miRTarBase - #MIRT364735


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pre-miRNA Information
pre-miRNA hsa-mir-3679   
Genomic Coordinates chr2: 134127125 - 134127192
Description Homo sapiens miR-3679 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-3679-5p
Sequence 6| UGAGGAUAUGGCAGGGAAGGGGA |28
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 17 2 + 134127146 26487287 MiREDiBase
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN28578769 23 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1490236859 15 dbSNP
rs982355045 16 dbSNP
rs1053094244 17 dbSNP
rs893220051 23 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol TOR1B   
Synonyms DQ1
Description torsin family 1 member B
Transcript NM_014506   
Expression
Putative miRNA Targets on TOR1B
3'UTR of TOR1B
(miRNA target sites are highlighted)		 
>TOR1B|NM_014506|3'UTR
   1 GCTCCTATCCAGATGGGGTAGGAGACAGCTGGGAGGCTCCGCACGCCAGAGGCCTTGCCTTTCAGAAGAACCCTGAAGAC
  81 CGCTTTGGGGTTTTGCCTGTTTGCACCTTAGACTTTTGGGTATAGAATCTTTTTTTTGAGAAGAGGTCTCACTCCGTCAT
 161 CCAAGCTGGAGTGCAGTGGTGCAATCCTCAACTCACTGCAACCTCCGCTCCCGGTTTGAGTGATTCTCATGCCTCAGCCT
 241 CCCGAGTAGCTGGGATTACAGGCATGAGCCACTGTGCCCAGCTGGGATATAGAATCTAAGAGTTGATTGTGGAAAACACG
 321 TGAATCTATTGCGCGCATTTGTCATTTAGCAAGATGGCAGCAGTCCAGCTGTTCTTTGCAGCTGGAGATGAACTTTTAAA
 401 AATCCCCTTCACACTTAATGTACTGACCGAGACAGAAGTACCTGAAAACAGCTGTGCATGGCAGGCCCGGCAATAGCTTC
 481 TGACCCACAGCACCCGCGCCTCAGAAGCTACGGTCACAACTAAAGGAGTCCAGGGACTTGCTGCAGGCTGGGGGGCACTG
 561 GGTGGTTCTCACCAGCAGGCTGCGGGGCACTGTGTTCTCATTGGCCAAAAACATCCTTTTGCTCTGTCTCGTTCTTTACA
 641 CAGAGTTCACTGACTTGAAGTATACTCAGTTAAAATCGGGGCTGGAGGTGCAGACGGTGTCTGACCGGAGGATGTGGCCG
 721 TGCCCGCCGAGCACTCTTGATCTGAGCTGACCTGTGTGTGTGTGTGGGGGGGGGTGGGGCCTTCACCTAAGACCTCTGCA
 801 GCAGACCTGGACAGACAGGCCCCTCCCGCCTGTCCATCGCTCTAGCTGCTAATACAGCCCTGGCTGTGGAATCCTTCACC
 881 GTCTCAGCTGGTATCAGCCCCAGCCTGCCTTGTGCCATATCTCAGCTTGGATCTCTGCTAGAGTCCCCCCAACCATATAT
 961 CATAGAGTTGAATCACAATGAGACCGTTGGCTTTGAATTTGAGTCGTTGGTTCCCATGGTGAGATGCTTGTTAAGACTTT
1041 ATACTTGGGTCAATCTCTCACTTTATTTTGTAGAACCATTTGAAATCCTAGGATGTGCTTGTTCTGGAAGGATGACATGG
1121 GCCCAGACTGAACAAGTCAGCTTGATGATCTTAAATGATGGAAGTATAGGACGTTGCTTATTTTAAAACAAGGGAAGGAC
1201 ACAAAATGGAATGACTGCTTAGTCCTTTCTCAGATACTCTTAAAACAATTTTTTATTGTTAAATTTGTGGTAATACATGG
1281 TCACAACCGTGGATCAAACAAGGTCAGTCTAAAGTGGCAGGTCCTAGGTGTGACCTGATACCACCACCCTTTGTGGCAGC
1361 ACCGGGCTGGACTGCCCTGATCCCTGGGACGTGAGACTTAGCTTCCAGCCAGTGTGAATCATTGTATCTGTCTCATAATC
1441 ACAGCACAGCTGCAGACACAACAACGTGCAGCATTTTTTACATAAAAATATGGTAGAATTAATTTATGACATGGAAATGC
1521 CTTACGTGGTATCACACTTAGTCTTGAAAAAAACACCAAGGTGACGTTTAAAATTTTTAGTACATATCCTCAAATTGGAG
1601 CTAAGTTATACTTCTTTTATAACCTTTTGGGCATCTGGTCGAGAGAAGACAAGATTTTCTCTATTTACAGTGAGGCAATA
1681 AATATGTTTGCCACCTTTGGACTGCCAAAAAAAAAAAAAAAAAA
