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Table 2 Possible changes in MSAP MH profiles from Figure 1 and their interpretation

From: How to interpret Methylation Sensitive Amplified Polymorphism (MSAP) profiles?

Plants
1MH1 → MH2 methylation change MSAP pattern (Figure 1) 7interpretation
2(-, -) → (+, +) 3s(mCmC → CC) 4S5(4 → 1) ambiguous
  6s(mCmC → CC) and l(CmC → CC) S(5 → 1)  
  s(CC → mCmC) L(1 → 4)  
  s(CmC → mCmC) and l(CmC → CC) L(3 → 4)  
(-, -) → (+, -) s(mCmC → CmC) S(4 → 2) or S(5 → 3) ambiguous
  s(mCmC → CmC) and l(CC → CmC) S(4 → 3)  
  s(mCmC → CmC) and l(CmC → CC) S(5 → 2)  
  s(CmC → mCmC) L(3 → 5)  
  s(CC → mCmC) and l(CC → CmC) L(1 → 5)  
(-, -) → (-, +) l(CmC → CC) L(3 → 2) ambiguous
  s(CC → CmC) L(1 → 2)  
(+, +) → (-, -) s(CC → mCmC) S(1 → 4) ambiguous
  s(CC → mCmC) and l(CC → CmC) S(1 → 5)  
  s(mCmC → CC) L(4 → 1)  
  s(mCmC → CmC) and l(CC → CmC) L(4 → 3)  
(+, +) → (+, -) s(CC → CmC) S(1 → 2) methylation
  s(CC → CmC) and l(CC → CmC) S(1 → 3)  
  l(CC → CmC) L(4 → 5)  
(+, +) → (-, +) s(mCmC → CmC) L(4 → 2) hypomethylation
(+, -) → (-, -) s(CmC → mCmC) S(2 → 4) or S(3 → 5) ambiguous
  s(CmC → mCmC) and l(CC → CmC) S(2 → 5)  
  s(CmC → mCmC) and l(CmC → CC) S(3 → 4)  
  s(mCmC → CmC) L(5 → 3)  
  s(mCmC → CC) and l(CmC → CC) L(5 → 1)  
(+, -) → (+, +) s(CmC → CC) S(2 → 1) hypomethylation
  s(CmC → CC) and l(CmC → CC) S(3 → 1)  
  l(CmC → CC) L(5 → 4)  
(+, -) → (-, +) s(mCmC → CmC) and l(CmC → CC) L(5 → 2) hypomethylation
(-, +) → (-, -) s(CmC → CC) L(2 → 1) ambiguous
  l(CC → CmC) L(2 → 3)  
(-, +) → (+, +) s(CmC → mCmC) L(2 → 4) methylation
(-, +) → (+, -) s(CmC → mCmC) and l(CC → CmC) L(2 → 5) methylation
Vertebrates
MH1 → MH2 sequence change MSAP pattern (Figure 1) interpretation
(-, -) → (+, +) 8new CCGG - mutation
(-, -) → (+, -) new CmCGG - mut. + met.
(-, -) → (-, +) l(CmC → CC) L(3 → 2) ambiguous
  s(CC → CmC) L(1 → 2)  
(+, +) → (-, -) CCGG loss - mutation
(+, +) → (+, -) s(CC → CmC) S(1 → 2) methylation
(+, +) → (-, +) new internal CmCGG - mut. + met.
(+, -) → (-, -) CmCGG loss - mutation
  new internal CmCGG -  
(+, -) → (+, +) s(CmC → CC) S(2 → 1) hypomethylation
  s(CmC → CC) and l(CmC → CC) S(3 → 1)  
(+, -) → (-, +) (CmC → CC) and new int. CmCGG - mutation
(-, +) → (-, -) s(CmC → CC) L(2 → 1) ambiguous
  l(CC → CmC) L(2 → 3)  
(-, +) → (+, +) internal CmCGG loss - mutation
(-, +) → (+, -) (CC → CmC) and int. CmCGG loss - mutation
  1. 1MH1 and MH2 represent the original (control) and a changed MSAP profile, respectively.
  2. 2- and + in parentheses denote the absence and the presence of a band in MspI (M) and HpaII (H) lanes.
  3. 3s and l indicate restriction sites in Figure 1 (the "methylation change" and "sequence change" columns).
  4. 4S and L indicate specific MSAP fragments (the "MSAP pattern column") according their lengths from Figure 1.
  5. 5The numbers in parenthesis correspond to the methylation states of the sequence and the MSAP profiles in Figure 1.
  6. 6Some MSAP profile changes are explained by two methylation changes (both s and l MspI/HpaII sites).
  7. 7Interpretation for each MH1→MH2 profile change is noted in the interpretation column.
  8. 8Majority of possible MSAP profile changes in vertebrates are explained by gain or loss of the restriction site and therefore are expected to be very rare.
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