pre-miRNA Information
pre-miRNA hsa-mir-378f   
Genomic Coordinates chr1: 23929070 - 23929147
Description Homo sapiens miR-378f stem-loop
Comment None
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-378f
Sequence 52| ACUGGACUUGGAGCCAGAAG |71
Evidence Experimental
Experiments Illumina
Editing Events in miRNAs
Modification Type Position on miR Chromosome DNA Strand Genomic Position (hg38) List of PMIDs Variant details
A-to-I 18 1 + 23929138 29233923 MiREDiBase
A-to-I 19 1 + 23929139 29233923 MiREDiBase
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol REST   
Synonyms NRSF, WT6, XBR
Description RE1 silencing transcription factor
Transcript NM_005612   
Expression
Putative miRNA Targets on REST
3'UTR of REST
(miRNA target sites are highlighted)
>REST|NM_005612|3'UTR
   1 TGAAACTTTGAACAAGGTTTCAGTTCTTAGTTTGTAAGGTATATTACATTTTATATTCATTTATGATAGCAGACAACCTT
  81 TTAAGATTGCTTTAATTAGTATCTGATGTTGATTTTTAAGTGGCATTCTTTTCCTTAGGACTTTTTATGTATACCTGTTG
 161 ATTGTTGTGTAAATTTTAGTAAATCTAAGAGAGTGTACTAAACCAGCAGGTATCTGTTAGCTTATGTGTTTAATTGAAAT
 241 TAGAAGGCTAAGATGGTATAACAGCATTTTATTGCTTTGTCCAGCTACAACTTGTCATTTTTTTCTCCATGTCTTATCTT
 321 CCTGTTTCACTTTAGTTTATTCTTCGTTTTTTATTGAGATCTATAAAAAATTGGCTTACTTAATAGCAAATTACTTGAAG
 401 AATTTGCCTGCTTTATATAAAGTTAGCACTTTAAGATTTTTTTTTTTAGAGATGAGAAGACATTTAAATTGAAGAAAAAT
 481 TCCCCCAGCAATAGACAGTCTATCAGTCCAAGTATTTACTTCCTGAGTTTTGATCAATATTTTTTATTTGTGTATGTTAA
 561 TCGTCATAAAAACAGTGATTTTGGTGTGTTTTTTATTTTGGTGCTTTAATGGCTTAAGATGTTGCACATTTTTTTTTTCT
 641 TTTGGTTTCTGTTTATGTTTTTTTGCCTATGCAGTTAAATTTTTCCTAGAAATAGCATTTGTGTTGAACAGTAACACTTT
 721 ATACATATATATATGCATGTTTATTTTGTTTGGCGTCTTTGGAGGGATGCTTTTAGACTTGTTTGCAAAAGGGCAGTTTT
 801 CTTTTTCTTTGCTGCAGTTGTCTATTTTGCAGAATAATAGTGTGTGCAAGTTTGTGAGCAAATGAAATATGCAGGTTCAA
 881 TCTATTGATTTTGATTTTTACATCTTATATCTATGCCAGAATCTGTATTTCATATAACTTATTTATTTCGAATGGATGTA
 961 GTAAATTCACAGCTATCAGTTTTGATTTTGCAATAAATAAACCACTAGGTTGCATGTCGAACAAATTTTTATCTCAAATA
1041 CCAACCATCAGTTTTTTTTTTCATGTGTTTTGGTACAGCTAATTCCTAATTGTAGAGTGTTAAATGTTTGAGGAGAACCT
1121 TTTCTCATAGATGGTTGGTGTTCATATGGCTACTTTACAATAAAGAGAACTGTAAGTGATATTTGGAAACTACAAACCTG
1201 GAATTAGGAGATATAATTATTCCTTCAAGTTTTATAGAATATCACTTGGGAGATTCCAAAGCCATAGCTATTACGCGGCA
1281 AACCTAGGATAAGAAAGGTAGTATGAGTGCTGGTAGACCAGCTGCAACTTTCCTATACAGTGAAAAAGGCTGGTGAAACA
1361 AGTACAGTCCAGATTTTTTAAAATCATACTTTCTCAGGGATCTCCACAAACTGGTGGGTGTCCTGGCTGTCTGTGTGATA
1441 GCCTCTTTCTATAGGTGAGGCCTCAAATGAATTGCAGCTATCCTGGTGTTCCTATGAGGGCACTTTGTATGAAAAAGGGC
1521 ATGTACTCCAAAACATTTTTGTAGGTTCTTTGGCCAGTTGCCAAAGAGTGTGAAAGAATCCAATAGAGGATTTTTCTTAC
1601 TGATAGCAGTCATTCATTGCAGTAAAATAAAATATGATCCCATTAGGGAATCTTGAATTCTGACCTCCCATACTCCGTTT
1681 TGAAATAACCACTTTATATTTCATTTTTTAAAAATCTGATGATCTCTTTGAGGCAGGTTTCAGATTTGGCAGTACAACAT
1761 GAAAGATTAGGAAAAGCATTAATAACGTGTGGGTGGAAAGCTTGTTAAAAATCTGAGAGTGAAGTTTGAGTTAAAAGTTG
1841 TTTGAACATGGCATTGACTGGGAGGCCAAAGATTTAAAGAAGCGGAAGATTCTTCTCTTAAGACATGAGGAGTAAGTTGT
1921 GTGATAATGGTATGTGTTTTGTGTGCATGAATGGACATTGTAAATGTTGAATTCTAGGCTCCGACAATCATTGTCAACAG
2001 AAGATCAAGCTGCAAATATTTATGTTTTAAAACTTAAATTATAAAGCTAGTTAAGTCTTTCTAATGACTAGTTTTAATGT
2081 TCATGGGTACATTTTACCTAAGTTACCGTTTACATTGTATAGAAAAAGATACATCTTAAGCACAGATTGGTTATTAGGAA
2161 TTAGTTTGGGGAAGAGGTTTTTTTGTGGATTCTTTCATACTGCAAAGAAAAACCATTTGCCTTTTGGGGAATTGAGCTAA
2241 CTTCTAATCTAGTCTTAAGACTAGAATGCTAAAAACAAAAACATGAAGGAAATTAAAACCCCTTATTATTAAATTGATTT
2321 GTAAAAACATTGTTACTGGAAATTTATTGGACTTGAGGCCTTCCTCCAGAAAATAAGGACTTGATTGTCAGGCCTATATT
2401 AGGTTCTGAACCTTAATGCCATGTATTTGTACTTACTAAAAATTGTTTCAATGAAAAGTACATTAGCAGTATGAACTTCT
2481 GGTCCAGTTGGAAGTTTTTCCATTTGAAAAATGTGATGTTTGCATGGAACTGTTTGAAACTTTTTTATTTTCTAGTCCCC
2561 CTCCCCCACACTGGATAGAATTTAGCCTAGAATTTTCCCTTTGGATAAAAGAACAAAAATTGAACATGTTATTTGTAAAT
2641 TGATGTTTAGTAATTAGTGATAAACTTGAAATACTAGCATATATTATAAGCCTTAATCTTAGGTAGTCTTATGAAAATGA
2721 ATCTCTTAACTATCTTTTGAACCTGTATTCACATTGGTTTTCAAGATATTTTAAGTTATATTTTTTCCTCTTTTCAGAGC
2801 TGCTTCTTATTCTGGGGCTACTTTTTTTTTTAGTTGTGTAATTCACAAAGGGCTGCATTTTTTTTTTTTTTTAATAAGGC
2881 TTATAACTATGGCTGGATCTTTTGCTCTAGTCTTCTAAGAAGGGCCATTTTATTTTTTAGAGTCACTTCTAAAGTCATGT
2961 GGTAATTAACTTTGGAGACTGTTTTGCGTATGAGTGCTGATACAAATTAAAACCCAAGTAGACCTCATTGCATGTCACCC
