Table 4.
Differentially methylated regions and expression data from potential distally regulated genes based on in silico high-throughput chromosome conformation capture analysis
| All (GDM vs control) | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Proximal gene: RNA-Seq | Hi-C gene interactions: RNA-Seq | |||||||||||
| Chr | DMR start-end | No. CpGs | UCSC regulatory region | Methyl % | ERRBS q | Name | Log FC | P | Name | Log FC | P | Full form |
| 2 | 143626118- 143626133 | 2 | Strong enhancer/ exon 1 | –9.8 | 0.01 | KYNU | 0.91 | .24 | ARHGAP15 (RHG15)* | 2.01 | .02 | Rho GTPase activating protein 15 |
| 9 | 137537491- 137537663 | 2 | Strong or weak enhancer/ exon 1 | –25.6 | 0 | COL5A1 | –0.19 | .77 | MIR3689A | –3.18 | .002 | MicroRNA 3689a |
| 19 | 55477808- 55478162 | 3 | Active promoter/ exon 1 | –21.9 | 0.01 | NLRP2 | –0.77 | .34 | KIR3DL1 | 2.64 | .01 | Killer cell immunoglobulin- like receptor, 3 Ig domains and long cytoplasmic tail 1 |
| FCAR | 2.33 | .03 | Fc fragment of IgA receptor | |||||||||
| NCR1 | 3.12 | .003 | Natural cytotoxicity triggering receptor 1 | |||||||||
| Female (GDM vs control) | ||||||||||||
| Proximal gene: RNA-Seq | Hi-C gene interactions: RNA-Seq | |||||||||||
| Chr | DMR start-end | No. CpGs | UCSC regulatory region | Methyl % | ERRBS q | Name | Log FC | P | Name | Log FC | P | Full form |
| 1 | 38899434- 38899466 | 2 | Exon 1 | 31.6 | 0.001 | RHBDL2 | 0.12 | .83 | POU3F1 | –3.21 | .04 | POU class 3 homeobox 1 |
| 7 | 95025855- 95025906 | 2 | CpG island/active promoter/ intergenic | 15.6 | 0.03 | PON3/PON1 | 0.49/– 0.20 | 0.62/0.78 | DYNC1I1 | 1.49 | .03 | Dynein cytoplasmic 1 intermediate chain 1 |
| 8 | 143879721- 143879783 | 2 | CpG island/exon 1 | -23 | 0.02 | RP11-706C16.8 | 0.01 | 0.99 | SLURP1 | –2.39 | .02 | Secreted LY6/PLAUR domain containing 1 |
| CYP11B2 | 3.52 | .02 | Cytochrome P450 family 11 subfamily B member 2 | |||||||||
| 9 | 137625891- 137626053 | 2 | Strong enhancer/ exon 1 | 33.9 | 0.01 | COL5A1 | –0.5 | 0.5 | MIR3689A | –4.96 | .002 | MicroRNA 3689A |
| MIR3689F | –2.46 | .02 | MicroRNA 3689F | |||||||||
| 19 | 55477808- 55478162 | 3 | Active/weak promoter exon 1 | -35.2 | 0.01 | NLRP2 | –1.66 | 0.14 | LILRA2 | 3.84 | .008 | Leukocyte immunoglobulin- like receptor 2 |
| KIR3DL1 | 3.53 | .02 | Killer cell immunoglobulin- like receptor, 3 Ig domains, and long cytoplasmic tail 1 | |||||||||
| NCR1 | 4.04 | .005 | Natural cytotoxicity triggeringreceptor 1 | |||||||||
| Male (GDM vs control) | ||||||||||||
| Proximal gene: RNA-Seq | Hi-C interacting genes: RNA-Seq | |||||||||||
| Chr | DMR start-end | No. CpGs | UCSC regulatory region | Methyl % | ERRBS q | Name | Log FC | P | Name | Log FC | P | Full form |
| 3 | 49471923- 49472056 | 2 | Intergenic | 11.6 | 0.004 | NICN1 | 0.45 | .31 | MIR425 | –2.81 | .005 | MicroRNA 425 |
| 11 | 130416252- 130416291 | 2 | Intergenic | 16.9 | 0.015 | ADAMTS15 | –1.11 | .24 | ADAMTS8 | –3.15 | .04 | ADAM metallopeptidase with thrombospondin type 1 motif 8 |
| 12 | 53069066- 53069130 | 2 | Exon 9 | 7.7 | 0.01 | KRT1 | 0 | 1 | KRT83 | 4.42 | .001 | Keratin 83 |
| KRT78 | 2.99 | .01 | Keratin 6B | |||||||||
| KRT6C | 2.62 | .05 | Keratin 6C | |||||||||
| KRT5 | 3.68 | .04 | Keratin 5 | |||||||||
| KRT4 | 2.59 | .03 | Keratin 4 | |||||||||
| KRT78 | 2.84 | .006 | Keratin 78* all type 2 keratins in a cluster on chromosome 12q1 | |||||||||
| 17 | 5925022- 5925042 | 2 | Intergenic | 19.1 | 0.008 | WSCD1 | –0.01 | .99 | LOC339166 | 2.13 | .02 | Noncoding RNA LOC339166 |
| 22 | 38522378- 38522389 | 2 | Exon 10/weak enhancer | 7.4 | 0.01 | PLA2G6 | 0.28 | .62 | SOX10 | –2.08 | .04 | SRY-box 10 |
| LOC400927 (TPTEP2) | –3.47 | .003 | Transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 | |||||||||
Abbreviations: Chr, chromosome; DMR, differentially methylated regions; ERRBS, enhanced reduced representation bisulfite sequencing; FC, fold change; GDM, gestational diabetes; Hi-C, high-throughput chromosome conformation capture; Ig, immunoglobulin; RNA-Seq, RNA sequencing; SOX10, SRY-box transcription factor 10; UCSC, University of California Santa Cruz.