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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