3041 TATGAATGTTGACAATGGAAGGAATACCTTGCCTGTAGTATACTGTCACTTCTGGATTGATAAGCTGAGGAAGAAAGTTA
3121 AGTTTCTTTTTTACATAAGTCAGAAAAACTTACAGCTGGTGTTCCTAGTTTCCTGGTTGACCTCAGCAGATGAAGTGAAC
3201 AGATAGTGTTAATTCAGATTGAAGAAATTATCTGAATCTTGGTTTGTGTAGATTTACAATCTACATGCAATATTAACTAA
3281 ATCAGATAGCTTTTACAGTTTCACATGTGTACATAGGTTCCCTCCCGGTCCCTTCCATATCCATTAGTTATTGAACTTTC
3361 TAAACTGGCATTGAAACATTACAACAATGTTTTGTTGCACCAATTTTATAAACTTAAGCAGTGCAATACGTGTTACTTTT
3441 CTGAGGCAAACCAAAGGTAAATTTCTCAAGGTTCTTGCTGCCTTCTTTAGCAGCATTTGATGGAAGATCTTTTATACATT
3521 TGTAATAGATAAAAATAAACCAGATTGCAAATCCTTTTTTAAAATCCTAAACCATGTACCAAGTTTTTGGTCCAAATTAT
3601 GTAGGATAAGTTAAACTTAAATTGCATTCTATTAACCAATATGAGTGTATTTCTGTAAGCATAGTTATGTTGAAATAAAG
3681 TTTTAAAAACCA
Target sites Provided by authors   Predicted by miRanda    DRVs    SNPs    DRVs & SNPs
miRNA-target interactions
(Predicted by miRanda)
ID Duplex structure Position Score MFE
1
miRNA  3' gaagaccgagguUCAGGUCa 5'
                      ||||||| 
Target 5' tgaaacaagtacAGTCCAGa 3'
1354 - 1373 140.00 -9.80
2
miRNA  3' gaAGAC-CGAGGUUCAGGUCa 5'
            | ||  ||:| :|||||| 
Target 5' agTATGAACTTCTGGTCCAGt 3'
2468 - 2488 138.00 -16.31
3
miRNA  3' gaaGACCGAGGUUCAGGUca 5'
             | | || : ||||||  
Target 5' agaCAGTCTATCAGTCCAag 3'
493 - 512 129.00 -8.30
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
1178578 152 ClinVar
COSN31598583 16 COSMIC
COSN7496094 208 COSMIC
COSN26827808 423 COSMIC
COSN9045677 536 COSMIC
COSN21958367 544 COSMIC
COSN31962270 564 COSMIC
COSN31657271 748 COSMIC
COSN28981730 1062 COSMIC
COSN17286607 1546 COSMIC
COSN15912395 1977 COSMIC
COSN21104754 2109 COSMIC
COSN1298708 2586 COSMIC
COSN22698480 3404 COSMIC
COSN24324104 3669 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1336936895 2 dbSNP
rs772278505 7 dbSNP
rs1230728158 9 dbSNP
rs1289068538 14 dbSNP
rs760840538 15 dbSNP
rs200137905 16 dbSNP
rs1257978702 19 dbSNP
rs1336763256 20 dbSNP
rs1470760885 23 dbSNP
rs760970217 25 dbSNP
rs771157425 34 dbSNP
rs777034707 35 dbSNP
rs1409231394 41 dbSNP
rs759954686 42 dbSNP
rs765732930 43 dbSNP
rs1250506393 44 dbSNP
rs762391711 48 dbSNP
rs1043869611 57 dbSNP
rs571466291 60 dbSNP
rs1185291160 61 dbSNP
rs1441729494 66 dbSNP
rs1365923374 68 dbSNP
rs1406735624 70 dbSNP
rs1000173060 71 dbSNP
rs1204318176 73 dbSNP
rs1031013524 75 dbSNP
rs1306078518 77 dbSNP
rs770018766 79 dbSNP
rs1334115375 83 dbSNP
rs1351818364 89 dbSNP
rs536844723 97 dbSNP
rs1441556997 108 dbSNP
rs1013680176 118 dbSNP
rs1327683964 119 dbSNP
rs972824793 120 dbSNP
rs1315147835 125 dbSNP
rs557258216 142 dbSNP
rs1386073119 143 dbSNP
rs1319446146 150 dbSNP
rs781667 152 dbSNP
rs1386906761 156 dbSNP
rs1161190412 158 dbSNP
rs931227818 161 dbSNP
rs1049707640 163 dbSNP
rs1375816483 165 dbSNP
rs536276722 168 dbSNP
rs909034757 169 dbSNP
rs962003504 172 dbSNP
rs1208386148 177 dbSNP
rs1447752650 180 dbSNP
rs911049680 184 dbSNP
rs1208367351 188 dbSNP
rs145052321 196 dbSNP
rs1041088680 198 dbSNP
rs1293123737 205 dbSNP
rs1360591905 207 dbSNP
rs1225443684 208 dbSNP
rs902623197 209 dbSNP
rs533864838 215 dbSNP
rs1362360418 217 dbSNP
rs1296175436 227 dbSNP
rs922963350 228 dbSNP
rs763331656 231 dbSNP
rs999502917 232 dbSNP
rs1181925122 233 dbSNP
rs1327770292 243 dbSNP
rs1321341979 246 dbSNP
rs1404543708 250 dbSNP
rs1366173503 255 dbSNP
rs1054202649 263 dbSNP
rs572986400 264 dbSNP
rs1427703042 265 dbSNP
rs1388427380 268 dbSNP
rs560639617 270 dbSNP
rs774570488 275 dbSNP
rs1185948432 277 dbSNP
rs558648586 283 dbSNP
rs1012910012 290 dbSNP
rs1050040609 292 dbSNP
rs4864608 293 dbSNP
rs150938778 296 dbSNP
rs760637695 298 dbSNP
rs28613467 306 dbSNP
rs1035412021 311 dbSNP
rs1273300999 317 dbSNP
rs370943826 318 dbSNP
rs1272700136 325 dbSNP
rs556136695 326 dbSNP
rs972390071 330 dbSNP
rs1345951278 332 dbSNP
rs1304682219 334 dbSNP
rs1410404805 335 dbSNP
rs1369805251 340 dbSNP
rs763635931 346 dbSNP
rs551502862 347 dbSNP
rs564036650 347 dbSNP
rs952448612 356 dbSNP
rs1421977787 359 dbSNP
rs985329111 360 dbSNP
rs911158935 362 dbSNP
rs1384083580 364 dbSNP
rs1248631961 365 dbSNP
rs1023624013 370 dbSNP
rs943848882 372 dbSNP
rs779444757 375 dbSNP
rs969491698 375 dbSNP
rs1006283329 376 dbSNP
