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. 2018 Aug 17;47(6):1910–1937. doi: 10.1093/ije/dyy153

Table 4.

Candidate genes exhibiting associations between nutritional exposures during periconception and pregnancy and offspring DNA methylation. Links between methylation at nutrition-sensitive genes and offspring phenotype are also included

Gene/region of Interest Genomic featuresc Exposure (↑/↓: increased/decreased) Outcome (↑/↓: increased/decreased) Coordinates of ROI in studiesd,e (number of CpGs on 450ka and EPICb arrays)
Blue = ME
Brown = imprinted
Yellow = ME and imprinted
ABCA1 (ATP Binding Cassette Subfamily A Member 1) Promoter marks; CpG island; binding site for multiple TFs Famine ↑Methylation47 chr9: 107, 690, 502-107, 690, 821 (1)a(5)b
ACADM (Acyl-CoA Dehydrogenase, C-4 To C-12 Straight Chain) Multiple TFs binding sites; Promoter mark; Active Enhancer mark ↑Folate ↑Methylation61 chr1: 76, 189, 707-76, 190, 008 (6)a(7)b
BOLA3 (BolA Family Member 3) Enhancer and Promoter marks; CpG island; binding site for multiple TFs Rainy season conception ↑Methylation30 chr2: chr2: 74, 357, 632-74, 357, 837 (1)a,b
CRH (Corticotropin-Releasing Hormone) Enhancer mark ↑Choline ↓Methylation60 chr8: 67, 090, 692-67, 091, 132 (5)a(8)b
CYS1 (Cystin 1) Multiple TFs binding sites; Promoter mark ↑Folate ↓Methylation50 chr2: 10, 220, 719
DNMT1 (DNA Methyltransferase 1) Multiple TFs binding sites; Promoter mark; Active Enhancer mark ↑Folate ↑Methylation44, ↓Methylation42 chr19: 10, 305, 774-10, 305, 811 (2)a,b
Multiple TFs binding sites; Promoter mark; Active Enhancer mark ↑Folic acid ↓Methylation44 chr19: 10, 305, 774-10, 305, 811 (2)a,b
Multiple TFs binding sites; Promoter mark; Active Enhancer mark ↑Choline ↑Methylation44, ↑↓Methylation42 chr19: 10, 305, 774-10, 305, 811 (2)a,b
Multiple TFs binding sites; Promoter mark; Active Enhancer mark ↑Betaine ↑Methylation42 chr19: 10, 305, 774-10, 305, 811 (2)a,b
EXD3 (FLJ20433) (exonuclease 3'-5' domain containing 3)  Active Enhancer mark; CpG island Rainy season conception ↑Methylation30 chr9: 140, 312, 206-140, 312, 339
FAM150B (Family With Sequence Similarity 150, Member B) None Famine ↑Methylation48 chr2: 366, 113 (1)a,b 
FZD7 (Frizzled Class Receptor 7) Multiple TFs binding sites; Promoter mark ↑Folate ↑methylation61 chr2: 202, 901, 045-202, 901, 470 (5)a(4)b
GNASAS (Guanine Nucleotide Binding Protein (G Protein), Alpha Stimulating Activity Antisense RNA 1) Enhancer marks; Multiple TFs binding sites Famine (periconceptional)/Famine (late gestation) ↑Methylation/ ↓Methylation47 chr20: 57, 425, 815-57, 426, 108 (3) a,b
CpG island; MYC binding site UNIMMAP (supplementation) ↓Methylation53 chr20: 57, 429, 802-57, 430, 242 (1)a(2)b
H19 Multiple TFs binding sites ↑Methylation ↑Birthweight56 chr11: 2, 011, 131-2, 011, 275 (2)a,b