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' aggggAAGGGACG-GUAUAGGAGu 5'
               ||::: |: ||||||||| 
Target 5' taaaaTTTTTAGTACATATCCTCa 3'
 1569 - 1592 158.00 -15.90
2 
miRNA  3' aggGGAAGGG--ACGGUAUAGGAGu 5'
             ||| ||:  |||||||| ||| 
Target 5' cagCCTGCCTTGTGCCATAT-CTCa 3'
 901 - 924 126.00 -20.90
3 
miRNA  3' agGGGAAGGGACGGUAUAGGAGu 5'
            | ||  |:||  :||| ||| 
Target 5' ttCACTGACTTGAAGTATACTCa 3'
 646 - 668 125.00 -13.50
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN26999400 41 COSMIC
COSN15316938 42 COSMIC
COSN5854726 60 COSMIC
COSN30523001 102 COSMIC
COSN1374149 123 COSMIC
COSN31482391 236 COSMIC
COSN5119503 409 COSMIC
COSN26437146 496 COSMIC
COSN31550287 513 COSMIC
COSN30165467 522 COSMIC
COSN26553213 580 COSMIC
COSN30119827 584 COSMIC
COSN4894226 603 COSMIC
COSN6603102 631 COSMIC
COSM6273942 646 COSMIC
COSN31480487 658 COSMIC
COSN26856561 731 COSMIC
COSN27881995 758 COSMIC
COSN32061725 764 COSMIC
COSN28866359 766 COSMIC
COSN20070548 768 COSMIC
COSN15148228 771 COSMIC
COSN47713 776 COSMIC
COSN30132060 800 COSMIC
COSN21964437 1007 COSMIC
COSN2311468 1033 COSMIC
COSN30003601 1187 COSMIC
COSN29688143 1426 COSMIC
COSN9701129 1435 COSMIC
rs12634 1675 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs550970341 2 dbSNP
rs770812700 2 dbSNP
rs78211824 3 dbSNP
rs1264900165 6 dbSNP
rs756575894 7 dbSNP
rs200753107 8 dbSNP
rs749719628 13 dbSNP
rs769138304 17 dbSNP
rs773048199 18 dbSNP
rs573081703 19 dbSNP
rs775861794 19 dbSNP
rs1350904706 20 dbSNP
rs770598172 21 dbSNP
rs78173949 30 dbSNP
rs566958922 33 dbSNP
rs765279934 38 dbSNP
rs199892031 41 dbSNP
rs78957005 42 dbSNP
rs200742722 45 dbSNP
rs757428205 46 dbSNP
rs1286599403 48 dbSNP
rs1227860532 50 dbSNP
rs750457372 52 dbSNP
rs202045629 56 dbSNP
rs1351119089 60 dbSNP
rs1203849088 68 dbSNP
rs575421708 71 dbSNP
rs1394758185 75 dbSNP
rs1236486372 82 dbSNP
rs753428077 83 dbSNP
rs1386002730 97 dbSNP
rs954358662 100 dbSNP
rs1157888255 104 dbSNP
rs904746321 123 dbSNP
rs1185385567 130 dbSNP
rs577501387 130 dbSNP
rs1423150844 133 dbSNP
rs987711598 143 dbSNP
rs879275386 149 dbSNP
rs1266485603 154 dbSNP
rs1208291853 156 dbSNP
rs72755214 157 dbSNP
rs1270057744 160 dbSNP
rs973941375 163 dbSNP
rs151030428 168 dbSNP
rs1421150162 180 dbSNP
rs964733179 185 dbSNP
rs749321256 192 dbSNP
rs1457418060 194 dbSNP
rs1169312350 195 dbSNP
rs773503520 207 dbSNP
rs927980167 208 dbSNP
rs952570987 213 dbSNP
rs939321872 214 dbSNP
rs577262242 215 dbSNP
rs1339813033 222 dbSNP
rs542127314 226 dbSNP
rs1247139879 231 dbSNP
rs891696492 232 dbSNP
rs1465493651 233 dbSNP
rs768614422 243 dbSNP
rs11558553 244 dbSNP
rs1355659194 245 dbSNP
rs1271740710 260 dbSNP
rs1362896486 264 dbSNP
rs904351771 265 dbSNP
rs1297297040 267 dbSNP
rs1435432690 268 dbSNP
rs1366909017 270 dbSNP
rs1321096314 271 dbSNP