rs1040868936 377 dbSNP
rs1016126110 384 dbSNP
rs923992722 385 dbSNP
rs962144789 388 dbSNP
rs529515427 396 dbSNP
rs1323733484 404 dbSNP
rs1274556080 406 dbSNP
rs1284967661 413 dbSNP
rs1226345500 419 dbSNP
rs1053913829 420 dbSNP
rs1349859851 430 dbSNP
rs1202698501 433 dbSNP
rs893791300 435 dbSNP
rs11336958 437 dbSNP
rs1332220916 437 dbSNP
rs1443072466 437 dbSNP
rs397879276 437 dbSNP
rs1469494998 438 dbSNP
rs1030696398 443 dbSNP
rs542133568 447 dbSNP
rs767469589 447 dbSNP
rs1471805740 452 dbSNP
rs1407948997 463 dbSNP
rs1446007704 467 dbSNP
rs1178245367 471 dbSNP
rs542627366 483 dbSNP
rs1012272757 484 dbSNP
rs1235260946 487 dbSNP
rs985782527 489 dbSNP
rs559281722 497 dbSNP
rs1186459035 498 dbSNP
rs1372239768 501 dbSNP
rs1461546610 501 dbSNP
rs1264603936 503 dbSNP
rs910204702 506 dbSNP
rs1045319238 510 dbSNP
rs1169558258 511 dbSNP
rs947151132 520 dbSNP
rs1376812522 524 dbSNP
rs906798329 529 dbSNP
rs190192306 538 dbSNP
rs200337062 543 dbSNP
rs373699773 543 dbSNP
rs528464115 547 dbSNP
rs1336089455 555 dbSNP
rs180739700 564 dbSNP
rs141330981 567 dbSNP
rs1454740328 567 dbSNP
rs935532783 574 dbSNP
rs898034452 575 dbSNP
rs1326184033 577 dbSNP
rs1421405056 582 dbSNP
rs1412262985 584 dbSNP
rs1182513211 587 dbSNP
rs994317112 588 dbSNP
rs1228851407 600 dbSNP
rs1444694845 601 dbSNP
rs1052615138 603 dbSNP
rs369294506 604 dbSNP
rs1026766029 614 dbSNP
rs1485313220 620 dbSNP
rs1261105986 622 dbSNP
rs952461390 623 dbSNP
rs1319923999 628 dbSNP
rs985107795 628 dbSNP
rs1236737468 629 dbSNP
rs1245395870 629 dbSNP
rs1317194809 629 dbSNP
rs796271772 629 dbSNP
rs1433190517 640 dbSNP
rs143550781 640 dbSNP
rs1272413795 645 dbSNP
rs1320877755 646 dbSNP
rs1222375599 650 dbSNP
rs1263152412 652 dbSNP
rs1462392361 654 dbSNP
rs1018117261 655 dbSNP
rs1206393948 656 dbSNP
rs753343306 657 dbSNP
rs949604457 658 dbSNP
rs1045104435 670 dbSNP
rs965271667 679 dbSNP
rs1386582549 694 dbSNP
rs530762846 696 dbSNP
rs1195325041 697 dbSNP
rs1375867092 698 dbSNP
rs756962604 699 dbSNP
rs1188108914 721 dbSNP
rs1006314462 725 dbSNP
rs905172710 725 dbSNP
rs1016726033 726 dbSNP
rs935212913 729 dbSNP
rs1294051589 731 dbSNP
rs564577801 732 dbSNP
rs1225331661 733 dbSNP
rs1307197686 736 dbSNP
rs1430031914 738 dbSNP
rs1384316657 739 dbSNP
rs993775893 755 dbSNP
rs989953092 756 dbSNP
rs915348445 763 dbSNP
rs1367932506 764 dbSNP
rs948008374 767 dbSNP
rs1373341121 772 dbSNP
rs1045099275 773 dbSNP
rs1172042505 775 dbSNP
rs778550402 780 dbSNP
rs750029901 789 dbSNP
rs1199797060 812 dbSNP
rs1384768177 816 dbSNP
rs1383119528 817 dbSNP
rs939583284 821 dbSNP
rs1249519460 825 dbSNP
rs1036651561 826 dbSNP
rs550475964 830 dbSNP
rs1404826960 840 dbSNP
rs1480332139 843 dbSNP
rs1251924967 859 dbSNP
rs985981629 863 dbSNP
rs1325031192 867 dbSNP
rs1236505142 870 dbSNP
rs1017241679 871 dbSNP
rs968315742 877 dbSNP
rs1327411148 881 dbSNP
rs1350860021 883 dbSNP
rs978390559 884 dbSNP
rs1396626027 885 dbSNP
rs147719648 905 dbSNP
rs934409730 908 dbSNP
rs755332703 909 dbSNP
rs918064507 911 dbSNP
rs1200026980 912 dbSNP
rs1176968172 914 dbSNP
rs1269758786 915 dbSNP
rs1027125011 916 dbSNP
rs1481449711 917 dbSNP
rs949636705 920 dbSNP
rs1181039163 921 dbSNP
rs1045304735 924 dbSNP
rs905200353 926 dbSNP
rs758778395 935 dbSNP
rs1251353844 939 dbSNP
rs1197562610 944 dbSNP
rs1363440298 946 dbSNP
rs1460199710 947 dbSNP
rs386674682 947 dbSNP
rs115752183 950 dbSNP
rs1159084357 950 dbSNP
rs114040635 951 dbSNP
rs1160675813 952 dbSNP
rs186088023 959 dbSNP
rs965053783 961 dbSNP
rs1336807452 962 dbSNP
rs527718486 969 dbSNP
rs1308520280 970 dbSNP
rs1424629882 970 dbSNP
rs1449821707 972 dbSNP
rs1404969402 973 dbSNP
rs112072087 974 dbSNP
rs1030947000 975 dbSNP
rs1157724702 976 dbSNP
rs1346921806 978 dbSNP
rs1454252629 979 dbSNP
rs956722211 985 dbSNP
rs989341768 986 dbSNP
rs915278718 993 dbSNP
rs1184144636 996 dbSNP
rs1442833514 1004 dbSNP
rs571949421 1015 dbSNP
rs1030591767 1017 dbSNP
rs890263026 1019 dbSNP
rs1389182420 1020 dbSNP
rs770418236 1024 dbSNP
rs1305602332 1025 dbSNP
rs980892929 1032 dbSNP
rs778055054 1036 dbSNP
rs1007434045 1040 dbSNP
rs1240697374 1050 dbSNP
rs1017508739 1052 dbSNP
