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Table 1 Characteristics of each region investigated

From: Quantitative analysis of DNA methylation at all human imprinted regions reveals preservation of epigenetic stability in adult somatic tissue

Assay Chr Location P-O-O methylation mark Germ-line/somatic Average somatic methylation Location within gene CpG island CTCF CpG density
DIRAS3 (3) 1 68285444 Maternal Somatic 70.22 Gene body Exonic Yes YV 6.2
DIRAS3 (2) 1 68288969 Maternal Germ-line# 50.42 Promoter/Ex 1 Yes N 5.6
DIRAS3 (1) 1 68290053 Maternal Germ-line# 46.09 5' upstream (GPR) Yes YV 5.4
ZDBF2 2 206834066 Paternal Germ-line 47.65 Intergenic No Y 1.4
NAP1L5 4 89837958 Maternal Germ-line 50.16 Embeded gene promoter No N 7.2
ZAC 6 144371274 Maternal Germ-line 40.83 Isoform promoter Yes N 11.2
IGF2R-2 6 160346534 Unknown Unknown 81.34 Gene body intronic Yes N 6.6
SLC22A1 6 160475377 Unknown Unknown 82.78 Gene body Exonic Yes N 5.6
SLC22A3 6 160688909 Unknown Unknown 39.89 Promoter/Ex 1 Yes YV 7.6
MEST (s) 7 129913465 Maternal Somatic 28.15 Isoform promoter Yes Y 8.2
MEST 7 129918562 Maternal Germ-line 45.84 Isoform promoter Yes Y 7
GRB10 (g) 7 50817567 Maternal Germ-line 45.47 Isoform promoter Yes YV 12.6
GRB10 (s) 7 50829108 Maternal Somatic 19.19 Isoform promoter Yes YV 6
PEG10 7 94123850 Maternal Germ-line 55.63 Promoter Yes Y 6.4
PON1 7 94791675 Unknown Unknown 34.04 Promoter/Ex 1 Yes N 4.6
INPP5FV2 10 121568151 Maternal Germ-line 60.89 Isoform promoter Yes YV 11.2
H19 DMR 11 1977714 Paternal Germ-line 45.23 5' upstream (GPR) No Y 5.8
IGF2 (2) 11 2110885 Paternal Somatic 35.41 Gene body Exonic Yes N 6.2
IGF2 (0) 11 2126069 Paternal Somatic 54.59 Isoform promoter No N 2.2
KCNQ1 11 2422247 Unknown Unknown 22.27 5' upstream (GPR) Yes YV 6.8
KvDMR 11 2678628 Maternal Germ-line 50.68 antisense RNA promoter Yes YV 5.6
KCNQ1DN 11 2847182 Unknown Unknown 26.22 5' upstream (GPR) Yes N 11.4
CDKN1C 11 2861764 None None 12.07 Gene body Exonic Yes Y 10.8
OSBPL5 (3) 11 3098345 Unknown Unknown 82.66 Gene body Exonic Yes N 4.2
RB1 13 47791152 Maternal Germ-line 59.47 Gene body intronic Yes N 6.4
DLK 14 100262671 Paternal Somatic 56.05 Promoter/Ex 1 Yes N 9.2
IG-DMR 14 100345582 Paternal Germ-line 58.17 Intergenic No N 2.4
MEG3-US 14 100360453 Paternal Somatic 49.55 Intergenic Yes N 6.6
MEG3 14 100361829 Paternal Somatic 48.99 Promoter/Ex 1 Yes YV 6.2
RTL 14 100419312 None None 88.27 Gene body Exonic Yes N 6.4
MKRN3 15 21362387 Unknown Unknown 62.44 Gene body Exonic No N 4.4
SNRPN 15 22751911 Maternal Germ-line 47.12 Isoform promoter Yes N 7.8
UBE3A 15 23234499 None None 3.15 Promoter/Ex 1 Yes Y 9.6
ATP10A 15 23658720 None None 13.82 Promoter/Ex 1 Yes N 5.4
GABRB3 15 24425436 Unknown Unknown 47.8 Isoform promoter Yes YV 7.6
GABRA5 15 24663372 Unknown Unknown 87.29 Promoter/Ex 1 Yes YV 13
TCEB3C 18 42797692 None None 86.52 Embedded gene pronoterd Yes YV 7.6
NLRP2 19 60186163 Unknown Unknown 61.93 Gene-body Exonic Yes N 7
PEG3/ZIM2 19 62043527 Maternal Germ-line 49.92 Gene body intronic Yes N 9.2
USP29 19 62322335 Unknown Unknown 43.27 Intergenic Yes N 7.4
ZIM3 19 62348129 Unknown Unknown 74.21 Promoter/Ex 1 No N 1
MCTS2 20 21441323 Maternal Germ-line 44.72 Embedded gene promoter Yes Y 6.6
NNAT 20 35582455 Maternal Germ-line 77.93 Embedded gene promoter Yes YV 5.2
BLCAP 20 35589631 None None 8.37 Promoter/Ex 1 Yes YV 7.6
L3MBTL 20 41576732 Maternal Germ-line 51.23 Gene body Exonic (Ex1) Yes Y 7.6
NESP 20 56848977 Paternal Somatic 45.7 Isoform promoter Yes Y 9.2
NESPAS 20 56860398 Maternal Somatic 47.53 Isoform promoter Yes N 6.4
GNAS XL 20 56864018 Maternal Germ-line 43.98 Isoform promoter Yes N 5.6
GNAS 1A 20 56898576 Maternal Somatic 25.1 Isoform promoter Yes N 12
  1. Characteristics of each assay: Average somatic methylation is the average level for Brain, Breast, Colon, Heart, Kidney, Liver and Placenta. Genomic localization was analysed by BLASTing the amplicon against UCSC genomic sequence. The location of the amplicon in context of each gene sequence was recorded.
  2. GPR = general promoter region; CpG Island amplicon is within an UCSC annotated CpG island; CTCF binding is determined by analysis of ENCODE tracts on UCSC, (Y = Yes); binding in a tissue specific manner (YV = Yes variable); N = not binding; CpG density was calculated by taking the mid-point of the amplicon used for each assay and analysing the sequence 250bp each side (500bp in total); density is given as No. of CpGs per 100bp; # = the DMR for DIRAS3 could be either DMR1 or DMR2.
  3. Chr = chromosome