rs1385743672 273 dbSNP
rs774979273 287 dbSNP
rs1390763542 291 dbSNP
rs1164962045 293 dbSNP
rs1218296461 295 dbSNP
rs375314946 297 dbSNP
rs760845600 298 dbSNP
rs1325825820 304 dbSNP
rs908359842 308 dbSNP
rs1278454120 313 dbSNP
rs559947930 320 dbSNP
rs185610000 321 dbSNP
rs1451145440 325 dbSNP
rs1195713522 330 dbSNP
rs542028304 333 dbSNP
rs562333783 334 dbSNP
rs116214334 335 dbSNP
rs1015132092 336 dbSNP
rs1344684122 342 dbSNP
rs962235922 349 dbSNP
rs551334475 362 dbSNP
rs188921301 363 dbSNP
rs904797166 398 dbSNP
rs936234498 414 dbSNP
rs1470634000 420 dbSNP
rs191156923 429 dbSNP
rs115221907 430 dbSNP
rs1422756468 436 dbSNP
rs1357939790 444 dbSNP
rs1412739495 451 dbSNP
rs566816944 453 dbSNP
rs1378340686 460 dbSNP
rs1201676676 461 dbSNP
rs1482074852 464 dbSNP
rs1251740873 469 dbSNP
rs1345640045 470 dbSNP
rs1019025257 497 dbSNP
rs939354308 498 dbSNP
rs1399615852 499 dbSNP
rs988104188 503 dbSNP
rs1345264420 510 dbSNP
rs913894413 512 dbSNP
rs945983975 513 dbSNP
rs535967595 516 dbSNP
rs1349282879 521 dbSNP
rs1347626060 526 dbSNP
rs1224155923 527 dbSNP
rs1357267789 530 dbSNP
rs183708168 534 dbSNP
rs900544677 541 dbSNP
rs996197676 553 dbSNP
rs1274356428 556 dbSNP
rs1042959053 558 dbSNP
rs1343462470 560 dbSNP
rs1471661862 564 dbSNP
rs1027625800 571 dbSNP
rs1207447641 577 dbSNP
rs904382223 583 dbSNP
rs569068525 584 dbSNP
rs931804639 585 dbSNP
rs537739171 588 dbSNP
rs1443298228 601 dbSNP
rs984027523 602 dbSNP
rs1206394005 603 dbSNP
rs1015471882 607 dbSNP
rs866443116 611 dbSNP
rs756133045 615 dbSNP
rs1235343279 616 dbSNP
rs1483947844 623 dbSNP
rs1181872631 626 dbSNP
rs1283455815 629 dbSNP
rs890164663 631 dbSNP
rs917015563 632 dbSNP
rs1338976294 634 dbSNP
rs749460253 635 dbSNP
rs1455813113 637 dbSNP
rs1412039185 638 dbSNP
rs780676874 638 dbSNP
rs1382532215 642 dbSNP
rs1354781129 644 dbSNP
rs1401597759 646 dbSNP
rs1333794675 649 dbSNP
rs1357577340 650 dbSNP
rs1450314984 652 dbSNP
rs1412282487 653 dbSNP
rs1303487055 657 dbSNP
rs1181740106 661 dbSNP
rs1376161789 662 dbSNP
rs1473348348 666 dbSNP
rs1444444607 673 dbSNP
rs1311250236 676 dbSNP
rs749790395 678 dbSNP
rs948446728 679 dbSNP
rs1464154608 681 dbSNP
rs141116203 682 dbSNP
rs577521526 685 dbSNP
rs746665295 696 dbSNP
rs897494161 697 dbSNP
rs936286745 707 dbSNP
rs1296147386 708 dbSNP
rs1228772795 717 dbSNP
rs1053291155 720 dbSNP
rs1367628045 721 dbSNP
rs1433240741 726 dbSNP
rs866679392 727 dbSNP
rs1433008560 728 dbSNP
rs1322935381 730 dbSNP
rs1329482012 735 dbSNP
rs1241785909 743 dbSNP
rs1387542007 747 dbSNP
rs1280585800 752 dbSNP
rs1353665429 753 dbSNP
rs1449175769 753 dbSNP
rs1487234611 753 dbSNP
rs3217180 753 dbSNP
rs1325360143 755 dbSNP
rs1294468962 760 dbSNP
rs1272291456 761 dbSNP
rs376708846 761 dbSNP
rs1227397945 762 dbSNP
rs200600696 762 dbSNP
rs1365645434 763 dbSNP