rs1204848384 1052 dbSNP
rs1381449363 1052 dbSNP
rs140595812 1053 dbSNP
rs1315079013 1060 dbSNP
rs999843369 1062 dbSNP
rs1358441662 1063 dbSNP
rs1223214597 1064 dbSNP
rs1031323156 1066 dbSNP
rs1479577521 1068 dbSNP
rs1387108751 1073 dbSNP
rs192197922 1077 dbSNP
rs545602834 1082 dbSNP
rs1037006317 1084 dbSNP
rs1384706509 1087 dbSNP
rs1419926575 1090 dbSNP
rs1180709339 1091 dbSNP
rs1473898906 1091 dbSNP
rs918084333 1098 dbSNP
rs564991109 1102 dbSNP
rs1192982911 1108 dbSNP
rs557237311 1109 dbSNP
rs1264259059 1132 dbSNP
rs930776065 1135 dbSNP
rs1220933398 1144 dbSNP
rs1359278187 1147 dbSNP
rs1049235160 1151 dbSNP
rs1380167442 1154 dbSNP
rs888153582 1160 dbSNP
rs1368018517 1165 dbSNP
rs942239308 1168 dbSNP
rs1431254347 1171 dbSNP
rs1460876405 1182 dbSNP
rs1301007650 1183 dbSNP
rs1404269003 1190 dbSNP
rs1366041159 1192 dbSNP
rs1038135228 1194 dbSNP
rs866706864 1198 dbSNP
rs184080847 1202 dbSNP
rs1396556878 1208 dbSNP
rs1475838919 1211 dbSNP
rs1426251639 1214 dbSNP
rs542866271 1215 dbSNP
rs1312451887 1222 dbSNP
rs1051815983 1227 dbSNP
rs1270218938 1229 dbSNP
rs559610654 1235 dbSNP
rs1435534087 1240 dbSNP
rs1316816012 1241 dbSNP
rs1271628491 1246 dbSNP
rs1059741 1257 dbSNP
rs1059740 1258 dbSNP
rs528500809 1260 dbSNP
rs1340963612 1275 dbSNP
rs1007386751 1276 dbSNP
rs1203683407 1277 dbSNP
rs550288590 1278 dbSNP
rs186053445 1287 dbSNP
rs1352863648 1290 dbSNP
rs1328198047 1296 dbSNP
rs1000090843 1298 dbSNP
rs1402725536 1301 dbSNP
rs1480987411 1304 dbSNP
rs1174798724 1305 dbSNP
rs1714003 1311 dbSNP
rs1200820593 1313 dbSNP
rs1480300558 1320 dbSNP
rs1031773791 1340 dbSNP
rs1193457091 1342 dbSNP
rs1469010010 1356 dbSNP
rs1231822677 1358 dbSNP
rs759754653 1368 dbSNP
rs1014431585 1369 dbSNP
rs1260848370 1380 dbSNP
rs1184617404 1387 dbSNP
rs1416360732 1392 dbSNP
rs1024092988 1396 dbSNP
rs1284911682 1397 dbSNP
rs771809574 1400 dbSNP
rs1222024369 1402 dbSNP
rs781031215 1403 dbSNP
rs1372444827 1409 dbSNP
rs969791607 1410 dbSNP
rs980958211 1413 dbSNP
rs926763737 1414 dbSNP
rs963634429 1417 dbSNP
rs1407326324 1418 dbSNP
rs1178614165 1426 dbSNP
rs973656146 1428 dbSNP
rs919253429 1431 dbSNP
rs929289011 1444 dbSNP
rs530876526 1446 dbSNP
rs550763721 1450 dbSNP
rs912000710 1451 dbSNP
rs943444502 1452 dbSNP
rs1038857885 1456 dbSNP
rs1463068981 1459 dbSNP
rs904343287 1460 dbSNP
rs760674050 1467 dbSNP
rs1316328025 1472 dbSNP
rs1284844683 1478 dbSNP
rs1241012367 1481 dbSNP
rs1053009411 1491 dbSNP
rs1338490024 1495 dbSNP
rs567424680 1498 dbSNP
rs1383711516 1500 dbSNP
rs1359563449 1507 dbSNP
rs1059739 1519 dbSNP
rs1213963367 1521 dbSNP
rs891701163 1531 dbSNP
rs1160515230 1541 dbSNP
rs1422007033 1548 dbSNP
rs1296191564 1549 dbSNP
rs1308223856 1550 dbSNP
rs1013958763 1552 dbSNP
rs1444938813 1557 dbSNP
rs1220558637 1562 dbSNP
rs1257824873 1564 dbSNP
rs1261284016 1573 dbSNP
rs1184616035 1574 dbSNP
rs1461064437 1581 dbSNP
rs1204515052 1582 dbSNP
rs150493651 1584 dbSNP
rs1357113590 1601 dbSNP
rs1289683743 1610 dbSNP
rs1485091824 1616 dbSNP
rs1322613875 1633 dbSNP
rs1315079152 1636 dbSNP
rs1213217469 1638 dbSNP
rs1186519440 1640 dbSNP
rs905638732 1641 dbSNP
rs753717050 1643 dbSNP
rs1402403202 1647 dbSNP
rs1033864930 1649 dbSNP
rs1173660386 1656 dbSNP
rs1424721327 1664 dbSNP
rs1427936836 1669 dbSNP
rs546954356 1671 dbSNP
rs963537457 1676 dbSNP
rs974070779 1677 dbSNP
rs138269723 1678 dbSNP
rs1343273015 1679 dbSNP
rs1429763919 1691 dbSNP
rs566754619 1692 dbSNP
rs1026600883 1693 dbSNP
rs1402984507 1694 dbSNP
rs867530596 1696 dbSNP
rs951015120 1697 dbSNP
rs1281502988 1704 dbSNP
rs761321874 1704 dbSNP
rs538653869 1710 dbSNP
rs558238778 1711 dbSNP
rs1224418912 1717 dbSNP
rs1344229132 1719 dbSNP
rs1283174199 1725 dbSNP
rs1280996855 1728 dbSNP
rs1392284060 1730 dbSNP
rs1315287968 1733 dbSNP
rs1295884592 1753 dbSNP
rs1215531115 1755 dbSNP
rs1354744055 1757 dbSNP
rs911863181 1759 dbSNP
rs1479320521 1760 dbSNP
rs1489572971 1774 dbSNP
rs1428562090 1775 dbSNP
rs1197852587 1779 dbSNP
rs943473884 1787 dbSNP
rs974757569 1788 dbSNP
rs1258932979 1802 dbSNP
rs1480470065 1809 dbSNP
rs1192633345 1818 dbSNP
rs1321897103 1819 dbSNP
rs1262854447 1821 dbSNP
rs925794537 1822 dbSNP
