pre-miRNA Information
pre-miRNA hsa-mir-3160-1   
Genomic Coordinates chr11: 46451805 - 46451889
Description Homo sapiens miR-3160-1 stem-loop
Comment None
RNA Secondary Structure
pre-miRNA hsa-mir-3160-2   
Genomic Coordinates chr11: 46451807 - 46451887
Description Homo sapiens miR-3160-2 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-3160-3p
Sequence 54| AGAGCUGAGACUAGAAAGCCCA |75
Evidence Experimental
Experiments Illumina
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN30582333 1 COSMIC
COSN1535547 3 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1396368683 1 dbSNP
rs1162409303 2 dbSNP
rs1404378453 12 dbSNP
rs1171960732 14 dbSNP
rs1324633375 16 dbSNP
rs1187765019 16 dbSNP
rs1300058326 19 dbSNP
rs1432898407 21 dbSNP
rs1011279103 22 dbSNP
Putative Targets

miRNA Expression profile
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol GDE1   
Synonyms 363E6.2, MIR16
Description glycerophosphodiester phosphodiesterase 1
Transcript NM_016641   
Expression
Putative miRNA Targets on GDE1
3'UTR of GDE1
(miRNA target sites are highlighted)
>GDE1|NM_016641|3'UTR
   1 ACTTTCACGGTGGGACGAAACGGGTTCAGAAACTGCCAGGGGCCTCATACAGGGATATCAAAATACCCTTTGTGCTAGCC
  81 CAGGCCCTGGGGAATCAGGTGACTCACACAAATGCAATAGTTGGTCACTGCATTTTTACCTGAACCAAAGCTAAACCCGG
 161 TGTTGCCACCATGCACCATGGCATGCCAGAGTTCAACACTGTTGCTCTTGAAAATCTGGGTCTGAAAAAACGCACAAGAG
 241 CCCCTGCCCTGCCCTAGCTGAGGCACACAGGGAGACCCAGTGAGGATAAGCACAGATTGAATTGTACAGTTTGCAGATGC
 321 AGATGTAAATGCATGGGACATGCATGATAACTCAGAGTTGACATTTTAAAACTTGCCACACTTATTTCAAATATTTGTAC
 401 TCAGCTATGTTAACATGTACTGTAGACATCAAACTTGTGGCCATACTAATAAAATTATTAAAAGGAGCACTAAAGGAAAA
 481 CTGTGTGCCAAGCATCATATCCTAAGGCATACGGAATTTGGGGAAGCCACCATGCAATCCAGTGAGGCTTCAGTGTACAG
 561 CAACCAAAATGGTAGGGAGGTCTTGAAGCCAATGAGGGATTTATAGCATCTTGAATAGAGAGCTGCAAACCACCAGGGGG
 641 CAGAGTTGCATTTTTCCAGGCTTTTTAGGAAGCTCTGCAACAGATGTGATCTGATCATAGGCAATTAGAACTGGAAGAAA
 721 CTTCCAAAAATATCTAGGTTTGTCCTCATTTTACAAATGAGGAAACTAAACTCTGTGGAAGGGAAGGGGTTGCCTCAAAA
 801 GTCACAGCTTAGCTGGGCACAGTGGCTCATGCCGATAATCCCAGCAATTCAGAAAGCTGAGGCAGGAGGATTACTTGAGG
 881 CCAGACTGGGCAATATAGCAAGACCCCATCTCTAAAAAATTAGGCATGGTGGTGCATGCCTGTATTCCCAGCTACTCAGG
 961 AGGTTGAGGTGGGAGGATCACTTGAGCCCAGAAGTTCAAGGCTGCAATGAGCCATGATTACACCACGGCACTACAACCTT
1041 GGTGGCACAGTGAGAACCTGACTCTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGATAACTAGAACTTCTAGAACATCT
1121 TGTTTACAGTTAGCCAGAAACTATACAAGTGGTTTAACATGCATTATCTTACTCAATCCATACAAAAGTCTTATGGAGGT
1201 GTTAGCACTCTTTCTACTGATGAAGAACTGAGGTACTTCATAAAACCACTTACCCAAGGTGTCTTGAGTCTGGTACAACT
1281 GGCATTCAAATCTAGGTCAGTCTGCCCCCAGAGCCACTACCCTTACCCCTCACTGAATCTGCCTTTATATTGTTGAGCCC
1361 ATGACCCCAAACTGCTCTTTCCAATTTGAACTTCCAGGGATTTTATTGTGAACTTACATAGCAACATTAAAATGAAGTTG
1441 AATTGTTTTTAATGGCAACGCCGTCTGTCTCCTCTAGCTTACCGCTTCTCACCTTTCAACCCCATCTGTGGCCTTTGTCC