rs147944259 763 dbSNP
rs376119823 763 dbSNP
rs1306658809 764 dbSNP
rs71481355 764 dbSNP
rs1423925252 765 dbSNP
rs758847973 765 dbSNP
rs764184445 765 dbSNP
rs3217179 766 dbSNP
rs553747620 766 dbSNP
rs1287033793 767 dbSNP
rs1300771015 767 dbSNP
rs1040907896 768 dbSNP
rs1220509 768 dbSNP
rs1181430767 769 dbSNP
rs542740092 769 dbSNP
rs996237664 770 dbSNP
rs887772534 771 dbSNP
rs1274677767 772 dbSNP
rs2287368 772 dbSNP
rs1015515190 773 dbSNP
rs1394666661 773 dbSNP
rs1449316208 774 dbSNP
rs878877554 776 dbSNP
rs1380794932 779 dbSNP
rs1014102876 781 dbSNP
rs1024535659 785 dbSNP
rs1156586064 786 dbSNP
rs543552355 790 dbSNP
rs1423056465 792 dbSNP
rs879248035 793 dbSNP
rs1425526710 795 dbSNP
rs1486351147 799 dbSNP
rs1162944390 801 dbSNP
rs969976109 804 dbSNP
rs979807182 808 dbSNP
rs1208189220 811 dbSNP
rs111440015 817 dbSNP
rs957032072 818 dbSNP
rs879134315 820 dbSNP
rs1035108274 823 dbSNP
rs952893657 825 dbSNP
rs988396412 828 dbSNP
rs1376785934 829 dbSNP
rs1454310215 830 dbSNP
rs181233451 832 dbSNP
rs960812723 837 dbSNP
rs1319404535 839 dbSNP
rs944923005 840 dbSNP
rs1291751530 841 dbSNP
rs1457320118 843 dbSNP
rs1385694038 850 dbSNP
rs1317609090 857 dbSNP
rs1447364001 859 dbSNP
rs1043181 860 dbSNP
rs1388562420 880 dbSNP
rs752291029 881 dbSNP
rs764154660 882 dbSNP
rs913925791 883 dbSNP
rs968061508 891 dbSNP
rs1208640361 892 dbSNP
rs979099301 901 dbSNP
rs932090713 903 dbSNP
rs925869112 905 dbSNP
rs1248646998 906 dbSNP
rs1340423341 907 dbSNP
rs1296462666 908 dbSNP
rs78683824 910 dbSNP
rs887824271 913 dbSNP
rs1196980714 914 dbSNP
rs1298540914 918 dbSNP
rs1238306787 920 dbSNP
rs1050182388 928 dbSNP
rs2287367 932 dbSNP
rs1427604821 936 dbSNP
rs1244728126 943 dbSNP
rs866082261 950 dbSNP
rs1475856966 953 dbSNP
rs1014568894 957 dbSNP
rs527798364 958 dbSNP
rs1480119298 962 dbSNP
rs897524968 974 dbSNP
rs994486472 979 dbSNP
rs1049799058 986 dbSNP
rs867846461 987 dbSNP
rs1272646814 988 dbSNP
rs1171438220 990 dbSNP
rs1345539681 996 dbSNP
rs1285150127 1004 dbSNP
rs1407886684 1006 dbSNP
rs1399735910 1007 dbSNP
rs1032724685 1008 dbSNP
rs184944123 1009 dbSNP
rs1398926757 1020 dbSNP
rs1170991025 1029 dbSNP
rs1469385994 1031 dbSNP
rs1202293023 1035 dbSNP
rs549202865 1044 dbSNP
rs1384187478 1050 dbSNP
rs751555901 1054 dbSNP
rs1182987095 1056 dbSNP
rs960844943 1058 dbSNP
rs1439861073 1063 dbSNP
rs560564292 1066 dbSNP
rs1276092457 1069 dbSNP
rs1202595869 1076 dbSNP
rs529353272 1078 dbSNP
rs1021019974 1079 dbSNP
rs912863921 1092 dbSNP
rs1043182 1112 dbSNP
rs1328399118 1117 dbSNP
rs968456529 1118 dbSNP
rs1444143348 1125 dbSNP
rs976735391 1127 dbSNP
rs757220961 1133 dbSNP
rs77334779 1139 dbSNP
rs1406993901 1143 dbSNP
rs1178669003 1160 dbSNP
rs922166062 1162 dbSNP
rs979434602 1167 dbSNP
rs559373963 1168 dbSNP
rs925875171 1173 dbSNP