MYC and CTCF binding sites; Active promoter mark; weak enhancer mark ↑Methylation ↑Small for gestational age92 chr11: 2, 019, 727-2, 019, 921 (7)a(6)b
Multiple TFs binding sites ↑ Omega-3 PUFA ↓Methylation64 chr11: 2, 024, 197-2, 024, 340
Multiple TFs binding sites ↑Folic acid ↓Methylation51 chr11: 2, 024, 254-2, 024, 261
Enhancer Mark; CTCF-binding site ↑Methylation ↓Birth length, ↑weight in adulthood, ↑adult BMI, ↑adult blood pressure62 chr11: 2, 021, 072-2, 021, 291 (2)a,b
HSD11B2 (Hydroxysteroid 11-Beta Dehydrogenase 2) (HSD2) Multiple TFs binding sites; CpG island ↑Methylation ↓Neonatal ponderal index, ↑birthweight, ↑adult adiposity, ↑adult blood pressure62 chr16: 67464346-67464649 (3)a(4)b
Multiple TFs binding sites; Promoter mark; Active Enhancer mark; CpG island ↑Meat and fish intake ↑Methylation62 chr16: 67, 464, 981-67, 465, 111 (1)a(2)b
Multiple TFs binding sites, Active Enhancer mark ↓Methylation ↑Risk of being in a poorly regulated neurobehavioral profile103,104 chr16: 67, 464, 387-67, 464, 417
IGF2 (Insulin-like Growth Factor 2) POL2A binding site ↑Folic acid ↓Methylation44 chr11: 2, 151, 629-2, 151, 721 (3) a,b
POL2A binding site ↑Folate ↑Methylation56 chr11: 2, 151, 629-2, 151, 721 (3) a,b
1 reported SNP (rs3741210) ↑Omega-3 PUFA ↑Methylation64 chr11: 2, 169, 425-2, 169, 556
CTCF binding site; Enhancer mark; 2 reported SNPs (rs3741210, rs3741208) ↑Folic acid ↑Methylation52 chr11: 2, 169, 459 -2, 169, 796
CTCF binding site; Enhancer mark; 2 reported SNPs (rs3741210, rs3741208) ↑Methylation ↓Birthweight52 chr11: 2, 169, 459 -2, 169, 796
CTCF binding site; Enhancer mark; 2 reported SNPs (rs3741210, rs3741208) Famine ↓Methylation45,46 chr11: 2, 169, 459-2, 169, 796
POL2A and USF1 binding sites; 1 CpG island; 1 reported SNP (rs1803647) ↑Folic acid ↑Methylation58 chr11: 2, 154, 262-2, 154, 977 (5)a,b
Multiple TFs binding sites; Promoter mark; Active Enhancer mark ↑Methylation ↑ADHD in early‐onset persistent youth63 (37)a(35)b,f
Multiple TFs binding sites; Promoter mark; Active Enhancer mark High‐fat and ‐sugar diet ↑Methylation63 (37)a(35)b,f
POL2A binding site; Promoter mark; Active Enhancer mark; CpG island ↑Omega-3 PUFA ↑Methylation64 chr11: 2, 159, 107-2, 159, 965 (3)a(4)b
EZH2 and CTCF binding site; Promoter mark; CpG island ↑Vitamin B12 ↓Methylation59 chr11: 2, 161, 115-2, 161, 275 (4)a,b
CTCF binding site; Enhancer mark; 2 reported SNPs (rs3741210, rs3741208) Famine ↓Methylation46 chr11: 2, 169, 385-2, 169, 489
Enhancer mark Famine ↓Methylation46 chr11: 2, 170, 541-2, 170, 644
CTCF binding site; Enhancer mark; 2 reported SNPs (rs3741210, rs3741208) ↓Methylation ↑Small for gestational age83 chr11: 2, 169, 458-2, 169, 796
EZH2, RAD21 and CTCF binding site; Promoter mark; CpG island Famine ↑Methylation46 chr11: 2, 160, 906-2, 161, 372 (14)a(13)b
