SNVs in the 3′UTR disrupting the validated seed match of TP53:miRNA
| TP53 3′UTR and miRNA† . | Consequential pairing† . | Seed match‡ . | No. of patients* . | |
|---|---|---|---|---|
| Seed + m8 + 1A . | Other . | |||
| Pos. 93-98 | 5′ CUUUGAACCCUUGCU––UGCAAUA | 7mer-1A | 1(1) | 0 |
| |::||||||||| | ||||
| hsa-miR-25/92a | 3′ AGUCUGGCUCUGUUCACGUUAC | |||
| |x|||| | ||||
| nSNV 93G>A | 5′ CUUUGAACCCUUGCU––UACAAUA | NO | ||
| Pos. 287-292 | 5′ UGCAGUUAAGGGUUAGUUUACA | 7mer-1A | 1(1) | 0 |
| |||| ||||||| | ||||
| hsa-miR-30d | 3′ GAAGGUCAGCCCCUA––CAAAUGU | |||
| |||| x|||||| | ||||
| nSNV 287G>A | 5′ UGCAGUUAAGGGUUAAUUUACA | NO | ||
| Pos.734-739 | 5′ AAGACUUGUUUUAUGCUCAGGGU | 7mer-m8 | 6(4) | 3(2) |
| ||| ||||||| | ||||
| hsa-miR-125b | 3′ AGUGUUCAAUCCCAGAGUCCCU | |||
| ||| x|||x|xx | ||||
| nSNV 733C>T | 5′ AAGACUUGUUUUAUGUUCAGGGU | NO | ||
| nSNV 737G>C | 5′ AAGACUUGUUUUAUGCUCACGGU | NO | ||
| nSNV 737G>A | 5′ AAGACUUGUUUUAUGCUCAAGGU | NO | ||
| nSNV 739G>A | 5′ AAGACUUGUUUUAUGCUCAGGAU | NO | ||
| nSNV 739G>C | 5′ AAGACUUGUUUUAUGCUCAGGCU | NO | ||
| nSNV 740U>A | 5′ AAGACUUGUUUUAUGCUCAGGGA | 8mer | ||
| Pos. 736-741 | 5′ GACUUGUUUUAUGCUCAGGGUCA | 8mer | 6(5) | 0 |
| ||||||| | ||||
| hsa-miR-504 | 3′ CUAUCUCACGUCUGGUCCCAGA | |||
| ||x|xx| | ||||
| nSNV 737G>C | 5′ GACUUGUUUUAUGCUCAAGGUCA | NO | ||
| nSNV 737G>A | 5′ GACUUGUUUUAUGCUCACGGUCA | NO | ||
| nSNV 739G>A | 5′ GACUUGUUUUAUGCUCAGGAUCA | NO | ||
| nSNV 739G>C | 5′ GACUUGUUUUAUGCUCAGGCUCA | NO | ||
| nSNV 740U>A | 5′ GACUUGUUUUAUGCUCAGGGCCA | NO | ||
| Pos. 804-809 | 5′ UGGGUCUCGCUUUGUUGCCCAGG | 7mer-m8 | 3(2) | 4(3) |
| :||||||:||||||||||||| | ||||
| hsa-miR-1285 | 3′ UCCAGAGUGAAACAACGGGUCU | |||
| :||||||:||||||||xx||| | ||||
| nSNV 805C>T | 5′ UGGGUCUCGCUUUGUUGTCCAGG | NO | ||
| nSNV 806C>T | 5′ UGGGUCUCGCUUUGUUGCTCAGG | NO | ||
| Pos. 967-972 | 5′ GGGGUCUCACAGUGUUGCCCAGG | 7mer-m8 | 5(2) | 2(2) |
| :|||||||| ||||||| | ||||
| hsa-miR-1285 | 3′ UCCAGAGUGAAACAACGGGUCU | |||
| :|||||||| ||||||| | ||||
| nSNV 968C>T | 5′ GGGGUCUCACAGUGUUGTCCAGG | NO | ||
| nSNV 969C>T | 5′ GGGGUCUCACAGUGUUGCTCAGG | NO | ||
| Pos. 1065-1070 | 5′ CCACGUCCAGCUGGAAGGGUCA | 7mer-1A | 4(3) | 1(1) |
| |||||| | ||||