rs144940713 1174 dbSNP
rs1258135136 1185 dbSNP
rs1471378394 1192 dbSNP
rs985992972 1199 dbSNP
rs147949345 1201 dbSNP
rs1182650620 1203 dbSNP
rs909310863 1209 dbSNP
rs940733891 1212 dbSNP
rs1196218998 1219 dbSNP
rs1264887988 1227 dbSNP
rs1206300303 1228 dbSNP
rs1483552077 1237 dbSNP
rs750182932 1242 dbSNP
rs1225367775 1249 dbSNP
rs1354059517 1256 dbSNP
rs1181049904 1267 dbSNP
rs1314098873 1273 dbSNP
rs1036077854 1275 dbSNP
rs1245599503 1278 dbSNP
rs918971983 1288 dbSNP
rs537604765 1289 dbSNP
rs930321392 1290 dbSNP
rs1048693445 1294 dbSNP
rs1344643494 1301 dbSNP
rs896466223 1306 dbSNP
rs1402929542 1309 dbSNP
rs950030255 1312 dbSNP
rs916579543 1323 dbSNP
rs1046058033 1340 dbSNP
rs1445557818 1346 dbSNP
rs905748167 1354 dbSNP
rs1178716424 1359 dbSNP
rs528417485 1364 dbSNP
rs1032776992 1367 dbSNP
rs1242174483 1374 dbSNP
rs1217943652 1377 dbSNP
rs547356418 1388 dbSNP
rs1056725194 1391 dbSNP
rs1222967242 1392 dbSNP
rs1010380277 1394 dbSNP
rs896665181 1399 dbSNP
rs1383542298 1400 dbSNP
rs1212993720 1408 dbSNP
rs77357177 1418 dbSNP
rs749457754 1420 dbSNP
rs1432898154 1421 dbSNP
rs975736587 1424 dbSNP
rs1303025442 1425 dbSNP
rs1029258602 1427 dbSNP
rs1284707247 1427 dbSNP
rs768826450 1428 dbSNP
rs1043186 1429 dbSNP
rs1427545695 1429 dbSNP
rs984977040 1434 dbSNP
rs1476720597 1441 dbSNP
rs909361716 1444 dbSNP
rs940784621 1450 dbSNP
rs1223079757 1458 dbSNP
rs1490790533 1461 dbSNP
rs1272182922 1463 dbSNP
rs1001345243 1466 dbSNP
rs534120640 1467 dbSNP
rs1273907030 1469 dbSNP
rs748717817 1473 dbSNP
rs1216426052 1474 dbSNP
rs75003318 1474 dbSNP
rs77796236 1475 dbSNP
rs1209419183 1476 dbSNP
rs78586989 1485 dbSNP
rs113285477 1488 dbSNP
rs1254014191 1497 dbSNP
rs986043858 1497 dbSNP
rs1343676608 1523 dbSNP
rs772516959 1526 dbSNP
rs1406070260 1527 dbSNP
rs917964109 1536 dbSNP
rs773573361 1538 dbSNP
rs761097371 1547 dbSNP
rs553471680 1553 dbSNP
rs905798967 1560 dbSNP
rs190150141 1566 dbSNP
rs930436335 1567 dbSNP
rs1054238338 1574 dbSNP
rs17418918 1577 dbSNP
rs1010029451 1583 dbSNP
rs750107170 1585 dbSNP
rs1176424051 1596 dbSNP
rs1480809160 1598 dbSNP
rs181855991 1601 dbSNP
rs10988522 1606 dbSNP
rs376867658 1610 dbSNP
rs1321567769 1617 dbSNP
rs901561279 1620 dbSNP
rs762482136 1641 dbSNP
rs1326291789 1642 dbSNP
rs937628452 1649 dbSNP
rs1056735130 1654 dbSNP
rs1374456382 1669 dbSNP
rs12634 1675 dbSNP
rs945541049 1677 dbSNP
rs1176516484 1680 dbSNP
rs750124139 1684 dbSNP
rs544780743 1686 dbSNP
rs953634564 1693 dbSNP
rs374145471 1698 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' aggggaagggacgguaUAGGAGu 5'
                          |||||| 
Target 5' --------------caAUCCUCa 3'
 		1 - 9
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]
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 ENST00000259339.2 | 3UTR | CAAUCCUCAACUCACUGCAACCUC