EZH2, ZBTB7A and CTCF binding site; Promoter mark; CpG island Famine ↑Methylation46 chr11: 2, 161, 550-2, 161, 846 (1)a(2)b
Enhancer mark; 1 reported SNPs (rs3741210) ↓Methylation ↑Small for gestational age95 chr11: 2, 169, 467-2, 169, 640
POLR2A and ZBTB7A binding site Famine ↓Methylation46 chr11: 2, 155, 447-2, 155, 736 (1)a,b
CpG island; USF1 and POL2A binding sites ↑Methylation ↑Birthweight, birth height, head and thorax circumference at birth91 chr11: 2, 154, 263-2, 154, 457 (2)a,b
None ↑Methylation ↑Birthweight90 chr11: 2, 169, 518-2, 169, 499
CTCF and REST binding sites; CpG island ↑Methylation ↑TG and TG: HDL102 chr11: 2, 160, 374-2, 160, 610 (4)a,b
IGF2R (Insulin-like Growth Factor 2 Receptor) CpG island; associated with SNP rs677882 and rs8191722 ↑UNIMMAP (supplementation) ↓Methylation53 chr6: 160, 426, 403-160, 426, 850
IGF2/H19 ICR None ↑Methylation ↓Head circumference between 1–10 years; ↑subcutaneous fat measures at age 17 years97 chr11: 2, 064, 402-2, 064, 717
IL10 (Interleukin 10) Enhancer and Promoter marks; binding site for multiple TFs Famine ↑Methylation47 chr1: 206, 946, 011-206, 946, 339 (2)a(3)b
INSIGF (Insulin- Insulin-like Growth Factor 2) None Famine ↓Methylation46,47 chr11: 2, 182, 336-2, 182, 640 (5)a(4)b
LASP1 (LIM And SH3 Protein 1) Multiple TFs binding sites; Promoter marks; Enhancer marks; 4 CpG islands; 25 reported SNPs ↑Folate ↑Methylation61 chr17: 37, 123, 638-37, 123, 949 (9)a,b
LEP (Leptin) None ↑Folate ↓Methylation42,44 chr7: 127, 881, 035-127, 881, 054
None ↑Betaine ↓Methylation42 chr7: 127, 881, 035-127, 881, 054
None ↑Folic acid ↑Methylation42 chr7: 127, 881, 035-127, 881, 054
CpG island; CEBP binding site; 2 reported SNPs (rs791620, rs2167270) Famine ↑Methylation47 chr7: 127, 881, 054-127, 881, 410 (4)a(6)b
CpG island; CEBP binding site; 2 reported SNPs (rs791620, rs2167270) ↑Methylation ↑Small for gestational age94 chr7: 127, 881, 127-127, 881, 350 (4)a(6)b
CpG island; 1 reported SNP (rs2167270) ↓Methylation ↑BMI100 chr7: 127, 881, 280-127, 881, 300 (2)a(3)b
CpG island; CEBP binding site; 2 reported SNPs (rs791620, rs2167270) ↓Methylation ↑BMI; ↑hip circumference98 chr7: 127, 881, 126-127, 881, 474 (3)a(4)b
CpG island; CEBP binding site; 2 reported SNPs (rs791620, rs2167270) ↑Methylation ↑Fasting LDL-C98 chr7: 127, 881, 126-127, 881, 474 (3)a(4)b
CpG island ↓Methylation ↑BMI99 chr7: 127, 881, 036 -127, 881, 057
CpG island; CEBP binding site; 2 reported SNPs (rs791620, rs2167270) ↑Methylation ↑Lethargy and hypotonicity105 chr7: 127, 881, 127-127, 881, 350 (4)a(6)b
CpG island; CEBP binding site; 2 reported SNPs (rs791620, rs2167270) ↓Methylation ↑HDL101 chr7: 127, 881, 053-127, 881, 410 (4)a(6)b
LY6E (Lymphocyte Antigen 6 Family Member E) Multiple TFs binding sites; Promoter mark; Active Enhancer mark ↑Folate ↓Methylation61 chr8: 144, 120, 106-144, 120, 706 (8)a(9)b
