pre-miRNA Information
pre-miRNA hsa-mir-3179-1   
Genomic Coordinates chr16: 14901508 - 14901591
Description Homo sapiens miR-3179-1 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases
pre-miRNA hsa-mir-3179-2   
Genomic Coordinates chr16: 16300159 - 16300242
Description Homo sapiens miR-3179-2 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases
pre-miRNA hsa-mir-3179-3   
Genomic Coordinates chr16: 18411894 - 18411977
Description Homo sapiens miR-3179-3 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases
pre-miRNA hsa-mir-3179-4   
Genomic Coordinates chr16: 18494493 - 18494576
Description Homo sapiens miR-3179-4 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-3179
Sequence 52| AGAAGGGGUGAAAUUUAAACGU |73
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1351100204 1 dbSNP
rs1398613616 4 dbSNP
rs1340262765 20 dbSNP
rs1229893475 21 dbSNP
Putative Targets

miRNA Expression profile
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol TGIF1   
Synonyms HPE4, TGIF
Description TGFB induced factor homeobox 1
Transcript NM_003244   
Other Transcripts NM_170695 , NM_173207 , NM_173208 , NM_173209 , NM_173210 , NM_173211 , NM_174886   
Expression
Putative miRNA Targets on TGIF1
3'UTR of TGIF1
(miRNA target sites are highlighted)
>TGIF1|NM_003244|3'UTR
   1 CCCATTTTCAAGCAAAACAGTTCTCAGAAATGTCATGATTGCCGGGGTGAAGGCAAGAGATGAATTGCATTATTTTATAT
  81 ATTTTTTATTAATATTTGCACATGGGATTGCTAAAACAGCTTCCTGTTACTGAGATGTCTTCAATGGAATACAGTCATTC
 161 CAAGAACTATAAACTTAAAGCTACTGTAGAAACAAAGGGTTTTCTTTTTTAAATGTTTCTTGGTAGATTATTCATAATGT
 241 GAGATGGTTCCCAATATCATGTGATTTTTTTTTTCCTCCCCTTCCCTTTTTTTGTTATTTTTTCAGACTGTGCAATACTT
 321 AGAGAACCTATAGCATCTTCTCATTCCCATGTGGAACAGGATGCCCACATACTGTCTAATTAATAAATTTTCCATTTTTT
 401 TTCAAACAAGTATGAATCTAGTTGGTTGATGCCTTTTTTTTCATGACATAATAAAGTATTTTCTTTAAAAAAAAAAAAAA
 481 AAA
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' ugcAAAUUUAAAGUGGGGAAGa 5'
             |||   || | ||||||| 
Target 5' attTTTTTTTTCCTCCCCTTCc 3'
264 - 285 155.00 -12.40
2
miRNA  3' ugcaaAUUUAAAGUGGGGAAGa 5'
               |||||||: || :||: 
Target 5' attaaTAAATTTT-CCATTTTt 3'
379 - 399 104.00 -6.70
3
miRNA  3' ugcaAAUUU-----AAAGUGGGGAAGa 5'
              |||:|     | | :| :|||| 
Target 5' atacTTAGAGAACCTATAGCATCTTCt 3'
315 - 341 102.00 -6.11
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
326711 20 ClinVar
326712 134 ClinVar
326713 265 ClinVar
326714 337 ClinVar
326715 408 ClinVar
326716 434 ClinVar
COSN31599516 9 COSMIC
COSN30705872 28 COSMIC
COSN31555417 28 COSMIC
COSN32052967 28 COSMIC
COSN22859456 38 COSMIC
COSN31599713 43 COSMIC
COSN30180586 46 COSMIC
COSN30499844 61 COSMIC
COSN30160187 63 COSMIC
COSN31581054 85 COSMIC
COSN31598398 108 COSMIC
COSN28040711 193 COSMIC