rs935881162 1823 dbSNP
rs1053362760 1835 dbSNP
rs891737681 1840 dbSNP
rs949997397 1846 dbSNP
rs1045439715 1847 dbSNP
rs1467865072 1860 dbSNP
rs1405102600 1870 dbSNP
rs1362185998 1872 dbSNP
rs1467582885 1883 dbSNP
rs1422724112 1884 dbSNP
rs1179813516 1885 dbSNP
rs1418551338 1886 dbSNP
rs1001288850 1891 dbSNP
rs905504801 1891 dbSNP
rs1242922070 1895 dbSNP
rs1345041206 1895 dbSNP
rs1201381717 1896 dbSNP
rs1405638523 1897 dbSNP
rs1347814421 1898 dbSNP
rs1276626964 1905 dbSNP
rs1237752897 1907 dbSNP
rs1353835405 1911 dbSNP
rs1310748584 1927 dbSNP
rs1450020774 1929 dbSNP
rs1016660291 1931 dbSNP
rs898231897 1952 dbSNP
rs1223389023 1958 dbSNP
rs995039165 1974 dbSNP
rs1382754956 1976 dbSNP
rs1157963809 1979 dbSNP
rs1420182486 1980 dbSNP
rs1381014415 1983 dbSNP
rs1160458138 1984 dbSNP
rs1026884715 1997 dbSNP
rs1242741450 2002 dbSNP
rs568947939 2013 dbSNP
rs1285437517 2017 dbSNP
rs1356267151 2026 dbSNP
rs562930220 2035 dbSNP
rs1444457431 2042 dbSNP
rs1260036117 2044 dbSNP
rs1205081738 2050 dbSNP
rs537503780 2056 dbSNP
rs1287626682 2064 dbSNP
rs1490637153 2065 dbSNP
rs1223158457 2068 dbSNP
rs987659190 2069 dbSNP
rs1018903152 2072 dbSNP
rs1469344830 2080 dbSNP
rs1324492565 2084 dbSNP
rs1317305935 2085 dbSNP
rs1400537998 2090 dbSNP
rs1177402104 2091 dbSNP
rs1362370853 2096 dbSNP
rs1382001088 2097 dbSNP
rs1300174055 2099 dbSNP
rs557135900 2100 dbSNP
rs1422793899 2105 dbSNP
rs1442536453 2108 dbSNP
rs1473869439 2109 dbSNP
rs964646258 2109 dbSNP
rs1371713061 2115 dbSNP
rs974705151 2118 dbSNP
rs1478469155 2131 dbSNP
rs149192051 2139 dbSNP
rs866660640 2148 dbSNP
rs1490053615 2154 dbSNP
rs957917416 2157 dbSNP
rs1211281893 2170 dbSNP
rs79178673 2172 dbSNP
rs1406973264 2178 dbSNP
rs1342341593 2181 dbSNP
rs1281267054 2189 dbSNP
rs1404216301 2198 dbSNP
rs988692511 2200 dbSNP
rs1324219329 2201 dbSNP
rs1407361770 2202 dbSNP
rs145032340 2205 dbSNP
rs1170474050 2215 dbSNP
rs1466441832 2217 dbSNP
rs1426183385 2220 dbSNP
rs1352809933 2233 dbSNP
rs950017797 2243 dbSNP
rs1441819871 2248 dbSNP
rs138876445 2253 dbSNP
rs1435774463 2264 dbSNP
rs57467543 2265 dbSNP
rs1379664086 2268 dbSNP
rs1244243531 2280 dbSNP
rs190469406 2281 dbSNP
rs1319772614 2284 dbSNP
rs1260969571 2294 dbSNP
rs1222836817 2295 dbSNP
rs565094052 2311 dbSNP
rs1368131413 2318 dbSNP
rs905535895 2324 dbSNP
rs781474291 2330 dbSNP
rs1334245222 2332 dbSNP
rs1330970187 2334 dbSNP
rs1038039294 2339 dbSNP
rs1402928962 2348 dbSNP
rs1174650796 2351 dbSNP
rs898273196 2356 dbSNP
rs994294030 2360 dbSNP
rs1173866903 2382 dbSNP
rs1270332547 2385 dbSNP
rs1436708293 2386 dbSNP
rs1047908842 2394 dbSNP
rs1178890153 2397 dbSNP
rs1458773426 2403 dbSNP
rs1239620139 2404 dbSNP
rs1459653309 2409 dbSNP
rs1209151129 2412 dbSNP
rs1182786429 2416 dbSNP
rs1280612079 2420 dbSNP
rs1221965226 2422 dbSNP
rs1348663972 2437 dbSNP
rs886566220 2438 dbSNP
rs1009110821 2450 dbSNP
rs1473761581 2455 dbSNP
rs1166070236 2456 dbSNP
rs1019187573 2465 dbSNP
rs1417535200 2470 dbSNP
rs1360286291 2482 dbSNP
rs1336749493 2484 dbSNP
rs964926677 2488 dbSNP
rs1379170247 2489 dbSNP
rs141926610 2491 dbSNP
rs544429034 2494 dbSNP
rs1382983427 2495 dbSNP
rs1450671427 2500 dbSNP
rs957491946 2501 dbSNP
rs989280202 2505 dbSNP
rs778425134 2513 dbSNP
rs1213580166 2515 dbSNP
rs1487885802 2517 dbSNP
rs1247696546 2518 dbSNP
rs749772043 2523 dbSNP
rs1285489577 2526 dbSNP
rs561356399 2530 dbSNP
rs529945966 2531 dbSNP
rs1356178168 2535 dbSNP
rs1313147989 2536 dbSNP
rs750159884 2541 dbSNP
rs971186656 2541 dbSNP
rs1268927822 2556 dbSNP
rs1339220449 2561 dbSNP
rs546793039 2568 dbSNP
rs1298331648 2573 dbSNP
rs1259370792 2575 dbSNP
rs1420954665 2576 dbSNP
rs1321015555 2579 dbSNP
rs1202610255 2580 dbSNP
rs927235179 2583 dbSNP
rs1423975229 2595 dbSNP
rs34341200 2597 dbSNP
rs560470495 2599 dbSNP
rs1184561014 2601 dbSNP
rs567183828 2608 dbSNP
rs1263782489 2612 dbSNP
rs532271391 2625 dbSNP
rs1489328880 2627 dbSNP
rs1038052667 2636 dbSNP
rs1221126974 2649 dbSNP
rs374292810 2651 dbSNP
rs929743622 2678 dbSNP
rs1047216060 2687 dbSNP
rs1340493978 2691 dbSNP
rs775482448 2696 dbSNP
rs1425830457 2700 dbSNP
rs527842667 2702 dbSNP
rs1402347720 2708 dbSNP