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
HNSC 0.847 0.18 0.500 0.33 3 Click to see details
LUSC -0.664 0.27 -1.000 0.5 3 Click to see details
THCA 0.601 0.29 0.500 0.33 3 Click to see details
STAD 0.522 0.33 0.500 0.33 3 Click to see details
STAD 0.522 0.33 0.500 0.33 3 Click to see details
STAD 0.522 0.33 0.500 0.33 3 Click to see details
STAD 0.522 0.33 0.500 0.33 3 Click to see details
STAD 0.522 0.33 0.500 0.33 3 Click to see details
STAD 0.522 0.33 0.500 0.33 3 Click to see details
55 hsa-miR-3679-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT114494 PNN pinin, desmosome associated protein 2 2
MIRT169967 DNAJB9 DnaJ heat shock protein family (Hsp40) member B9 2 6
MIRT182181 POU2F1 POU class 2 homeobox 1 2 2
MIRT189380 TXLNA taxilin alpha 2 4
MIRT364735 TOR1B torsin family 1 member B 2 2
MIRT445477 KDM6A lysine demethylase 6A 2 2
MIRT446333 ATP5C1 ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1 2 2
MIRT446386 SYNCRIP synaptotagmin binding cytoplasmic RNA interacting protein 2 2
MIRT446971 SLCO4C1 solute carrier organic anion transporter family member 4C1 2 2
MIRT449793 C1orf109 chromosome 1 open reading frame 109 2 2
MIRT451211 PIN1 peptidylprolyl cis/trans isomerase, NIMA-interacting 1 2 2
MIRT452098 NUCB2 nucleobindin 2 2 2
MIRT454036 DDT D-dopachrome tautomerase 2 2
MIRT461708 ZNF426 zinc finger protein 426 2 2
MIRT464957 TWIST1 twist family bHLH transcription factor 1 2 2
MIRT465775 TMOD3 tropomodulin 3 2 2
MIRT466925 STC2 stanniocalcin 2 2 2
MIRT471388 PDPR pyruvate dehydrogenase phosphatase regulatory subunit 2 2
MIRT473585 MAT2A methionine adenosyltransferase 2A 2 2
MIRT476070 GRIN2A glutamate ionotropic receptor NMDA type subunit 2A 2 2
MIRT477324 EPHA2 EPH receptor A2 2 2
MIRT478244 DDX3X DEAD-box helicase 3, X-linked 2 4
MIRT480449 C16orf72 chromosome 16 open reading frame 72 2 6
MIRT481866 ANKRD50 ankyrin repeat domain 50 2 2
MIRT492032 TSG101 tumor susceptibility 101 2 4
MIRT493737 GRAP2 GRB2-related adaptor protein 2 2 2
MIRT495623 PPP1R1C protein phosphatase 1 regulatory inhibitor subunit 1C 2 2
MIRT497590 SLC23A1 solute carrier family 23 member 1 2 2
MIRT504702 ZNF117 zinc finger protein 117 2 2
MIRT507794 CDKN1B cyclin dependent kinase inhibitor 1B 2 2
MIRT510653 TMED7 transmembrane p24 trafficking protein 7 2 4
MIRT525534 FSIP2 fibrous sheath interacting protein 2 2 2
MIRT531149 CYGB cytoglobin 2 2
MIRT536003 MED13 mediator complex subunit 13 2 2
MIRT537056 GPR180 G protein-coupled receptor 180 2 2
MIRT538297 CSNK2A1 casein kinase 2 alpha 1 2 2
MIRT544755 C8orf33 chromosome 8 open reading frame 33 2 2
MIRT544927 MIS18BP1 MIS18 binding protein 1 2 2
MIRT556973 HSPA4L heat shock protein family A (Hsp70) member 4 like 2 2
