Table 4.
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.
Number of CpGs covered on Infinium HumanMethylation450K BeadChip array.
Number of CpGs covered on Infinium MethylationEPIC array.
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).
Coordinates based on genome build hg19. The BiSearch Web server122 was used to find genomic coordinates for ROIs where only primers were available.
HumanMethylation450 v1.2 and Infinium MethylationEPIC v1.0 B4 Manifest Files were referred to report ROI coverage on Illumina Infinium Methylation BeadChip arrays.
A total of 37 probes from 450k array were found within the gene and considered for analysis.