Table 1.
Oligonucleotide primersequences used for RT-qPCR, ChIP-qPCR, 5-hmC and 5-mC Chop-qPCR, hmeDIP-qPCR, and subcloning. All sequences correspond to the X. tropicalis genome except where indicated
| For RT-qPCR | |
|---|---|
| Gene | Primer sequence (5’ → 3’) |
| ef1a | Forward: CTATCCCCGCCAAACATCT |
| Reverse: CCATCTCAGCAGCTTCCTTC | |
| gadd45α | Forward: CTCAATGTGGACCCAGACAA |
| Reverse: CAGGGTGAAGTGGATCTGTAAA | |
| gadd45β | Forward: GACCTCCACTGCATTCTAGTTT |
| Reverse: CCACTGACTCCTGCTTCTATATTC | |
| gadd45γ | Forward: GGAAGAAGTTCACGGACAAGA |
| Reverse: GGGCAGAGACCAATAGTTCAT | |
| tdg | Forward: GGGATCAATCCAGGTCTTATGG |
| Reverse: TCCAGACAAGAACAGACACTTC | |
| tet2 | Forward: GGTTACTGCTTGCTTGGATTT |
| Reverse: CACGATTGTCTTCTCTGGTTAAAG | |
| tet3 | Forward: ATCTGACATCTCCAACCAAGAG |
| Reverse: GTCCAGAACCCAGATGTGTATAA | |
| idh1 | Forward: GGACAGTAACCCGGCATTATAG |
| Reverse: CCTCTTGTCCAGGCAAAGATAG | |
| idh2 | Forward: GCACTGGCCACTCTGAAATA |
| Reverse: CATTGGGACTCTTCCACATCTT | |
| idh3a | Forward: GCTAATCCCACTGCTCTTCTT |
| Reverse: CAGAGCCTTCCCAGATTTGAT | |
| idax | Forward: TGCCAAAGGTCTGTGTGTC |
| Reverse: TCCTCTGACCTCTAGTGAAGTG | |
| apobec2 | Forward: CCCTGCTTCTTCTTTCATGTTTC |
| Reverse: AATACTTGACCCTCAGGTCTTTC | |
| Firefly luciferase | Forward: CTTCGAGGAGGAGCTATTCTTG |
| Reverse: GTCGTACTTGTCGATGAGAGTG | |
| Renilla luciferase | Forward: CATGGGATGAATGGCCTGATA |
| Reverse: CAACATGGTTTCCACGAAGAAG | |
| For 5-hmC chop-qPCR | |
| X. tropicalis dnmt3a-TRE-A | Forward: CTTTGCCGGTGCCAACA |
| Reverse: CTGCTTCCCACAATCCCTT | |
| For 5-mC chop-qPCR | |
| Genomic region | Primer sequence (5’ → 3’) |
| X. laevis dnmt3a-TRE-B | Forward: TGA CTC TGC GCT GTG A |
| Reverse: AGG CTA CGT ACC CCT CTC AGT CT | |
| X. laevis control genomic regiona | Forward: TTC CCA TGG GTC CCT GTA AGT |
| Reverse: GGG AGC TTT TTG CTG CAG AA | |
| For hmeDIP-qPCR | |
| Genomic region | Primer sequence (5’ → 3’) |
| dnmt3a TRE-A | Forward: CACAGAAATGCAAGGGATTG |
| Reverse: CTGTAGTGCTGCTCAGTG | |
| dnmt3a TRE-B | Forward: TGACTCTGCGCAGTGA |
| Reverse: AGGCTACGTACCCCTCTCAGTCT | |
| For ChIP-qPCR | |
| Genomic region | Primer sequence (5’ → 3’) |
| dnmt3a TRE-A | Forward: CAGTAAAGGCACCCTGAG |
| Reverse: CATAAAGATTTCTGCCGTACAC | |
| thrb TRE | Forward: CCCCTATCCTTGTTCGTCCTC |
| Reverse: GCGCTGGGCTGTCCT | |
| gadd45γ TRE region | Forward: AGTGTTTATGCACGGGAAGG |
| Reverse: CCGGCAATTTGGTCGCTTATT | |
| tet3 TRE region | Forward: GTGTGTGTAGGCTGAATCTCTAAG |
| Reverse: AAGCCTGAGAGGGAAGAAGA | |
| ifabp promoter | Forward: CCCTACATTGGTTGAGCCAGTTTT |
| Reverse: TCAAAGGCCATGGTGATTGGT | |
| thrb exon 5 | Forward: CCCCGAAAGTGAAACTCTAACTCT |
| Reverse: CCACACCGAGTCCTCCATTTT | |
| tet2 TRE region | Forward: GTGGAGTGGATCACACAAGTAA |
| Reverse: TAGCTGGAGGCAGTCTATGT | |
| Sox9 promoter | Forward: ACGTGAAAGTGGAGCAGTGT |
| Reverse: TCTTCAGCAAAGGCACCCAA | |
| dnmt3a exon 2 | Forward: AACACTCCTCACCCACAAATAG |
| Reverse: GGGAATCTCTCCGCAAAGTAA | |
| klf9 synergy module (KSM) | Forward: CCGTCCCTTCTTTTGTGTACATT |
| Reverse: GCTGTTCGTGCCACTTTGC | |
| idax TRE region | Forward: CGAGAGATCAGCTGCACAATA |
| Reverse: ATGTCCAAGGTAAGGGTGTATG | |
| idh2 | Forward: FATAGGACGAGTAAGGGCAAAC |
| Reverse: GGCAAAGGTCACCCTGTAA | |
| For subcloning the tet2 TRE region (610 bp b ) into pGL4.23 | |
| Primer sequence | |
| Forward: AAACTCGAGGGAGTTCTGCCTGCCTTCTAG | |
| Reverse: TGTGAAGCTTCAGCGTAAATTGTGTCTATTTC | |
| For EMSA | |
| Genomic region | Primer sequence (5’ → 3’) |
| X. tropicalis dnmt3a TRE-B | Forward: AAG TGC AGC GAT GGG AGG G |
| Reverse: AAT CAT TCT TGG CTG CGC CC | |
| X. tropicalis klf9 synergy module (KSM) | Forward: ATACTCGAGCCCTGTACCATTTAGGGCC |
| Reverse: ATAAAGCTTAGCGCCGCTTTAAGAAAT |
a No Hinp1I restriction sites contained within the DNA sequence.
b The full DNA sequence is given in Supplemental Table 4 (62).