1521 AGGCCCACAGCTTAGCCATGGCTTCCCTCCTGCATCCCTGCCGTGGGTTGCTGGCCTCACACTTGCAGCAGCTGGACAGT
1601 GATTTTAGAAGGCCACCAGTCCCCATAGCTATGTGACAATGAGAAGCAAACTTTTTTGTGACAGATTGTATTGGCATAGG
1681 CATGATAGATGGGGATTGGTACGTTTTGAATCAGCATTTGCAAAAAAATTGTCTTGAATTTTAAAATAAACAACAAAGAT
1761 TTGTTCATTGAGTGCAAAAAAAAAAAAAAAAAAAAAAAAA
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' acccgAAAGAUCAGAGUCGAga 5'
               ||| ||  |||||||  
Target 5' aaataTTTGTA--CTCAGCTat 3'
389 - 408 137.00 -10.30
2
miRNA  3' acCCGAAAGA----UCAGAGUCGAGa 5'
            ||:|  ||    |||| |||||: 
Target 5' ggGGTTGCCTCAAAAGTCACAGCTTa 3'
786 - 811 118.00 -17.80
3
miRNA  3' acCCGAAAGAUCAGAGUCGAGa 5'
            ||||||:|||    ||||| 
Target 5' caGGCTTTTTAGG--AAGCTCt 3'
657 - 676 115.00 -21.20
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN31585155 17 COSMIC
COSN31598050 21 COSMIC
COSN30577852 59 COSMIC
COSN30494902 65 COSMIC
COSN30447875 68 COSMIC
COSN31602377 79 COSMIC
COSN30103175 81 COSMIC
COSN30454977 92 COSMIC
COSN31508981 125 COSMIC
COSN8230199 126 COSMIC
COSN30577714 144 COSMIC
COSN31602539 188 COSMIC
COSN23641719 488 COSMIC
COSN23191467 1050 COSMIC
COSN6081170 1182 COSMIC
COSN32150645 1219 COSMIC
COSN8391077 1245 COSMIC
COSN24952865 1453 COSMIC
COSN21516386 1768 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs747575581 5 dbSNP
rs770737790 5 dbSNP
rs1341784379 7 dbSNP
rs201160961 8 dbSNP
rs757947752 9 dbSNP
rs1325676021 11 dbSNP
rs778448691 14 dbSNP
rs562476032 16 dbSNP
rs1044644814 17 dbSNP
rs372112650 19 dbSNP
rs1412238952 21 dbSNP
rs764064115 22 dbSNP
rs756105412 31 dbSNP
rs202202853 35 dbSNP
rs766545567 36 dbSNP
rs762964578 40 dbSNP
rs1167532071 42 dbSNP
rs930997096 44 dbSNP
rs773445992 48 dbSNP
rs1257398108 50 dbSNP
rs765383538 51 dbSNP
rs972523456 54 dbSNP
rs1041582880 60 dbSNP
rs574197701 61 dbSNP
rs1011452499 66 dbSNP
rs943852302 67 dbSNP
rs1157531849 72 dbSNP
rs555491834 76 dbSNP
rs534239283 77 dbSNP
rs985291658 78 dbSNP
rs953958930 79 dbSNP
rs184843372 83 dbSNP
rs1403983999 84 dbSNP
rs1433148309 91 dbSNP
rs1261759104 93 dbSNP
rs1279809884 97 dbSNP
rs1056070256 106 dbSNP
rs1221914962 108 dbSNP
rs1283465668 109 dbSNP
rs558011192 117 dbSNP
rs1021579793 124 dbSNP
rs937095927 126 dbSNP
rs1484653298 137 dbSNP
rs1294074606 145 dbSNP
rs1284867535 150 dbSNP
rs1198389541 153 dbSNP
rs773525301 158 dbSNP
rs539484386 159 dbSNP
rs1175916839 160 dbSNP
rs1380163294 172 dbSNP
rs990515336 175 dbSNP
rs1349752694 177 dbSNP
rs1045496121 180 dbSNP
rs956071572 187 dbSNP
rs772292696 189 dbSNP
rs192796293 190 dbSNP
rs1428180596 201 dbSNP
rs550842789 203 dbSNP
rs535898301 204 dbSNP
rs1355979802 214 dbSNP
rs1232389537 231 dbSNP
rs186701458 231 dbSNP
rs564469686 232 dbSNP
rs1248123489 233 dbSNP