rs890869320 2712 dbSNP
rs1343112868 2714 dbSNP
rs1468478315 2718 dbSNP
rs1175956799 2728 dbSNP
rs749048078 2733 dbSNP
rs1398158487 2743 dbSNP
rs779027505 2746 dbSNP
rs1464878055 2748 dbSNP
rs1424017436 2749 dbSNP
rs1040499252 2751 dbSNP
rs1479381787 2753 dbSNP
rs1265363154 2769 dbSNP
rs900795015 2776 dbSNP
rs996358054 2780 dbSNP
rs1033034902 2781 dbSNP
rs1196940528 2788 dbSNP
rs1401105805 2791 dbSNP
rs1279591110 2803 dbSNP
rs957563541 2804 dbSNP
rs552158151 2806 dbSNP
rs1300068544 2810 dbSNP
rs1477028151 2820 dbSNP
rs568713231 2821 dbSNP
rs1020822516 2822 dbSNP
rs1369330360 2822 dbSNP
rs1328906252 2830 dbSNP
rs1346604938 2832 dbSNP
rs1445514334 2841 dbSNP
rs971469822 2845 dbSNP
rs1172467773 2852 dbSNP
rs537844004 2853 dbSNP
rs1203178728 2854 dbSNP
rs1172461555 2858 dbSNP
rs1309733547 2858 dbSNP
rs532015797 2858 dbSNP
rs56283756 2858 dbSNP
rs981295934 2858 dbSNP
rs1283236912 2869 dbSNP
rs1239243859 2871 dbSNP
rs1447553719 2873 dbSNP
rs1195725358 2874 dbSNP
rs1265499246 2875 dbSNP
rs1343556484 2881 dbSNP
rs1479493846 2885 dbSNP
rs927083476 2888 dbSNP
rs78136248 2890 dbSNP
rs1313459389 2893 dbSNP
rs1306378784 2898 dbSNP
rs1238980228 2902 dbSNP
rs974356659 2910 dbSNP
rs919609109 2914 dbSNP
rs929663988 2918 dbSNP
rs1157219538 2926 dbSNP
rs183044198 2933 dbSNP
rs1420891197 2952 dbSNP
rs1300574427 2953 dbSNP
rs1303380307 2957 dbSNP
rs1467470568 2963 dbSNP
rs912332380 2979 dbSNP
rs1156930906 2985 dbSNP
rs536471342 2988 dbSNP
rs1381131305 2989 dbSNP
rs1180948406 2995 dbSNP
rs1343175068 2998 dbSNP
rs943779677 3002 dbSNP
rs774868994 3003 dbSNP
rs1301290541 3004 dbSNP
rs900657569 3005 dbSNP
rs1332485202 3006 dbSNP
rs553117287 3015 dbSNP
rs1278788395 3018 dbSNP
rs1055084267 3024 dbSNP
rs1218787822 3030 dbSNP
rs766686644 3031 dbSNP
rs1339669757 3033 dbSNP
rs1313081681 3039 dbSNP
rs1289507483 3045 dbSNP
rs1358535184 3047 dbSNP
rs760477823 3050 dbSNP
rs866077415 3055 dbSNP
rs1361207102 3056 dbSNP
rs573493147 3057 dbSNP
rs866959505 3068 dbSNP
rs907299164 3073 dbSNP
rs1268090254 3075 dbSNP
rs1368254483 3077 dbSNP
rs1188671166 3081 dbSNP
rs776891408 3095 dbSNP
rs1179902959 3099 dbSNP
rs187055162 3115 dbSNP
rs559203164 3122 dbSNP
rs1207706645 3123 dbSNP
rs374331644 3123 dbSNP
rs958492066 3127 dbSNP
rs768373846 3134 dbSNP
rs544599688 3136 dbSNP
rs1424529843 3140 dbSNP
rs1027353821 3154 dbSNP
rs192732621 3155 dbSNP
rs1400477757 3157 dbSNP
rs982881907 3162 dbSNP
rs1320292631 3163 dbSNP
rs1392231613 3165 dbSNP
rs1403876214 3176 dbSNP
rs912202739 3182 dbSNP
rs868580797 3184 dbSNP
rs1389375510 3186 dbSNP
rs1463314322 3192 dbSNP
rs1421884504 3196 dbSNP
rs146294652 3214 dbSNP
rs776585304 3229 dbSNP
rs540442682 3230 dbSNP
rs1243413686 3236 dbSNP
rs1196119152 3238 dbSNP
rs1450734201 3239 dbSNP
rs1290111867 3242 dbSNP
rs1377096677 3252 dbSNP
rs1242064483 3264 dbSNP
rs1315865802 3267 dbSNP
rs975095545 3269 dbSNP
rs560347654 3270 dbSNP
rs1272057447 3273 dbSNP
rs1434369295 3278 dbSNP
rs1358675045 3296 dbSNP
rs1324492178 3298 dbSNP
rs570414848 3301 dbSNP
rs922113085 3302 dbSNP
rs1170406551 3304 dbSNP
rs534157866 3306 dbSNP
rs1266165369 3309 dbSNP
rs932176263 3314 dbSNP
rs1489500546 3316 dbSNP
rs532439851 3317 dbSNP
rs1422248126 3321 dbSNP
rs1054627999 3322 dbSNP
rs1237809737 3323 dbSNP
rs1458340384 3326 dbSNP
rs182754814 3327 dbSNP
rs562787052 3328 dbSNP
rs1383730054 3329 dbSNP
rs1423786306 3330 dbSNP
rs1199021044 3331 dbSNP
rs531236479 3337 dbSNP
rs1276378758 3352 dbSNP
rs764706277 3355 dbSNP
rs1344427391 3367 dbSNP
rs907163293 3370 dbSNP
rs1369762591 3372 dbSNP
rs772749731 3379 dbSNP
rs1297049877 3381 dbSNP
rs9055 3388 dbSNP
rs1447945816 3393 dbSNP
rs1356605251 3395 dbSNP
rs1338030163 3402 dbSNP
rs1448476682 3411 dbSNP
rs1334487422 3421 dbSNP
rs1332801217 3428 dbSNP
rs555861786 3430 dbSNP
rs1381746522 3431 dbSNP
rs1174966284 3435 dbSNP
rs1396598766 3438 dbSNP
rs995768958 3441 dbSNP
rs1379278303 3461 dbSNP
rs1179065042 3465 dbSNP
rs187782640 3481 dbSNP
rs1235472614 3483 dbSNP
rs1305631143 3484 dbSNP
rs951391195 3486 dbSNP
rs1225352828 3487 dbSNP
rs982699676 3489 dbSNP
rs1213084487 3494 dbSNP
rs1351837237 3508 dbSNP