MEG3 (Maternally Expressed 3) (GTL-2) CpG island; Promoter mark ↑Vitamin B6 ↑Methylation54 chr14: 101, 294, 220-101, 294, 391
CpG island; Promoter mark ↑Folate ↓Methylation56 chr14: 101, 294, 220-101, 294, 391
Enhancer and Promoter marks; CpG island; POLR2A binding site ↑ UNIMMAP (supplementation) ↓Methylation53 chr14: 101, 292, 283– 101, 292, 796 (4)a(5)b
CpG island; Promoter mark ↓Methylation ↑Birthweight56 chr14: 101, 294, 220-101, 294, 391
None Famine ↑Methylation47 chr14: 101, 291, 413-101, 291, 642 (5)a(6)b
MEST (Mesoderm-Specific Transcript) (PEG1) CpG island ↑UNIMMAP (supplementation) ↓Methylation53 chr7: 130, 131, 325-130, 131, 792 (11)a(9)b
Multiple TFs binding sites; Promoter mark; Enhancer mark; CpG island ↑Methylation ↑Small for gestational age93 chr7: 130, 125, 200-130, 126, 400 (16)a(17)b
MIRLET7BHG (MicroRNA Let-7b Host Gene) Active Enhancer mark ↑Omega-6 PUFA ↓Methylation66 chr22: 46, 473, 721 (1)a,b 
Active Enhancer mark ↓Methylation ↑Birthweight66 chr22: 46, 473, 721 (1)a,b 
NR3C1 (Nuclear Receptor Subfamily 3 Group C Member 1) (GR) Multiple TFs binding sites; Promoter mark; Enhancer mark; CpG island; 2 reported SNPs (rs10482604, rs10482605) ↑Methylation ↑Risk of being in a poorly regulated neurobehavioural profile103,104 chr5: 142, 783, 501-142, 783, 640 (4)a,b
Multiple TFs binding sites; Promoter mark; Enhancer mark; CpG island; 2 reported SNPs (rs10482604, rs10482605) ↑Choline ↑Methylation60 chr5: 142, 783, 501-142, 783, 908 (5)a(7)b
Multiple TFs binding sites; Promoter mark; Enhancer mark; CpG island ↑Methylation ↑Adult waist circumference, ↑adult BMI62 chr5: 142, 782, 759-142, 783, 164 (2)ab
Multiple TFs binding sites; Promoter mark; Enhancer mark; CpG island; 1 reported SNP (rs10482604) ↑Meat/fish and vegetable intake, ↓bread/potato intake in late pregnancy ↑Methylation62 chr5: 142, 783, 579-142, 783, 714 (3)a,b
Multiple TFs binding sites; Promoter mark; Enhancer mark; CpG island; 1 reported SNP (rs10482604) ↑Methylation ↓Adult blood pressure62 chr5: 142, 783, 578 -142, 783, 714 (3)a,b
OSBPL5/MRGPRG (Oxysterol-Binding Protein Like 5/MAS Related GPR Family Member G) Enhancer mark; CpG island Famine ↓Methylation48 chr11: 3, 225, 076 (1)a,b 
OTX2 (Orthodenticle Homeobox 2) CpG island; EZH2 binding site ↑Folate ↓Methylation50 chr14: 57, 278, 729 (1)a,b 
PAX8 (Paired Box8)  Multiple TFs binding sites; Promoter mark; Active Enhancer mark Rainy season conception ↑Methylation30 chr2: 113, 993, 262-113, 993, 391(2)a,b
chr2: 113, 992, 866-113, 993, 036(2)a,b
Multiple TFs binding sites; Promoter mark; Active enhancer mark Famine ↑Methylation49 chr2: 113, 992, 762-113, 993, 313 (8)a(7)b
PEG3 (Paternally Expressed 3) Multiple TFs binding sites; 2 CpG islands; 1 reported SNP (rs2302376) ↑Folate ↓Methylation56 chr19: 57, 351, 945-57, 352, 096 (4)a(3)b