rs1002975674 242 dbSNP
rs1357345872 245 dbSNP
rs1384001322 254 dbSNP
rs1338598485 255 dbSNP
rs549164343 260 dbSNP
rs1273970843 266 dbSNP
rs1435617049 268 dbSNP
rs1202806733 271 dbSNP
rs1237985670 272 dbSNP
rs1023125522 282 dbSNP
rs1445659391 286 dbSNP
rs1013124594 297 dbSNP
rs887987465 298 dbSNP
rs774783879 301 dbSNP
rs7135 309 dbSNP
rs1383983368 310 dbSNP
rs146678235 324 dbSNP
rs920077977 334 dbSNP
rs976009112 340 dbSNP
rs896837329 344 dbSNP
rs1465931655 346 dbSNP
rs758729768 355 dbSNP
rs570056516 358 dbSNP
rs1454422331 375 dbSNP
rs1020088710 379 dbSNP
rs374313286 382 dbSNP
rs1037130376 389 dbSNP
rs1008320913 392 dbSNP
rs943778174 407 dbSNP
rs779919317 408 dbSNP
rs967313338 409 dbSNP
rs1341686234 414 dbSNP
rs1426202965 422 dbSNP
rs1261896788 426 dbSNP
rs183920599 428 dbSNP
rs1257720137 430 dbSNP
rs1188179753 440 dbSNP
rs76065554 441 dbSNP
rs1011442784 452 dbSNP
rs1053138 467 dbSNP
rs893085977 483 dbSNP
rs543974197 484 dbSNP
rs573647601 485 dbSNP
rs561967642 488 dbSNP
rs1169492284 492 dbSNP
rs540454479 494 dbSNP
rs914436684 496 dbSNP
rs990095650 512 dbSNP
rs1173997657 513 dbSNP
rs1401348213 515 dbSNP
rs1382740428 518 dbSNP
rs1320251705 531 dbSNP
rs956209393 535 dbSNP
rs760470244 536 dbSNP
rs1225216074 542 dbSNP
rs1277798802 545 dbSNP
rs1324536569 548 dbSNP
rs924616404 554 dbSNP
rs1254655945 555 dbSNP
rs1277683121 563 dbSNP
rs981468136 571 dbSNP
rs971463332 576 dbSNP
rs1206209525 579 dbSNP
rs1357620320 585 dbSNP
rs1444768072 590 dbSNP
rs1332533903 592 dbSNP
rs1045850684 593 dbSNP
rs1023058493 594 dbSNP
rs745819260 606 dbSNP
rs1397735482 613 dbSNP
rs1048787490 615 dbSNP
rs1464554085 626 dbSNP
rs1454162159 629 dbSNP
rs1160210319 637 dbSNP
rs1422232781 641 dbSNP
rs1382780528 649 dbSNP
rs2521795 651 dbSNP
rs1475949975 657 dbSNP
rs1028299613 669 dbSNP
rs756817784 675 dbSNP
rs975703923 676 dbSNP
rs1299524066 677 dbSNP
rs1330865761 682 dbSNP
rs993747934 684 dbSNP
rs1352160846 685 dbSNP
rs964527165 689 dbSNP
rs898102539 692 dbSNP
rs912734301 697 dbSNP
rs1438163337 700 dbSNP
rs987288924 708 dbSNP
rs1490708726 710 dbSNP
rs1036650974 714 dbSNP
rs1219768860 715 dbSNP
rs1007890432 716 dbSNP
rs890834144 732 dbSNP
rs1020231062 733 dbSNP
rs1193965467 735 dbSNP
rs1183723337 736 dbSNP
rs567896122 747 dbSNP
rs990135409 756 dbSNP
rs1257443765 760 dbSNP
rs999618385 764 dbSNP
rs371782878 774 dbSNP
rs1282634082 775 dbSNP
rs1291990905 775 dbSNP
rs1390375704 778 dbSNP
rs575555435 781 dbSNP
rs1336692001 782 dbSNP
rs1375266975 785 dbSNP
rs1316409811 789 dbSNP
rs1360959583 802 dbSNP
rs1218825715 803 dbSNP
rs914427925 816 dbSNP
rs1480760064 821 dbSNP
rs1054718345 825 dbSNP
rs191486957 830 dbSNP
rs1024175320 833 dbSNP
rs542703368 834 dbSNP
rs1184109284 836 dbSNP
rs1325914025 839 dbSNP
rs1446521009 848 dbSNP