COSN26642246 211 COSMIC
COSN20114634 275 COSMIC
COSN31486181 293 COSMIC
COSN26647791 298 COSMIC
COSN26648860 305 COSMIC
COSN31566910 325 COSMIC
COSN8604526 336 COSMIC
COSN30118550 365 COSMIC
COSN30162987 400 COSMIC
COSN8604527 413 COSMIC
COSN31593909 420 COSMIC
COSN6120776 653 COSMIC
COSN58516 746 COSMIC
COSN25035620 760 COSMIC
COSN25490078 775 COSMIC
COSN22278487 798 COSMIC
COSN5425178 854 COSMIC
COSN6120779 1031 COSMIC
COSN22623880 1084 COSMIC
COSN1739258 1124 COSMIC
COSN6120781 1250 COSMIC
COSN22308598 1304 COSMIC
COSN27408669 1585 COSMIC
COSN27893083 1631 COSMIC
COSN1739259 1661 COSMIC
COSN9332280 1742 COSMIC
COSN8678309 1777 COSMIC
COSN22887885 1797 COSMIC
COSN1205414 1998 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1247279748 1 dbSNP
rs1231971234 5 dbSNP
rs1308225202 14 dbSNP
rs1374452107 15 dbSNP
rs1241852013 16 dbSNP
rs145621092 20 dbSNP
rs1355216701 21 dbSNP
rs1221785461 24 dbSNP
rs370491897 26 dbSNP
rs1300086123 28 dbSNP
rs756742227 29 dbSNP
rs1453791263 34 dbSNP
rs1390743487 35 dbSNP
rs75078688 37 dbSNP
rs781153445 41 dbSNP
rs900139143 43 dbSNP
rs745773389 44 dbSNP
rs563701713 45 dbSNP
rs775304618 50 dbSNP
rs1439258052 55 dbSNP
rs1348596934 61 dbSNP
rs1051495561 63 dbSNP
rs954279745 66 dbSNP
rs1166317308 68 dbSNP
rs1391494896 77 dbSNP
rs986932552 80 dbSNP
rs1192672324 86 dbSNP
rs890190970 87 dbSNP
rs912746852 90 dbSNP
rs1327015985 91 dbSNP
rs1225201155 92 dbSNP
rs1008420080 94 dbSNP
rs955748503 102 dbSNP
rs1032232953 103 dbSNP
rs1276786624 104 dbSNP
rs892060141 105 dbSNP
rs1307094723 111 dbSNP
rs529315164 114 dbSNP
rs1221273162 120 dbSNP
rs549486635 130 dbSNP
rs886053783 134 dbSNP
rs970083619 136 dbSNP
rs1044071985 138 dbSNP
rs980089529 141 dbSNP
rs1035802830 143 dbSNP
rs566210101 145 dbSNP
rs1248423071 146 dbSNP
rs1481742862 147 dbSNP
rs752943244 148 dbSNP
rs1200764848 153 dbSNP
rs1428579350 161 dbSNP
rs527462805 163 dbSNP
rs1473492597 165 dbSNP
rs983319248 169 dbSNP
rs907668404 185 dbSNP
rs1175505633 192 dbSNP
rs1056870215 193 dbSNP
rs1238239036 194 dbSNP
rs1212763873 199 dbSNP
rs111818038 206 dbSNP
rs1262848247 210 dbSNP
rs1229556071 215 dbSNP
rs1331788615 223 dbSNP
rs11571513 224 dbSNP
rs1390293418 227 dbSNP
rs1379499517 231 dbSNP
rs1304225890 232 dbSNP
rs1037555510 238 dbSNP
rs539732863 245 dbSNP
rs1208350262 248 dbSNP
rs1405083576 265 dbSNP
rs1491005622 265 dbSNP
rs199685547 265 dbSNP
rs34622075 265 dbSNP
rs565605009 265 dbSNP
rs71366664 265 dbSNP
rs78848135 265 dbSNP
rs886053784 265 dbSNP
rs77372929 266 dbSNP
rs1418571146 268 dbSNP
rs1414872313 270 dbSNP
rs921845212 271 dbSNP
rs1355942520 275 dbSNP
rs1462129889 279 dbSNP
rs1297112591 280 dbSNP
rs1348087150 282 dbSNP
rs1406761576 287 dbSNP
rs1466678731 292 dbSNP
rs1283811554 295 dbSNP
rs1344750218 298 dbSNP