rs1257452688 3513 dbSNP
rs1019244635 3515 dbSNP
rs756575199 3517 dbSNP
rs1200727035 3527 dbSNP
rs1448024507 3543 dbSNP
rs570907911 3547 dbSNP
rs921053940 3548 dbSNP
rs1182736897 3549 dbSNP
rs1417283855 3555 dbSNP
rs936415884 3578 dbSNP
rs28740801 3579 dbSNP
rs1420444434 3582 dbSNP
rs1411439987 3583 dbSNP
rs1427205008 3590 dbSNP
rs1169377007 3603 dbSNP
rs1423678080 3604 dbSNP
rs1043215 3605 dbSNP
rs1173801045 3609 dbSNP
rs1191369201 3611 dbSNP
rs1405173724 3611 dbSNP
rs1285320546 3617 dbSNP
rs946293619 3627 dbSNP
rs778925050 3630 dbSNP
rs1041956669 3632 dbSNP
rs1228088588 3639 dbSNP
rs1304316501 3642 dbSNP
rs928863800 3647 dbSNP
rs1398641782 3648 dbSNP
rs539216777 3655 dbSNP
rs1298270236 3662 dbSNP
rs1339293147 3662 dbSNP
rs1455075722 3668 dbSNP
rs559017822 3669 dbSNP
rs1163858401 3677 dbSNP
rs1405768998 3693 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 5978.0
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... "PAR-CLIP data was present in GSM714644. RNA binding protein: AGO2. Condition:completeT1 ...

- Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' gaagaccgagguucAGGUca 5'
                        ||||  
Target 5' cuuucucagggaucUCCAca 3'
17 - 36
2
miRNA  3' gaAGACCGAGGUUCAGguca 5'
            |:|  :|: || ||    
Target 5' -aUUU--UUUAAAAUCauac 3'
1 - 17
Article - Kishore S; Jaskiewicz L; Burger L; Hausser et al.
- Nature methods, 2011
Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.
LinkOut: [PMID: 21572407]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions TZM-bl
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... PAR-CLIP data was present in GSM1462574. RNA binding protein: AGO2. Condition:TZM-bl ami BaL ...

- Whisnant AW; Bogerd HP; Flores O; Ho P; et al., 2013, mBio.

Article - Whisnant AW; Bogerd HP; Flores O; Ho P; et al.
- mBio, 2013
UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.
LinkOut: [PMID: 23592263]
Experimental Support 3 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions MCF7
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... PAR-CLIP data was present in SRR1045082. RNA binding protein: AGO2. Condition:Untreated ...

- Farazi TA; Ten Hoeve JJ; Brown M; et al., 2014, Genome biology.

Article - Farazi TA; Ten Hoeve JJ; Brown M; et al.
- Genome biology, 2014
BACKGROUND: Various microRNAs (miRNAs) are up- or downregulated in tumors. However, the repression of cognate miRNA targets responsible for the phenotypic effects of this dysregulation in patients remains largely unexplored. To define miRNA targets and associated pathways, together with their relationship to outcome in breast cancer, we integrated patient-paired miRNA-mRNA expression data with a set of validated miRNA targets and pathway inference. RESULTS: To generate a biochemically-validated set of miRNA-binding sites, we performed argonaute-2 photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (AGO2-PAR-CLIP) in MCF7 cells. We then defined putative miRNA-target interactions using a computational model, which ranked and selected additional TargetScan-predicted interactions based on features of our AGO2-PAR-CLIP binding-site data. We subselected modeled interactions according to the abundance of their constituent miRNA and mRNA transcripts in tumors, and we took advantage of the variability of miRNA expression within molecular subtypes to detect miRNA repression. Interestingly, our data suggest that miRNA families control subtype-specific pathways; for example, miR-17, miR-19a, miR-25, and miR-200b show high miRNA regulatory activity in the triple-negative, basal-like subtype, whereas miR-22 and miR-24 do so in the HER2 subtype. An independent dataset validated our findings for miR-17 and miR-25, and showed a correlation between the expression levels of miR-182 targets and overall patient survival. Pathway analysis associated miR-17, miR-19a, and miR-200b with leukocyte transendothelial migration. CONCLUSIONS: We combined PAR-CLIP data with patient expression data to predict regulatory miRNAs, revealing potential therapeutic targets and prognostic markers in breast cancer.