rs368324124 865 dbSNP
rs1411069351 871 dbSNP
rs1162249407 877 dbSNP
rs1462709732 884 dbSNP
rs3179016 897 dbSNP
rs1048860529 908 dbSNP
rs930267944 919 dbSNP
rs1365276670 920 dbSNP
rs1385620252 927 dbSNP
rs971396340 931 dbSNP
rs915969419 932 dbSNP
rs900174176 938 dbSNP
rs1229122902 940 dbSNP
rs1040322023 942 dbSNP
rs1215551080 943 dbSNP
rs758070615 945 dbSNP
rs3179017 954 dbSNP
rs952252653 957 dbSNP
rs3179018 958 dbSNP
rs946118632 959 dbSNP
rs143264388 961 dbSNP
rs374108871 962 dbSNP
rs1421842604 967 dbSNP
rs565644523 969 dbSNP
rs1019159815 970 dbSNP
rs1177613300 976 dbSNP
rs553479416 981 dbSNP
rs957560186 986 dbSNP
rs534009195 989 dbSNP
rs766771810 996 dbSNP
rs11551688 1001 dbSNP
rs1302814530 1004 dbSNP
rs890802496 1007 dbSNP
rs1049444049 1010 dbSNP
rs187785060 1019 dbSNP
rs996588418 1024 dbSNP
rs551433202 1026 dbSNP
rs1156533654 1027 dbSNP
rs1438840350 1038 dbSNP
rs1223836782 1042 dbSNP
rs1395515219 1049 dbSNP
rs1264794877 1050 dbSNP
rs1054287350 1052 dbSNP
rs1195387346 1063 dbSNP
rs1310329929 1064 dbSNP
rs866008778 1064 dbSNP
rs3179019 1067 dbSNP
rs980417669 1070 dbSNP
rs1486232516 1071 dbSNP
rs934528271 1077 dbSNP
rs1477016027 1083 dbSNP
rs1245002418 1087 dbSNP
rs1198264433 1088 dbSNP
rs1447730175 1089 dbSNP
rs1288419869 1093 dbSNP
rs1214792526 1094 dbSNP
rs1353409168 1095 dbSNP
rs1175964010 1096 dbSNP
rs1200545439 1096 dbSNP
rs1218495782 1096 dbSNP
rs1218815977 1096 dbSNP
rs1223472099 1096 dbSNP
rs1284008180 1096 dbSNP
rs1295828282 1096 dbSNP
rs1307540387 1096 dbSNP
rs1318669956 1096 dbSNP
rs1339391418 1096 dbSNP
rs1346382255 1096 dbSNP
rs1365207635 1096 dbSNP
rs1405214970 1096 dbSNP
rs1413172899 1096 dbSNP
rs1427657080 1096 dbSNP
rs1454836025 1096 dbSNP
rs1479124664 1096 dbSNP
rs59519757 1096 dbSNP
rs1248736495 1098 dbSNP
rs1281534309 1098 dbSNP
rs1477243615 1098 dbSNP
rs1237083701 1101 dbSNP
rs148514696 1101 dbSNP
rs971367540 1103 dbSNP
rs924488676 1106 dbSNP
rs1273664187 1121 dbSNP
rs1442111930 1125 dbSNP
rs1045692231 1129 dbSNP
rs556721350 1143 dbSNP
rs1327745049 1152 dbSNP
rs915897293 1154 dbSNP
rs991517652 1159 dbSNP
rs3180351 1163 dbSNP
rs930738800 1176 dbSNP
rs920718366 1182 dbSNP
rs533205972 1198 dbSNP
rs1027374306 1219 dbSNP
rs972221566 1224 dbSNP
rs1279942453 1228 dbSNP
rs1375386697 1228 dbSNP
rs1237828029 1229 dbSNP
rs994592090 1248 dbSNP
rs1353065124 1249 dbSNP
rs148644736 1258 dbSNP
rs550523796 1264 dbSNP
rs1450102486 1266 dbSNP
rs1221234489 1267 dbSNP
rs1233849144 1274 dbSNP
rs987700158 1276 dbSNP
rs1412630380 1295 dbSNP
rs1177292690 1296 dbSNP
rs1380294261 1297 dbSNP
rs1444641073 1301 dbSNP
rs942935162 1302 dbSNP
rs1404425928 1310 dbSNP
rs891403306 1312 dbSNP
rs1187106021 1315 dbSNP
rs953651972 1317 dbSNP
rs1027932187 1321 dbSNP
rs1402167924 1327 dbSNP