| hsa-miR-504 | 3′ CUAUCUCACGUCUGGUCCCAGA | |||
| |x|x|x | ||||
| nSNV 1066G>A | 5′ CCACGUCCAGCUGGAAAGGUCA | NO | ||
| nSNV 1068G>A | 5′ CCACGUCCAGCUGGAAGGAUCA | NO | ||
| SNP 1070C>T | 5′ CCACGUCCAGCUGGAAGGGUUA | NO | ||
| nSNV 1071A>G | 5′ CCACGUCCAGCUGGAAGGGUCG | 6mer | ||
| Pos. 1084-1089 | 5′ GUCAACAUCUUUUACAUUCUGCAA | ? | 3(2) | 6(5) |
| || | | ||| | |||| | | ||||
| hsa-miR-15 | 3′ GUGUUUGGUAAUACACGACGAU | |||
| hsa-miR-16 | 3′ GCGGUUAUAAAUGCACGACGAU | |||
| | || ||||| | |||| | | ||||
| nSNV 1085C>T | 5′ GUCAACAUCUUUUACAUUCUGUAA | |||
| nSNV 1086A>G | 5′ GUCAACAUCUUUUACAUUCUGCGA | |||
| TP53 3′UTR and miRNA† . | Consequential pairing† . | Seed match‡ . | No. of patients* . | |
|---|---|---|---|---|
| Seed + m8 + 1A . | Other . | |||
| Pos. 93-98 | 5′ CUUUGAACCCUUGCU––UGCAAUA | 7mer-1A | 1(1) | 0 |
| |::||||||||| | ||||
| hsa-miR-25/92a | 3′ AGUCUGGCUCUGUUCACGUUAC | |||
| |x|||| | ||||
| nSNV 93G>A | 5′ CUUUGAACCCUUGCU––UACAAUA | NO | ||
| Pos. 287-292 | 5′ UGCAGUUAAGGGUUAGUUUACA | 7mer-1A | 1(1) | 0 |
| |||| ||||||| | ||||
| hsa-miR-30d | 3′ GAAGGUCAGCCCCUA––CAAAUGU | |||
| |||| x|||||| | ||||
| nSNV 287G>A | 5′ UGCAGUUAAGGGUUAAUUUACA | NO | ||
| Pos.734-739 | 5′ AAGACUUGUUUUAUGCUCAGGGU | 7mer-m8 | 6(4) | 3(2) |
| ||| ||||||| | ||||
| hsa-miR-125b | 3′ AGUGUUCAAUCCCAGAGUCCCU | |||
| ||| x|||x|xx | ||||
| nSNV 733C>T | 5′ AAGACUUGUUUUAUGUUCAGGGU | NO | ||
| nSNV 737G>C | 5′ AAGACUUGUUUUAUGCUCACGGU | NO | ||
| nSNV 737G>A | 5′ AAGACUUGUUUUAUGCUCAAGGU | NO | ||
| nSNV 739G>A | 5′ AAGACUUGUUUUAUGCUCAGGAU | NO | ||
| nSNV 739G>C | 5′ AAGACUUGUUUUAUGCUCAGGCU | NO | ||
| nSNV 740U>A | 5′ AAGACUUGUUUUAUGCUCAGGGA | 8mer | ||
| Pos. 736-741 | 5′ GACUUGUUUUAUGCUCAGGGUCA | 8mer | 6(5) | 0 |
| ||||||| | ||||
| hsa-miR-504 | 3′ CUAUCUCACGUCUGGUCCCAGA | |||
| ||x|xx| | ||||
| nSNV 737G>C | 5′ GACUUGUUUUAUGCUCAAGGUCA | NO | ||
| nSNV 737G>A | 5′ GACUUGUUUUAUGCUCACGGUCA | NO | ||
| nSNV 739G>A | 5′ GACUUGUUUUAUGCUCAGGAUCA | NO | ||
| nSNV 739G>C | 5′ GACUUGUUUUAUGCUCAGGCUCA | NO | ||
| nSNV 740U>A | 5′ GACUUGUUUUAUGCUCAGGGCCA | NO | ||
| Pos. 804-809 | 5′ UGGGUCUCGCUUUGUUGCCCAGG | 7mer-m8 | 3(2) | 4(3) |
| :||||||:||||||||||||| | ||||