MIRT561714 PPP2R2A protein phosphatase 2 regulatory subunit Balpha 2 2
MIRT563632 ZNF460 zinc finger protein 460 2 2
MIRT564705 ZNF322P1 zinc finger protein 322 pseudogene 1 2 2
MIRT572190 CALU calumenin 2 2
MIRT573900 MKI67 marker of proliferation Ki-67 2 2
MIRT576073 Poteg POTE ankyrin domain family, member G 2 2
MIRT576150 Hmox1 heme oxygenase 1 2 2
MIRT614848 PLEKHA6 pleckstrin homology domain containing A6 2 4
MIRT647592 FAM109B family with sequence similarity 109 member B 2 2
MIRT657009 KCNMB4 potassium calcium-activated channel subfamily M regulatory beta subunit 4 2 2
MIRT691268 GET4 golgi to ER traffic protein 4 2 2
MIRT695778 DENR density regulated re-initiation and release factor 2 2
MIRT698089 TPM1 tropomyosin 1 2 2
MIRT732571 IGLL5 immunoglobulin lambda like polypeptide 5 1 0
MIRT733722 NEDD4L neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase 3 0
MIRT734354 GREM1 gremlin 1, DAN family BMP antagonist 1 0
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-3679-5p 5-Fluorouracil approved 3385 Microarray CNE cells 22614822 2012 up-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-3679 Doxorubicin 31703 NSC123127 approved sensitive High Hepatocellular Carcinoma cell line (HepG2)
hsa-miR-3679-5p Platinum 23939 sensitive High Ovarian Cancer tissue
hsa-miR-3679-5p Doxorubicin 31703 NSC123127 approved sensitive High Breast Cancer cell line (MCF-7)
hsa-miR-3679-5p Curcumin 969516 NSC32982 approved sensitive High Breast Cancer cell line (MCF-7)
hsa-miR-3679-5p Osimertinib 71496458 NSC779217 approved resistant Low Non-Small Cell Lung Cancer tissue
hsa-miR-3679-5p Etoposide 36462 NSC141540 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-3679-5p Doxorubicin 31703 NSC123127 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-3679-5p Paclitaxel 36314 NSC125973 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-3679-5p Vinorelbine 44424639 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-3679-5p Vincristine 5978 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-3679-5p Gefitinib 123631 NSC715055 approved sensitive cell line (PC9)
hsa-miR-3679-5p Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-3679-5p Osimertinib 71496458 NSC779217 approved sensitive cell line (HCC827)
hsa-miR-3679-5p Paclitaxel 36314 NSC125973 approved resistant cell line (BAS)
hsa-miR-3679-5p Osimertinib 71496458 NSC779217 approved resistant cell line (H1975)
hsa-miR-3679-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-3679-5p Vemurafenib 42611257 NSC761431 approved sensitive cell line (LM16)
hsa-miR-3679-5p Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (1500 ng/ml)
hsa-miR-3679-5p Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (100 ng/ml)

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