rs1051307720 1333 dbSNP
rs946182368 1339 dbSNP
rs1383448001 1342 dbSNP
rs996950107 1346 dbSNP
rs913403632 1359 dbSNP
rs144020066 1361 dbSNP
rs1191727897 1365 dbSNP
rs1274041765 1367 dbSNP
rs1320434439 1368 dbSNP
rs370395981 1370 dbSNP
rs561481932 1374 dbSNP
rs1462172154 1392 dbSNP
rs1188968488 1396 dbSNP
rs149921525 1399 dbSNP
rs1472204716 1422 dbSNP
rs998671930 1425 dbSNP
rs183890769 1428 dbSNP
rs1168120036 1434 dbSNP
rs927272095 1454 dbSNP
rs2856615 1459 dbSNP
rs771327832 1460 dbSNP
rs564295381 1462 dbSNP
rs367803566 1463 dbSNP
rs575857848 1472 dbSNP
rs193031971 1476 dbSNP
rs1275796056 1483 dbSNP
rs577484272 1484 dbSNP
rs1027529122 1485 dbSNP
rs930643653 1493 dbSNP
rs574867373 1501 dbSNP
rs45457396 1503 dbSNP
rs1217129606 1505 dbSNP
rs1257856463 1508 dbSNP
rs1324761542 1509 dbSNP
rs1202676592 1511 dbSNP
rs1277188831 1516 dbSNP
rs964523268 1519 dbSNP
rs1193285925 1520 dbSNP
rs557743284 1522 dbSNP
rs1017672226 1528 dbSNP
rs553544849 1531 dbSNP
rs1008542731 1536 dbSNP
rs890123513 1543 dbSNP
rs1170730176 1551 dbSNP
rs1401494692 1554 dbSNP
rs114006199 1562 dbSNP
rs188542040 1563 dbSNP
rs1362648396 1570 dbSNP
rs1398345239 1571 dbSNP
rs891955351 1574 dbSNP
rs1054579923 1586 dbSNP
rs1411630637 1623 dbSNP
rs10572 1625 dbSNP
rs912041234 1633 dbSNP
rs1273520496 1635 dbSNP
rs1344944305 1639 dbSNP
rs987626669 1651 dbSNP
rs927377234 1659 dbSNP
rs1287585940 1666 dbSNP
rs1487045828 1675 dbSNP
rs1215414414 1683 dbSNP
rs1269230322 1686 dbSNP
rs183273232 1687 dbSNP
rs569162447 1694 dbSNP
rs1196495453 1699 dbSNP
rs550586177 1702 dbSNP
rs528897579 1703 dbSNP
rs567717515 1710 dbSNP
rs1418839788 1715 dbSNP
rs745636834 1719 dbSNP
rs950046634 1721 dbSNP
rs1297812982 1728 dbSNP
rs917258053 1729 dbSNP
rs1388832529 1754 dbSNP
rs1237303481 1757 dbSNP
rs1205784463 1758 dbSNP
rs1330994982 1759 dbSNP
rs1459499553 1763 dbSNP
rs1255541667 1767 dbSNP
rs983366129 1768 dbSNP
rs1217491084 1775 dbSNP
rs546294407 1778 dbSNP
Experimental Support 1 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.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' acccGAAAGA--UCAGAGUC-GAGa 5'
              ||  ||  |  ||| | ||| 
Target 5' ----CUCACUGCAACCUCUGCCUCc 3'
1 - 21
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 2 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 ERX177610. RNA binding protein: AGO2. Condition:KO_V_AGO_CLIP_2_12 PAR-CLIP data was present in ERX177625. RNA binding protein: AGO2. Condition:KO_D_AGO_CLIP_4_3 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]
Experimental Support 3 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions Prostate Tissue
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 SRX1760638. RNA binding protein: AGO2. Condition:AGO-CLIP-PC3-miR148 ...