Multiple TFs binding sites; 2 CpG islands; 1 reported SNP (rs2302376) ↑Folic acid ↓Methylation56 chr19: 57, 351, 945-57, 352, 096 (4)a(3)b
Multiple TFs binding sites; 2 CpG islands; 1 reported SNP (rs2302376) ↑Folic acid ↓Methylation58 chr19: 57, 351, 944-57, 352, 096 (4)a(3)b
PLAGL1 (PLAG1-Like Zinc Finger 1) (ZAC1) Multiple TFs binding sites; Promoter mark; Active Enhancer mark; CpG island ↑Folate ↓Methylation56 chr6: 144, 329, 109-144, 329, 231 (1)a,b
Multiple TFs binding sites; Promoter mark; Active Enhancer mark; CpG island ↑Methylation ↑Birthweight56 chr6: 144, 329, 109-144, 329, 231 (1)a,b
Multiple TFs binding sites; Promoter mark; CpG island ↑Methylation index ↑Fetal weight at 32 weeks of gestation, weight and BMI at 1 year40 chr6: 144, 329, 390-144, 329, 740 (4)a,b
Multiple TFs binding sites; Promoter mark; CpG island ↑ Vitamin B2 ↑Methylation index40 chr6: 144, 329, 390-144, 329, 740 (4)a,b
POMC (Proopiomelanocortin) Multiple TFs binding sites; Promoter mark; Active Enhancer mark; CpG island ↑Methylation ↑BMI43,96 chr2: 25, 384, 508-25, 384, 832 (3)a,b
Multiple TFs binding sites; Promoter mark; Active Enhancer mark; CpG island ↑SAM:SAH ratio; ↑betaine ↑Methylation43 chr2: 25, 384, 508-25, 384, 832 (3)a,b
PPAP2C (PLPP2) (Phosphatidic Acid Phosphatase 2c) CpG island Famine ↑Methylation48 chr19: 292, 167 (1)a,b 
PRDM9 (PR-Domain Containing Protein 9) Multiple transcription factor binding sites; Promoter mark, Active enhancer mark; 2 reported SNPs (rs10077095, rs1994929) Famine ↓Methylation49 chr5: 23, 507, 030-23, 507, 752 (12)a(11)b
RBM46 (RNA-Binding Motif Protein 46)  CpG island Rainy season conception ↑Methylation31 chr4: 155, 702, 818-155, 703, 110 (1)a,b
RXRA (Retinoid X Receptor Alpha) Multiple TFs binding sites; Enhancer mark ↑Methylation ↑Fat mass; % fat mass55 chr9: 137, 215, 697 -137, 216, 117 (1)a,b
Multiple TFs binding sites; Enhancer mark ↑Methylation ↑BMI55 chr9: 137, 215, 697 -137, 216, 117 (1)a,b
Multiple TFs binding sites; Enhancer mark ↑Carbohydrate intake  ↓Methylation55 chr9: 137, 215, 697 -137, 216, 117 (1)a,b
Multiple TFs binding sites; Enhancer mark ↑Methylation ↓Bone mineral content; % BMC75 chr9: 137, 215, 697 -137, 216, 117 (1)a,b
Multiple TFs binding sites; Promoter mark; Active Enhancer mark; CpG island ↑Folate ↓Methylation42 chr9: 137, 217, 097-137, 217, 132
Multiple TFs binding sites; Promoter mark; Active Enhancer mark; CpG island ↑Folate ↑Methylation44 chr9: 137, 217, 097-137, 217, 132
SLC38A2 (Solute Carrier Family 38 Member 2) Enhancer mark Famine ↑Methylation48 chr12: 46, 737, 123 (1)a,b 
SLITRK1 (SLIT And NTRK-like Family Member 1)  Promoter mark; Enhancer mark; CpG island Rainy season conception ↑Methylation30 chr13: 84, 453, 741-84, 453, 828
chr13: 84, 454, 210-84, 454, 281