| hsa-miR-1285 | 3′ UCCAGAGUGAAACAACGGGUCU | |||
| :||||||:||||||||xx||| | ||||
| nSNV 805C>T | 5′ UGGGUCUCGCUUUGUUGTCCAGG | NO | ||
| nSNV 806C>T | 5′ UGGGUCUCGCUUUGUUGCTCAGG | NO | ||
| Pos. 967-972 | 5′ GGGGUCUCACAGUGUUGCCCAGG | 7mer-m8 | 5(2) | 2(2) |
| :|||||||| ||||||| | ||||
| hsa-miR-1285 | 3′ UCCAGAGUGAAACAACGGGUCU | |||
| :|||||||| ||||||| | ||||
| nSNV 968C>T | 5′ GGGGUCUCACAGUGUUGTCCAGG | NO | ||
| nSNV 969C>T | 5′ GGGGUCUCACAGUGUUGCTCAGG | NO | ||
| Pos. 1065-1070 | 5′ CCACGUCCAGCUGGAAGGGUCA | 7mer-1A | 4(3) | 1(1) |
| |||||| | ||||
| hsa-miR-504 | 3′ CUAUCUCACGUCUGGUCCCAGA | |||
| |x|x|x | ||||
| nSNV 1066G>A | 5′ CCACGUCCAGCUGGAAAGGUCA | NO | ||
| nSNV 1068G>A | 5′ CCACGUCCAGCUGGAAGGAUCA | NO | ||
| SNP 1070C>T | 5′ CCACGUCCAGCUGGAAGGGUUA | NO | ||
| nSNV 1071A>G | 5′ CCACGUCCAGCUGGAAGGGUCG | 6mer | ||
| Pos. 1084-1089 | 5′ GUCAACAUCUUUUACAUUCUGCAA | ? | 3(2) | 6(5) |
| || | | ||| | |||| | | ||||
| hsa-miR-15 | 3′ GUGUUUGGUAAUACACGACGAU | |||
| hsa-miR-16 | 3′ GCGGUUAUAAAUGCACGACGAU | |||
| | || ||||| | |||| | | ||||
| nSNV 1085C>T | 5′ GUCAACAUCUUUUACAUUCUGUAA | |||
| nSNV 1086A>G | 5′ GUCAACAUCUUUUACAUUCUGCGA | |||
Number of patients carrying SNVs affecting putative miRNA binding. Unique SNVs are indicated in parentheses. SNVs affecting TP53:miRNA complementarity other than the seed match are not included. Underlining in the column 2 indicates the altered nucleotides.
Nucleotides in the TP53 3′ UTR are numbered starting from the one after the stop codon. Nucleotides complementary to the seed sequence (positions 2-7) of miRNAs are indicated. Position (pos.) numbers correspond to nucleotides that are complementary to the miRNA seed sequence (in bold). rs114831472, affecting miR-504 binding, is “SNP 1070C.T.” One miR-504 site overlaps with the miR-125b site. “x” indicates that base pairing is disrupted.
The 7mer-m8 site comprises the seed match supplemented by a Watson-Crick match to miRNA nucleotide 8. The 7mer-A1 site comprises the seed match supplemented by an A across from miRNA nucleotide 1. The 8mer site comprises the seed match supplemented by both m8 and A1. “NO” indicates that the seed match was abolished. “?” indicates unconventional interaction.