- Hamilton MP; Rajapakshe KI; Bader DA; Cerne et al., 2016, Neoplasia (New York, N.Y.).

Article - Hamilton MP; Rajapakshe KI; Bader DA; Cerne et al.
- Neoplasia (New York, N.Y.), 2016
MicroRNA (miRNA) deregulation in prostate cancer (PCa) contributes to PCa initiation and metastatic progression. To comprehensively define the cancer-associated changes in miRNA targeting and function in commonly studied models of PCa, we performed photoactivatable ribonucleoside-enhanced cross-linking immunoprecipitation of the Argonaute protein in a panel of PCa cell lines modeling different stages of PCa progression. Using this comprehensive catalogue of miRNA targets, we analyzed miRNA targeting on known drivers of PCa and examined tissue-specific and stage-specific pathway targeting by miRNAs. We found that androgen receptor is the most frequently targeted PCa oncogene and that miR-148a targets the largest number of known PCa drivers. Globally, tissue-specific and stage-specific changes in miRNA targeting are driven by homeostatic response to active oncogenic pathways. Our findings indicate that, even in advanced PCa, the miRNA pool adapts to regulate continuing alterations in the cancer genome to balance oncogenic molecular changes. These findings are important because they are the first to globally characterize miRNA changes in PCa and demonstrate how the miRNA target spectrum responds to staged tumorigenesis.
LinkOut: [PMID: 27292025]
CLIP-seq Support 1 for dataset GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000353258.3 | 3UTR | CUCACUGCAACCUCUGCCUCCUGGGUCCAAGCAAUUCUCCUG
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
Click to see details
118 hsa-miR-3160-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT066658 DYRK2 dual specificity tyrosine phosphorylation regulated kinase 2 2 2
MIRT075318 SF3B3 splicing factor 3b subunit 3 2 4
MIRT077083 EIF1 eukaryotic translation initiation factor 1 2 2
MIRT100381 HSPA1B heat shock protein family A (Hsp70) member 1B 2 6
MIRT135259 TMBIM6 transmembrane BAX inhibitor motif containing 6 2 4
MIRT184913 ZNF268 zinc finger protein 268 2 2
MIRT218862 CDKN1A cyclin dependent kinase inhibitor 1A 2 2
MIRT446580 FPR2 formyl peptide receptor 2 2 2
MIRT448834 FGD4 FYVE, RhoGEF and PH domain containing 4 2 2
MIRT449455 RNF13 ring finger protein 13 2 2
MIRT452284 CARD8 caspase recruitment domain family member 8 2 2
MIRT452628 FAM162A family with sequence similarity 162 member A 2 2
MIRT453454 GLG1 golgi glycoprotein 1 2 2
MIRT454188 AP1S3 adaptor related protein complex 1 sigma 3 subunit 2 6
MIRT454434 GTF2F1 general transcription factor IIF subunit 1 2 2
MIRT454575 NT5DC3 5'-nucleotidase domain containing 3 2 2
MIRT455555 TRAF1 TNF receptor associated factor 1 2 6
MIRT455841 MPL MPL proto-oncogene, thrombopoietin receptor 2 6
MIRT455969 BCAS4 breast carcinoma amplified sequence 4 2 4
MIRT456805 SIGLEC14 sialic acid binding Ig like lectin 14 2 2
