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Table 3 Analysis results for immediate and persistent changes in DNA methylation after ED exposure of G1 prospermatogonia

From: Deleterious effects of endocrine disruptors are corrected in the mammalian germline by epigenome reprogramming

   

Analysis level 1

Level 2

Level 3

Level 4

 

Sample A

Sample B

Sample A to B

Hits

Common in G1R and G2R

Hits

Common in MGCs and sperm

Hits

TGI

Hits

Group 1: CpG_G1R_MGC

Oil

BPA

Test 1

112

Test A (test 1 v 7)

1 (1)

    
 

BPA

Oil

Test 2

72

Test B (2 v 8)

3 (3)

    
 

Oil

VZ

Test 3

129

Test C (3 v 9)

0 (0)

Test Q (3 v 13)

1 (1)

Test C v G

0 (0)

 

VZ

Oil

Test 4

81

Test D (4 v 10)

0 (0)

Test R (4 v 14)

2 (1)

Test D v H

0 (0)

 

Oil

DEHP

Test 5

130

Test E (5 v 11)

4 (1)

    
 

DEHP

Oil

Test 6

120

Test F (6 v 12)

6 (3)

    

Group 2: CpG_G2R_MGC

Oil

BPA

Test 7

61

      
 

BPA

Oil

Test 8

98

      
 

Oil

VZ

Test 9

59

  

Test S (9 v 15)

4 (2)

  
 

VZ

Oil

Test 10

135

  

Test T (10 v 16)

2 (1)

  
 

Oil

DEHP

Test 11

89

      
 

DEHP

Oil

Test 12

167

      

Group 3: CpG_G1R_SPERM

Oil

VZ

Test 13

76

Test G (13 v 15)

4 (4)

    
 

VZ

Oil

Test 14

76

Test H (14 v 16)

4 (3)

    

Group 4:

          

CpG_G2R_SPERM

Oil

VZ

Test 15

196

      
 

VZ

Oil

Test 16

99

      

Group 5: Imp_G1R_MGC

Oil

BPA

Test 17

46

Test I (17 v 23)

0 (0)

    
 

BPA

Oil

Test 18

35

Test J (18 v 24)

0 (0)

    
 

Oil

VZ

Test 19

93

Test K (19 v 25)

1 (1)

Test U (19 v 29)

1 (1)

Test K v O

0 (0)

 

VZ

Oil

Test 20

51

Test L (20 v 26)

1 (1)

Test V (20 v 30)

0 (0)

Test L v P

0 (0)

 

Oil

DEHP

Test 21

83

Test M (21 v 27)

0 (0)

    
 

DEHP

Oil

Test 22

59

Test N (22 v 28)

1 (0)

    

Group 6: Impr_G2R_MGC

Oil

BPA

Test 23

30

      
 

BPA

Oil

Test 24

45

      
 

Oil

VZ

Test 25

29

  

Test X (25 v 31)

0 (0)

  
 

VZ

Oil

Test 26

120

  

Test Y (26 v 32)

4 (4)

  
 

Oil

DEHP

Test 27

27

      
 

DEHP

Oil

Test 28

111

      

Group 7: Impr_G1R_SPERM

Oil

VZ

Test 29

56

Test O (29 v 31)

3 (2)

    
 

VZ

Oil

Test 30

58

Test P (30 v 32)

1 (0)

    

Group 8: Impr_G2R_SPERM

Oil

VZ

Test 31

114

      
 

VZ

Oil

Test 32

93

      
  1. After in utero exposure of G1 MGC to vehicle control (‘oil’) or one of the EDs, the level of DNA methylation was measured in reprogrammed G1R and G2R fetal MGCs and adult spermatozoa by MIRA-chip and Nimblegen microarrays. CpG-promoter arrays were used in groups 1 to 4 and custom imprinting arrays were used in groups 5 to 7. At the first level of analysis, we performed 32 tests comparing the log2 ratio MIRA versus input values. To detect a change between sample A and B, peaks were identified in the average value (n = 3 for MGC and n = 2 for sperm) of A samples first and were compared with the MIRA intensity of the average of sample B at the same locations. The number of hits where a change occurred with greater than ±5% and Fisher’s exact test P value (P <0.05) were tabulated. At level two, we compared the results of two level-1 tests (in parentheses) to find common changes between G1R and G2R in MGCs (Tests A-F and I-N) and in sperm (Tests G-H and O-P); the number of common hits is provided and those that changed in the same direction are given in parentheses. At level three, we compared the results of two level-1 tests to find common changes between MGC and sperm in the same generation, G1R (Test Q-R and U-V) or G2R (S-T and X-Y). At level four, we compared the results of four level-1 tests in search for true transgenerational epigenetic inheritance: immediate effect in G1R MGCs, maintained into G1R sperm, G2R prospermatogonia, and G2R sperm, thereby having the potential to affect G3 soma. Note the low number of hits in levels 1 to 3 and lack of hits at level 4, even at the low cutoff values applied.
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Genome Biology

ISSN: 1474-760X

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