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Table 2 Genomic features of non-redundant tDMRs

From: Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis

 

chr6 coordinates (NCBI_35)

TSS

CTCF

H4K20 me1

PolII

H3K4 me2

H3K36 me3

H3K4 me3

DnaseI

H3K4 me1

CpG island

ECR

H2AZ

repeats %

CpG %

1

29823989–29826356

 

x

    

x

x

 

x

 

x

28.63

2.94

2

30000805–30003606

   

x

  

x

x

    

12.6

9.28

*3

30228982–30231712

            

26.44

2.64

*4

30247370–30249040

 

x

    

x

x

 

x

  

4.73

9.1

*5

30565890–30568365

  

x

x

 

x

x

     

11.95

4.77

6

30721858–30724158

      

x

    

x

5.91

10.52

7

30731648–30734384

            

42.71

2.27

8

30891136–30893651

            

95.08

5.24

9

31709197–31711626

          

x

 

79.93

5.01

*10

31803609–31806450

 

x

    

x

x

  

x

 

0

2.88

11

31841070–31843352

          

x

 

0

11.05

12

32020686–32023216

          

x

 

18.4

5.61

13

32056738–32058031

x

           

6.57

3.935

*14

32067481–32068550

            

0

3.09

*15

32071709–32072864

            

0

5.61

16

32073608–32074514

            

0

5.02

17

32074474–32074660

            

13.67

3.97

*18

32077678–32079121

            

0

5.35

*19

32081199–32081780

            

19.53

5.4

20

32088659–32090434

            

0

3.685

*21

32088718–32090526

            

0

3.41

*22

32090749–32092076

            

1.96

4.22

23

32092057–32093147

            

0

2.38

24

32094350–32095101

            

100

1.33

25

32098656–32099323

            

100

3.59

26

32099573–32100214

            

0

3.875

*27

32104734–32105602

            

0

5.29

*28

32107212–32107398

            

0

5.35

29

32109195–32110435

            

9.995

5.6

*30

32110416–32111859

            

19.53

5.4

31

32115381–32116535

          

x

 

0

7.27

32

32119000–32120024

          

x

 

0

7.61

33

32223988–32226638

      

x

  

x

  

4.19

11.09

34

32659407–32660508

      

x

x

 

x

  

9

5

35

32817677–32820582

            

20.44

2.96

36

32836042–32838492

            

9.42

7.26

37

33192620–33193912

 

x

          

32.79

6.5

*38

33372651–33375048

  

x

x

x

x

x

x

x

 

x

 

10.93

8.76

39

33389687–33392295

   

x

  

x

   

x

 

2.3

7.51

40

29830203–29832660

            

6.08

7.77

41

29889483–29892066

            

21.2

4.15

42

29937894–29939594

            

38.78

2.48

43

30484481–30486798

            

96.59

1.04

44

30491424–30493923

            

1.4

2

45

30526624–30528439

      

x

x

    

3.54

7.33

46

30527803–30529467

 

x

    

x

     

3.54

6.73

47

30534798–30537070

            

42.42

1.26

48

30881555–30884300

            

98.55

4.27

49

31092038–31094660

            

74.72

7.51

50

31270669–31273172

 

x

    

x

     

4.59

2.75

51

31454436–31456982

            

8.59

5.84

*52

32590480–32591619

            

44.47

2.11

53

32622631–32625110

            

91.09

5.97

54

33132309–33134479

       

x

    

24.37

1.01

55

33450625–33452501

            

84.66

2.88

  1. A total number of 55 non-redundant tDMRs were identified. tDMR co-ordinates on chromosome 6 are provided. tDMRs 1–39 are intragenic and 40–55 intergenic. Enrichment of genomic features, including CpG islands, DNAseI sites, TSSs, ECRs, CTCF binding sites, RNA PolII binding sites, histone marks (H4K20me1, H3K4me2, H3K4me3, H3K36me3, H3K4me1) and H2AZ was tested and marked by symbol 'x' if enrichment was statistically significant (P < 0.05). Percent CpG and repeat density were also determined and are shown for each tDMR. tDMRs 14 – 30 (intragenic) and 51 (intergenic) are mapping to the region encoding for C4A and C4B genes. Asterisks indicate the tDMRs that overlap with Affy_U95 expression array probes.
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BMC Medical Genomics

ISSN: 1755-8794

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