MIRT457320 DUSP19 dual specificity phosphatase 19 2 2
MIRT457366 POFUT2 protein O-fucosyltransferase 2 2 2
MIRT457684 ZNF587 zinc finger protein 587 2 2
MIRT458158 LYRM4 LYR motif containing 4 2 6
MIRT458641 SGPP2 sphingosine-1-phosphate phosphatase 2 2 2
MIRT459134 FADS6 fatty acid desaturase 6 2 2
MIRT459153 NARF nuclear prelamin A recognition factor 2 4
MIRT460460 NOM1 nucleolar protein with MIF4G domain 1 2 4
MIRT460974 STK17B serine/threonine kinase 17b 2 2
MIRT461439 ACSBG1 acyl-CoA synthetase bubblegum family member 1 2 2
MIRT461507 NEDD4L neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase 2 2
MIRT462490 GSR glutathione-disulfide reductase 2 2
MIRT462638 PHF5A PHD finger protein 5A 2 2
MIRT463279 ZFX zinc finger protein, X-linked 2 2
MIRT463360 ZFAND4 zinc finger AN1-type containing 4 2 2
MIRT465777 TMOD3 tropomodulin 3 2 2
MIRT466143 TMEM120B transmembrane protein 120B 2 2
MIRT468401 SETD3 SET domain containing 3 2 2
MIRT468998 RNPS1 RNA binding protein with serine rich domain 1 2 2
MIRT471574 PARD6B par-6 family cell polarity regulator beta 2 2
MIRT472108 NME2 NME/NM23 nucleoside diphosphate kinase 2 2 2
MIRT472125 NME1-NME2 NME1-NME2 readthrough 2 2
MIRT473020 MRPS14 mitochondrial ribosomal protein S14 2 2
MIRT473083 MORN4 MORN repeat containing 4 2 2
MIRT475598 HMGB2 high mobility group box 2 2 4
MIRT475937 GXYLT2 glucoside xylosyltransferase 2 2 8
MIRT476117 GPR157 G protein-coupled receptor 157 2 2
MIRT476406 GDE1 glycerophosphodiester phosphodiesterase 1 2 2
MIRT478003 DNAL1 dynein axonemal light chain 1 2 2
MIRT487969 IQSEC2 IQ motif and Sec7 domain 2 2 2
MIRT489418 TUBB2A tubulin beta 2A class IIa 2 2
MIRT491522 IL10RA interleukin 10 receptor subunit alpha 2 2
MIRT492673 PLEC plectin 2 2
MIRT493545 ICOSLG inducible T-cell costimulator ligand 2 2
MIRT513085 USP9X ubiquitin specific peptidase 9, X-linked 2 2
MIRT514009 CECR2 CECR2, histone acetyl-lysine reader 2 4
MIRT516683 ZNF860 zinc finger protein 860 2 2
MIRT518392 ZNF250 zinc finger protein 250 2 2
MIRT522683 LUZP1 leucine zipper protein 1 2 6
MIRT524488 CEP97 centrosomal protein 97 2 2
MIRT527457 CLEC12B C-type lectin domain family 12 member B 2 2
MIRT527705 IL17REL interleukin 17 receptor E like 2 2
MIRT531647 C19orf52 translocase of inner mitochondrial membrane 29 2 2
MIRT532381 UMPS uridine monophosphate synthetase 2 2
MIRT532588 MTHFD1 methylenetetrahydrofolate dehydrogenase, cyclohydrolase and formyltetrahydrofolate synthetase 1 2 2
MIRT533555 TPM4 tropomyosin 4 2 2
MIRT548371 ENTPD5 ectonucleoside triphosphate diphosphohydrolase 5 2 4
MIRT550250 PVR poliovirus receptor 2 2
MIRT552555 ZFP36L2 ZFP36 ring finger protein like 2 2 4
MIRT554113 SMARCE1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 2 2
MIRT554131 SMARCA5 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 2 2
MIRT561344 ZBTB18 zinc finger and BTB domain containing 18 2 2