LinkOut: [PMID: 24398324]
Experimental Support 4 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HCT116
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... PAR-CLIP data was present in ERX177604. RNA binding protein: AGO2. Condition:p53_V_AGO_CLIP_2_6 PAR-CLIP data was present in ERX177616. RNA binding protein: AGO2. Condition:p53_V_AGO_CLIP_3_6 PAR-CLIP data was present in ERX177628. RNA binding protein: AGO2. Condition:p53_V_AGO_CLIP_4_6 ...

- Krell J; Stebbing J; Carissimi C; Dabrowska et al., 2016, Genome research.

Article - Krell J; Stebbing J; Carissimi C; Dabrowska et al.
- Genome research, 2016
DNA damage activates TP53-regulated surveillance mechanisms that are crucial in suppressing tumorigenesis. TP53 orchestrates these responses directly by transcriptionally modulating genes, including microRNAs (miRNAs), and by regulating miRNA biogenesis through interacting with the DROSHA complex. However, whether the association between miRNAs and AGO2 is regulated following DNA damage is not yet known. Here, we show that, following DNA damage, TP53 interacts with AGO2 to induce or reduce AGO2's association of a subset of miRNAs, including multiple let-7 family members. Furthermore, we show that specific mutations in TP53 decrease rather than increase the association of let-7 family miRNAs, reducing their activity without preventing TP53 from interacting with AGO2. This is consistent with the oncogenic properties of these mutants. Using AGO2 RIP-seq and PAR-CLIP-seq, we show that the DNA damage-induced increase in binding of let-7 family members to the RISC complex is functional. We unambiguously determine the global miRNA-mRNA interaction networks involved in the DNA damage response, validating them through the identification of miRNA-target chimeras formed by endogenous ligation reactions. We find that the target complementary region of the let-7 seed tends to have highly fixed positions and more variable ones. Additionally, we observe that miRNAs, whose cellular abundance or differential association with AGO2 is regulated by TP53, are involved in an intricate network of regulatory feedback and feedforward circuits. TP53-mediated regulation of AGO2-miRNA interaction represents a new mechanism of miRNA regulation in carcinogenesis.
LinkOut: [PMID: 26701625]
CLIP-seq Support 1 for dataset GSM714644
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repA
Location of target site ENST00000309042.7 | 3UTR | AUUUUUUAAAAUCAUACUUUCUCAGGGAUCUCCACAAACUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset SRR1045082
Method / RBP PAR-CLIP / AGO2
Cell line / Condition MCF7 / Untreated
Location of target site ENST00000309042.7 | 3UTR | AUUUUUUAAAAUCAUACUUUCUCAGGGAUCUCCACAAACUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 24398324 / SRX388831
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000309042.7 | 3UTR | AUUUUUUAAAAUCAUACUUUCUCAGGGAUCUCCACAAACUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23592263 / GSE59944
CLIP-seq Viewer Link
MiRNA-Target Expression Profile
Dataset Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
27 hsa-miR-378f Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT463100 ZNF609 zinc finger protein 609 2 2
MIRT469371 REST RE1 silencing transcription factor 2 6
MIRT495441 KCNJ6 potassium voltage-gated channel subfamily J member 6 2 2
MIRT513606 VPS37B VPS37B, ESCRT-I subunit 2 2
MIRT520414 TXNL1 thioredoxin like 1 2 4
MIRT525111 PRKD2 protein kinase D2 2 2
MIRT525979 SPA17 sperm autoantigenic protein 17 2 2
MIRT527002 ARL8B ADP ribosylation factor like GTPase 8B 2 2
MIRT529215 CYP20A1 cytochrome P450 family 20 subfamily A member 1 2 2
MIRT529835 ARGFX arginine-fifty homeobox 2 2
MIRT532300 HAUS3 HAUS augmin like complex subunit 3 2 2
MIRT537577 ESYT2 extended synaptotagmin 2 2 2
MIRT543140 AKT1 AKT serine/threonine kinase 1 2 2
MIRT554924 RAP1B RAP1B, member of RAS oncogene family 2 2
MIRT564970 WTAP WT1 associated protein 2 2
MIRT570115 CACNG8 calcium voltage-gated channel auxiliary subunit gamma 8 2 2
MIRT652734 TGFB2 transforming growth factor beta 2 2 2
MIRT655948 NDST1 N-deacetylase and N-sulfotransferase 1 2 2
MIRT655997 MYRF myelin regulatory factor 2 2
MIRT684875 P4HB prolyl 4-hydroxylase subunit beta 2 2
MIRT692969 LGSN lengsin, lens protein with glutamine synthetase domain 2 2
MIRT693737 ACACA acetyl-CoA carboxylase alpha 2 2
MIRT710991 PPARGC1B PPARG coactivator 1 beta 2 2
MIRT712247 RCC2 regulator of chromosome condensation 2 2 2
MIRT718602 DCTPP1 dCTP pyrophosphatase 1 2 2
MIRT723499 WDR33 WD repeat domain 33 2 2
MIRT725448 HIPK3 homeodomain interacting protein kinase 3 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-378f Gemcitabine 60750 NSC613327 approved resistant High Pancreatic Cancer cell line (PANC-1)
hsa-miR-378f Fluorouracil 3385 NSC19893 approved resistant High Pancreatic Cancer cell line (PANC-1)
hsa-miR-378f Doxorubicin 31703 NSC123127 approved sensitive High Triple-Negative Breast Cancer cell line (MDA-MB-231, MDA-MB-468)
hsa-miR-378f Oxaliplatin 6857599 NSC266046 approved sensitive High Colorectal Cancer cell line (SW480, HCT-116)
hsa-miR-378f Erlotinib 176870 NSC718781 approved resistant High Head And Neck Squamous Cell Carcinoma cell line (HN6)
hsa-mir-378f Androstenedione+Anastrozole sensitive cell line (MCF-7)
hsa-miR-378f Osimertinib 71496458 NSC779217 approved sensitive cell line (PC9)
hsa-miR-378f Doxorubicin 31703 NSC123127 approved sensitive cell line (BAS)
hsa-miR-378f Osimertinib 71496458 NSC779217 approved sensitive cell line (H1975)
hsa-miR-378f Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (1500 ng/ml)
hsa-miR-378f Gemcitabine 60750 NSC613327 approved resistant cell line (Panc1-GR4)
hsa-miR-378f Gemcitabine 60750 NSC613327 approved resistant cell line (Panc1-GR3)

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