Table 2. . The 25 most abundant tRNA-derived fragments from HaCaT (>100 reads) are presented according to their sequence, ability to bind with Ago and similarity with known miRNAs.
| tRF ID | Type | Codon | Length | Sequence | Reads | Overlapping miRNAs | Bound with Ago | Predicted targets | Molecular function |
|---|---|---|---|---|---|---|---|---|---|
| 5030b | trf-5 | Glu GAG | 23 | TCCCTGGTGGTCTAGTGGTTAGG | 1593 | Yes | N/A | ||
| 1001 | trf-1 | Ser UCA | 20 | GAAGCGGGTGCTCTTATTTT | 810 | Yes | N/A | ||
| 3001a | trf-3 | Leu CUA, CUU | 18 | ATCCCACCGCTGCCACCA | 559 | miR-1260a | Yes | RPL4, USP9X, SAFB, E2F3, PITX1, UPF1, CDC37, PRDM10, HIST1H2AG, ZNF607, HIST3H2A, ENSA, AK2, HIST2H4B, PRPF31 | RNA binding, Structural constituent of ribosome, Receptor binding, Chaperone activity, DNA binding, Transcription factor activity |
| miR-1260b | |||||||||
| miR-4695-3p | |||||||||
| miR-6865-3p | |||||||||
| 3025b | trf-3 | Asp GAC | 22 | TCGATTCCCCGACGGGGAGCCA | 533 | Yes | N/A | ||
| 3003a | trf-3 | Cys UGC | 17 | TCCGGGTGCCCCCTCCA | 468 | Yes | PEPD, RPL23, PRPS2, MAZ, XBP1, COPA, C21orf91, SMEK1, ENO1, ETFB, SET, TAF15, RAB11A, LNPEP, PIBF1, ELL, TAF5, SLC35A3, DHX38, UBE2S, GPSM1, TRIAP1, MAP7D1, BIN3, TMSB10, NFYA, XPO4, GID4, GABARAPL1, MRPL39, PATL1, CAMKK2, TUBB, HNRNPR, PIK3R1, KLHDC10, PAX6, RNPS1, CIC, SNX25, DNMT3A, ZC3H13, RDH11, BAZ2A, SCAF11, MCC, SIPA1L2, LOC101930123 | GTPase activator activity, Phosphorylase activity, Enzyme inhibitor activity, DNA-methyltransferase activity, Transcription factor activity, RNA binding | |
| 1042 | trf-1 | Thr ACU | 28 | AACCGAGCGTCCAAGCTCTTTCCATTTT | 403 | Yes | N/A | ||
| 3014a | trf-3 | Ser UAC, UCU | 18 | ATCCTGCCGACTACGCCA | 389 | Yes | USP22 | A histone deubiquitinating component of the transcription regulatory histone acetylation (HAT) complex SAGA | |
| 5027b | trf-5 | Val GUG, GUU | 23 | GTTTCCGTAGTGTAGTGGTTATC | 362 | Yes | N/A | ||
| 3015b | trf-3 | Glu GAA | 22 | TCGACTCCCGGTGTGGGAACCA | 361 | Yes | N/A | ||
| 1037 | trf-1 | LeuTAG | 20 | ACCTCAGAAGGTCTCACTTT | 311 | miR-1285-3p | Yes | N/A | |
| 1030 | trf-1 | Ser UCU | 15 | GGAATGTCAGCTTTT | 298 | No | N/A | ||
| 1003 | trf-1 | Ser AGC | 26 | GCTAAGGAAGTCCTGTGCTCAGTTTT | 203 | Yes | N/A | ||
| 3020a | trf-3 | Ala GCA, GCU | 18 | TCCCCGGCACCTCCACCA | 194 | Yes | BCKDK, CNBP, ATP5B, TAF15, PA2G4, PRMT7, MINK1, FBL | Catalytic activity, Ubiquitin-specific protease activity, RNA binding, Protein serine/threonine kinase activity, Transcription regulator activity, Methyltransferase activity | |
| 3021a | trf-3 | Ala GCA, GCG | 18 | TCCCCGGCATCTCCACCA | 178 | Yes | RPS3, CSRP2, SLU7 | Involved in the repair of UV-induced DNA damage, development and cellular differentiation | |
| 5005c | trf-5 | Lys AAA | 31 | GCCCGGATAGCTCAGTCGGTAGAGCATCAGA | 162 | miR-6078 | Yes | N/A | |
| 5019a | trf-5 | Leu CUA, CUU | 16 | GGTAGCGTGGCCGAGC | 158 | Yes | N/A | ||
| 3009a | trf-3 | Leu CUU | 18 | ACCCCACTCCTGGTACCA | 157 | Yes | FECH, POLR2A, SERBP1, KDM5A, MICAL3, GHDC, GATSL1, DCTN5, SPHK2, CDKN1A, CHD4, TTC1, UBR5, FABP5, CTNNB1, MTAP, POLA2, SMARCB1, NIPSNAP1, PEA15, PDIA4, PCBP2, VTI1B, IPO7, AKAP13, RAB35, PTPN18, BAHD1, KCTD3, TRPM7, UBE2O, CCND1, DDOST, TGFBR1, ATXN2L, EIF3CL, GJC1, PTRF, ZNF790, KHSRP | DNA-directed DNA polymerase activity, Phosphorylase activity, Kinase binding, Transporter activity, Receptor signaling protein serine/threonine kinase activity, Ion channel activity | |
| 5004b | trf-5 | Gly GGC, GGG | 22 | GCATTGGTGGTTCAGTGGTAGA | 154 | Yes | N/A | ||
| 3025a | trf-3 | Asp GAC | 18 | TTCCCCGACGGGGAGCCA | 130 | Yes | RPL35A, SLC25A5, HCN2, ELP3, BTG1, PCBP2, ITPKC, RBM12B | Structural constituent of ribosome, Voltage-gated ion channel activity, Acyltransferase activity, Lipid kinase activity, ATP binding, Enzyme activator activity | |
| 3019a | trf-3 | Ala GCU | 18 | TCCCCAGTACCTCCACCA | 125 | Yes | GFI1, PRELID1, APMAP, GPATCH4 | Transription regulation activity | |
| 1004 | trf-1 | Asp GAC | 18 | GTGTGTAGCTGCACTTTT | 124 | No | N/A | ||
| 3008a | trf-3 | Val GUG, GUU | 17 | ACCGGGCGGAAACACCA | 115 | Yes | N/A | ||
| 1024 | trf-1 | Lys AAG | 15 | GCAACTGGTCGTTTT | 114 | Yes | N/A | ||
| 1026 | trf-1 | Ile AUU | 17 | TTCCGTGGGTTTGTTTT | 104 | No | N/A | ||
| 1041 | trf-1 | Gly GGU | 15 | TGCGGTACCACTTTT | 102 | No | N/A | ||
Each tRNA-derived fragment was corelated with mRNA targets using CLASH data meta-analysis and their predicted targets were also reported. Gene ontology enrichment analysis of the predicted gene targets shows putative participation in important molecular functions including ribosome structure and RNA binding, transcription regulator activity, DNA methyltransferase activity, phosphorylase activity, transcription factor activity and GTPase activity
MCC: Merkel-cell carcinoma.