MIRT561638 RUNX3 runt related transcription factor 3 2 2
MIRT566497 PBX2P1 PBX homeobox 2 pseudogene 1 2 2
MIRT570583 OTUD7B OTU deubiquitinase 7B 2 2
MIRT572731 MCTS1 MCTS1, re-initiation and release factor 2 2
MIRT574041 PEX26 peroxisomal biogenesis factor 26 2 2
MIRT575231 Fut1 fucosyltransferase 1 2 2
MIRT606811 BICD2 BICD cargo adaptor 2 2 2
MIRT621016 CLSTN3 calsyntenin 3 2 2
MIRT637852 PDCL3 phosducin like 3 2 2
MIRT640477 ZNF557 zinc finger protein 557 2 2
MIRT642827 LINC00346 long intergenic non-protein coding RNA 346 2 2
MIRT643887 IMP4 IMP4, U3 small nucleolar ribonucleoprotein 2 2
MIRT664874 PCNXL2 pecanex homolog 2 2 2
MIRT680528 PRIM2 DNA primase subunit 2 2 2
MIRT680648 KIAA1456 KIAA1456 2 2
MIRT680807 ZNF578 zinc finger protein 578 2 2
MIRT680921 STX2 syntaxin 2 2 2
MIRT681112 CEP57L1 centrosomal protein 57 like 1 2 2
MIRT681147 INTS7 integrator complex subunit 7 2 2
MIRT681966 TFCP2 transcription factor CP2 2 2
MIRT684316 GTF3C4 general transcription factor IIIC subunit 4 2 2
MIRT684906 GSG2 histone H3 associated protein kinase 2 2
MIRT685499 MED16 mediator complex subunit 16 2 2
MIRT685929 MOCS3 molybdenum cofactor synthesis 3 2 2
MIRT686875 SLC25A32 solute carrier family 25 member 32 2 2
MIRT688204 FNIP1 folliculin interacting protein 1 2 2
MIRT688791 CCNB1 cyclin B1 2 2
MIRT689227 RPS19 ribosomal protein S19 2 2
MIRT690470 ZNF33A zinc finger protein 33A 2 2
MIRT691982 PLCXD1 phosphatidylinositol specific phospholipase C X domain containing 1 2 2
MIRT694006 PPIL4 peptidylprolyl isomerase like 4 2 2
MIRT694529 TRIM72 tripartite motif containing 72 2 2
MIRT695420 ADH5 alcohol dehydrogenase 5 (class III), chi polypeptide 2 2
MIRT695784 HSD17B12 hydroxysteroid 17-beta dehydrogenase 12 2 2
MIRT697799 UBXN2A UBX domain protein 2A 2 2
MIRT698275 TMEM2 transmembrane protein 2 2 2
MIRT698317 TMEM136 transmembrane protein 136 2 2
MIRT699971 RREB1 ras responsive element binding protein 1 2 2
MIRT700717 PNO1 partner of NOB1 homolog 2 2
MIRT701721 MTMR12 myotubularin related protein 12 2 2
MIRT701879 MPLKIP M-phase specific PLK1 interacting protein 2 2
MIRT702959 HIF1A hypoxia inducible factor 1 alpha subunit 2 2
MIRT706178 ZNF716 zinc finger protein 716 2 2
MIRT706463 SPRED1 sprouty related EVH1 domain containing 1 2 2
MIRT718154 TTC33 tetratricopeptide repeat domain 33 2 2
MIRT718711 ANKRD18A ankyrin repeat domain 18A 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-3160-3p Gefitinib 123631 NSC715055 approved resistant cell line (PC9)
hsa-miR-3160-3p Osimertinib 71496458 NSC779217 approved resistant cell line (PC9)
hsa-miR-3160-3p Osimertinib 71496458 NSC779217 approved resistant cell line (HCC827)
hsa-miR-3160-3p Tripterygium wilfordii Hook F resistant tissue
hsa-miR-3160-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-3160-3p Paclitaxel/Docetaxel/Vinorelbine/Doxorubicin/Etoposide resistant cell line (Bads-200)

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