | — | 1417814_at |
| Psd3 | Pleckstrin and Sec7 domain containing 3 | 8 | 70220885 | 70221160 | — | — | — | — | 1418749_at |
| Tcof1 | Treacher Collins Franceschetti syndrome 1, homolog | 18 | 61013037 | 61013345 | — | — | — | — | 1423600_a_at |
| Uevld | UEV and lactate/malate dehyrogenase domains | 7 | 54224905 | 54225077 | — | — | — | — | 1421785_at |
| Wdr66 | WD repeat domain 66 | 5 | 123745990 | 123746262 | — | — | — | — | 1447215_at |
Abbreviations: FC, fold change; in/de, increased or decreased expression.
Genes of which both DNA methylation status and gene expression level were significantly altered by genotype (G; that is, 5-Htt+/− versus 5-Htt+/+), the environment (E; that is, prenatal stressed versus control mice) or in an interactive manner (G × E; that is, indicating those genes of which the effect of the environment depends upon the genotype) in the hippocampus of female mice. DNA methylation analysis was performed by applying hippocampal DNA enriched by methylated-DNA immunoprecipitation (MeDIP) on Affymetrix (Affy) Mouse Promoter 1.0R arrays. Gene expression data as described in van den Hove et al.4