Table 1.
Genomic location and core-sequence based orientation of the tested CTCF elements
| Tested CTCF site | Chromosomal location (mm10) | CTCF core motif orientation in endogenous site | Inserted CTCF sequence in forward orientation (Core motif in bold) | Inserted CTCF sequence in reverse orientation (Core motif in bold) |
|---|---|---|---|---|
| HS-94 | chr11: 32182671–32182738 | Forward | CCCAGGAGGCTGCATTACCACAGA TGGACAGTAGAGGGAGACAG AGATCGTGAGTTGAAAATTAAAAG | CTTTTAATTTTCAACTCACGATCT CTGTCTCCCTCTACTGTCCA TCTGTGGTAATGCAGCCTCCTGGG |
| HS-71 | chr11: 32205080–32205147 | Forward | CACGCGAGTGGCAACGGCAGGCCC CAGGCAGCAGGAGGCGCCCG CCTCCCAGCGTCACCTTGTTGGGT | ACCCAACAAGGTGACGCTGGGAGG CGGGCGCCTCCTGCTGCCTG GGGCCTGCCGTTGCCACTCGCGTG |
| HS-59 | chr11: 32217005–32217072 | Forward | CCTTGGAGCAGAAGCCACAATAAA TGACCACGAGGTGGCGCCAA CTGCCAAAAAAGGCATCGAGGCAG | CTGCCTCGATGCCTTTTTTGGCAG TTGGCGCCACCTCGTGGTCA TTTATTGTGGCTTCTGCTCCAAGG |
| HS-39 | chr11: 32237185–32237252 | Forward | TCATGGATTCAAAGCCACTGAGGC CTGGCCACTGGGGGCGCCAT TCGCCATTAAAAGGTCCTGCTGGG | CCCAGCAGGACCTTTTAATGGCGA ATGGCGCCCCCAGTGGCCAG GCCTCAGTGGCTTTGAATCCATGA |
| HS-38 | chr11: 32238628–32238695 | Reverse | CACCTGGTAGTGCTATGCACCCTG AGGCCACCAGAGGGTAGCAG AGGCCTACCCAGGACCTCAGTTTG | CAAACTGAGGTCCTGGGTAGGCCT CTGCTACCCTCTGGTGGCCT CAGGGTGCATAGCACTACCAGGTG |
| HS-29 | chr11: 32247237–32247304 | Forward | CAAATTCCTGTGTCCCTCCAAATT GGTCCACTGGGTGGCACTTG GAGGCCTCAAGCCCTGAGCTGTGC | GCACAGCTCAGGGCTTGAGGCCTC CAAGTGCCACCCAGTGGACC AATTTGGAGGGACACAGGAATTTG |
| Theta 1 | chr11: 32286905–32286972 | Reverse | CTCAAAGACGTCCTGAAACACAAG AGGCCGCCAGGGGGCGCTGC ATCGTTCCAGGATGCCTAGGTGTT | AACACCTAGGCATCCTGGAACGAT GCAGCGCCCCCTGGCGGCCT CTTGTGTTTCAGGACGTCTTTGAG |
| Theta 2 | chr11: 32300010–32300077 | Reverse | CTCAAAGATGTCCTGAAACACAAG AGGCCGCCAGGGGGCGCTGC ATCGTTCCAGGATGCCTAGGTGTT | AACACCTAGGCATCCTGGAACGAT GCAGCGCCCCCTGGCGGCCT CTTGTGTTTCAGGACATCTTTGAG |
| HS + 44 | chr11: 32321366–32321433 | Reverse | GAAAAGCCTTGCACCTACTTATAG TGGCCTGCAGGGGGCGCCCC AGAGACCTCCTGCCCGGTAGTCAT | ATGACTACCGGGCAGGAGGTCTCT GGGGCGCCCCCTGCAGGCCA CTATAAGTAGGTGCAAGGCTTTTC |
| HS + 48 | chr11: 32324813–32324880 | Reverse | CTTGGAGCTGCGAAGTTCCGAGTC CCGCCACACGGGGGTGCTCG TCGCCTTCTTATATCTCCGGTAGC | GCTACCGGAGATATAAGAAGGCGA CGAGCACCCCCGTGTGGCGG GACTCGGAACTTCGCAGCTCCAAG |
| HS + 65 | chr11: 32341265–32341332 | Reverse | CCAGGTTGGAGCACTACATCAATC TCTCCTGCAGGTGGCGCCCT TCCGCGCGACTCACTCTTATGGAC | GTCCATAAGAGTGAGTCGCGCGGA AGGGCGCCACCTGCAGGAGA GATTGATGTAGTGCTCCAACCTGG |
| HS + 66 | chr11: 32343076–32343143 | Forward | GTGTGTGAATGCAGGTGCCTACAG TGGACAGAAGAGGGCGCCAG ATCCTCTGGAGCTGGAGTTTCAGG | CCTGAAACTCCAGCTCCAGAGGAT CTGGCGCCCTCTTCTGTCCA CTGTAGGCACCTGCATTCACACAC |
| mouse β 3′HS1 | chr7: 103807045–103807112 | Reverse | AGAGCTCTGAGGCATGTTCTCAGT CAACCTCAAGGGGGCAGTAT TGAGCTTGGAATTCAGTATCAACT | AGTTGATACTGAATTCCAAGCTCA ATACTGCCCCCTTGAGGTTG ACTGAGAACATGCCTCAGAGCTCT |
| HoxA5|6 | chr6: 52204630–52204697 | Reverse | TCGGAAGCGAAGCGATGCGCCCAG TCTCCAGCGGGTGGCGCTCG AGTCCGACTGAACGGCGGCAACGG | CCGTTGCCGCCGTTCAGTCGGACT CGAGCGCCACCCGCTGGAGA CTGGGCGCATCGCTTCGCTTCCGA |
| H19-Igf2-m3 | chr7: 142580737–142580804 | Reverse | TTATGTGCAACAAGGGAACGGATG CTACCGCGCGGTGGCAGCAT ACTCCTATATATCGTGGCCCAAAT | ATTTGGGCCACGATATATAGGAGT ATGCTGCCACCGCGCGGTAG CATCCGTTCCCTTGTTGCACATAA |
| Sox9-CBS1 | chr11: 111537815–111537882 | Forward | GAAAATATTGTGCAAGGCAACATG TTACCAGCAGGTGGCAGTCC AGTAGACTTCTACAGAACTGTGGC | GCCACAGTTCTGTAGAAGTCTACT GGACTGCCACCTGCTGGTAA CATGTTGCCTTGCACAATATTTTC |
| Sox9-CBS2 | chr11: 111536194–111536261 | Forward | AAGAAAAGGTGTACTCTCCGTTGT CTACCGCCAGATGGCAGCAT GCACACACCAATTAAAATTTGTTC | GAACAAATTTTAATTGGTGTGTGC ATGCTGCCATCTGGCGGTAG ACAACGGAGAGTACACCTTTTCTT |
| Epha4-Pax3-R4 | chr1: 78008893–78008960 | Reverse | TACGACAGAGGCTGCGTCTCACTA TGTCCATGCGGGGGCGCTCT TTTGCAGTCTCTCTGCAGACCTCA | TGAGGTCTGCAGAGAGACTGCAAA AGAGCGCCCCCGCATGGACA TAGTGAGACGCAGCCTCTGTCGTA |
| Negative control | chr11: 32274291–32274358 | nil | AATGTAATGAAAATATGGCTAATTA ATCTTTACATTCTGTCTTGGCCA AGATGCAGAGAAGCGACAGT | nil |