Table 1.
Enzymes that generate protruding ends in the restriction fragments, which are complementary to the adaptors U-CG1, TA-1 and AATT-1
| Enzymes | Recognition sequence | Percentage coverage of CpGs in human gDNA (%) | Number of fragments (per kb) in CpG islands* | Number of fragments (per kb) in non-CpG islands* |
|---|---|---|---|---|
| HpaII (BsiSI) | CCGG | 8.6 | 3.98 | 1.18 |
| Hin6I (HinP1I) | GCGC | 6.4 | 3.98 | 0.61 |
| AciI (SsiI) | CCGC | 17.4 | 3.23 | 1.79 |
| Hin1I (AcyI, BsaHI) | GPuCGPyC | 2.0 | 1.92 | 0.11 |
| HpyCH4IV | ACGT | 6.6 | 1.31 | 1.08 |
| Bsu15I (ClaI, BspDI) | ATCGAT | 0.2 | <0.01 | 0.02 |
| NarI (MlyI) | GGCGCC | 0.6 | 1.08 | <0.01 |
| Bsp119I (BstBI, AsuII) | TTCGAA | 0.1 | 0.11 | <0.01 |
| Psp1406I (AclI, PspI) | AACGTT | 0.3 | <0.01 | 0.05 |
| XmiI (AccI) | GTMKAC | 0.1 | 0.19 | 0.34 |
| TasI | AATT | na | 0.80 | 2.88 |
| Csp6I | GTAC | na | 2.23 | 1.41 |
| MseI | TTAA | na | 0.80 | 2.88 |
| BfaI | CTAG | na | 1.56 | 1.55 |
Asterisk (*) indicates the number of 50 bp to 1.5 kb long (‘informative’) fragments, derived from several Mb of randomly selected CpG island and non-CpG island sequences on chromosomes 1, 2, 4, 5, 6, 9, 17, 19 and 20; bold numbers represent the most informative enzymes; na = not applicable; M = Adenine or Cytosine; K = Guanine or Thymine.