SPATC1L (C21orf56) (Spermatogenesis And Centriole Associated 1 Like) Multiple TFs binding sites; Promoter mark; Active Enhancer mark ↑Folate ↓Methylation61 chr21: 47, 604, 052-47, 604, 654 (5)a,b
STX11 (Syntaxin 11) Multiple TFs binding sites; Promoter mark; CpG island ↑Folate ↓Methylation50 chr6: 144, 471, 564 (1)a,b 
TACC1 (Transforming Acidic Coiled-Coil Containing Protein 1) Promoter mark; Enhancer mark Famine ↑Methylation48 chr8: 38, 586, 183 (1)a,b 
TFAP2A (Transcription Factor AP-2 Alpha) E2F1 and EZH2 binding site; Promoter mark; Active Enhancer mark; CpG island ↑Folate ↓Methylation50 chr6: 10, 411, 911 (1)a,b 
TMEM105 (Transmembrane Protein 105) Enhancer mark; Active Enhancer mark; CpG island Famine ↓Methylation48 chr17: 79, 283, 915 (1)a,b 
VTRNA2-1 (Vault RNA 2-1) Multiple TFs binding sites; Promoter mark; Active Enhancer mark; CpG island Rainy Season; ↑vitamin B2; ↑methionine; ↓dimethylglycine ↑Methylation41 chr5: 135, 415, 762-135, 416, 613 (15)a(13)b
WNT9A (Wnt Family Member 9A) NRF1 binding site; Promoter mark; Active Enhancer mark; CpG island ↑Folate ↑Methylation61 chr1: 228, 075, 423-228, 075, 749 (5)a(3)b
ZFP57 (Zinc Finger Protein 57) YY1 binding site; Promoter mark; Active Enhancer mark; multiple reported SNPs ↑Folate ↓Methylation61 chr6: 29, 648, 161-29, 649, 084 (24)a(25)b
Promoter mark; Active Enhancer mark; multiple reported SNPs Famine ↓Methylation49 chr6: 29, 648, 345-29, 649, 024 (19)a(18)b
ZFYVE28 (Zinc Finger FYVE-Type Containing 28)  Multiple TFs binding sites; Promoter mark; CpG island Rainy season conception ↑Methylation30 chr4: 2, 366, 658-2, 366, 739 (1)a,b
chr4: 2, 366, 909-2, 367, 003
ZNF385A (Zinc Finger Protein 385A) Multiple TFs binding sites; Promoter mark; CpG island Famine ↑Methylation48 chr12: 54, 764, 265 (1)a,b 

LBW, low birthweight; LDL-C, low-density lipoprotein cholesterol; ME, metastable epiallele; ROI, region of interest; SAH, s-adenosyl homocysteine; SAM, s-adenosyl methionine; UNIMMAP, United Nations International Multiple Micronutrient Preparation.

a

Number of CpGs covered on Infinium HumanMethylation450K BeadChip array.

b

Number of CpGs covered on Infinium MethylationEPIC array.

c

The following regulatory features were checked: enhancer/promoter marks (histone), overlapping binding sites for various transcription factors (e.g. CTCF, POL2A etc.) within region of interest (ROI) and presence of nearby reported GWAS single nucleotide polymorphisms (SNPs).

d

Coordinates based on genome build hg19. The BiSearch Web server122 was used to find genomic coordinates for ROIs where only primers were available.

e

HumanMethylation450 v1.2 and Infinium MethylationEPIC v1.0 B4 Manifest Files were referred to report ROI coverage on Illumina Infinium Methylation BeadChip arrays.

f

A total of 37 probes from 450k array were found within the gene and considered for analysis.