rs76499577 300 dbSNP
rs1314154217 311 dbSNP
rs1243354943 313 dbSNP
rs11571514 323 dbSNP
rs1274782911 331 dbSNP
rs886053785 337 dbSNP
rs1051360288 358 dbSNP
rs1308303366 362 dbSNP
rs1321032411 367 dbSNP
rs1436965878 372 dbSNP
rs569631047 386 dbSNP
rs1382783748 389 dbSNP
rs535121145 392 dbSNP
rs1288202930 394 dbSNP
rs1350545552 395 dbSNP
rs1458295843 395 dbSNP
rs1165506635 397 dbSNP
rs935045766 398 dbSNP
rs995873867 401 dbSNP
rs1249749265 403 dbSNP
rs1189660808 407 dbSNP
rs115682894 408 dbSNP
rs1260337749 419 dbSNP
rs1223937701 422 dbSNP
rs1205060697 424 dbSNP
rs1192271300 434 dbSNP
rs1489067849 434 dbSNP
rs397858239 434 dbSNP
rs1268841837 441 dbSNP
rs188912525 442 dbSNP
rs1358334747 448 dbSNP
rs1479715678 449 dbSNP
rs1188677622 450 dbSNP
rs192439935 452 dbSNP
rs1420587546 457 dbSNP
rs1428821515 461 dbSNP
rs1169299785 462 dbSNP
rs1368205734 467 dbSNP
rs891918279 480 dbSNP
rs1294502984 484 dbSNP
rs1303176743 484 dbSNP
rs1387313361 485 dbSNP
rs1392734413 488 dbSNP
rs1011742518 491 dbSNP
rs1364896617 493 dbSNP
rs1422791670 496 dbSNP
rs1365262640 501 dbSNP
rs1021916795 502 dbSNP
rs1434125520 505 dbSNP
rs1463657133 507 dbSNP
rs111809301 512 dbSNP
rs906098807 515 dbSNP
rs1371728729 518 dbSNP
rs1001556763 519 dbSNP
rs79394299 526 dbSNP
rs1434299598 532 dbSNP
rs960160932 537 dbSNP
rs1490039637 538 dbSNP
rs113796695 539 dbSNP
rs1015007948 542 dbSNP
rs963578417 544 dbSNP
rs1250572158 546 dbSNP
rs1361809126 547 dbSNP
rs973198007 549 dbSNP
rs1281297333 555 dbSNP
rs1332802755 555 dbSNP
rs921876710 556 dbSNP
rs73939394 557 dbSNP
rs987110539 558 dbSNP
rs911512212 559 dbSNP
rs1394573129 560 dbSNP
rs563864981 561 dbSNP
rs1466869477 562 dbSNP
rs1432155143 564 dbSNP
rs1174924742 565 dbSNP
rs1251948065 571 dbSNP
rs529270236 572 dbSNP
rs1021755906 576 dbSNP
rs968507854 578 dbSNP
rs1435770814 579 dbSNP
rs980149227 581 dbSNP
rs379584 589 dbSNP
rs938583046 597 dbSNP
rs750011225 603 dbSNP
rs559858429 604 dbSNP
rs1222854314 614 dbSNP
rs528614995 617 dbSNP
rs1329718042 624 dbSNP
rs1289116479 627 dbSNP
rs1444425463 632 dbSNP
rs907706892 635 dbSNP
rs757977031 646 dbSNP
rs1185097343 652 dbSNP
rs1396762692 653 dbSNP
rs547577192 664 dbSNP
rs898539667 666 dbSNP
rs1469760008 669 dbSNP
rs1043227193 671 dbSNP
rs1163668749 673 dbSNP
rs906129534 674 dbSNP
rs1413317922 677 dbSNP
rs1159838950 684 dbSNP
rs1468154408 685 dbSNP
rs1362925330 686 dbSNP
rs1187836415 687 dbSNP
rs1384068550 689 dbSNP
rs1049732346 695 dbSNP
rs1202769391 705 dbSNP
rs1465318958 706 dbSNP
rs1286254378 713 dbSNP
rs889812359 718 dbSNP
rs570632488 727 dbSNP
rs1057158523 729 dbSNP
rs895846496 731 dbSNP
rs1385201922 734 dbSNP
rs533026179 736 dbSNP
rs1345610716 744 dbSNP
rs757972978 745 dbSNP
rs419499 749 dbSNP
rs1452337534 754 dbSNP
rs1318243174 759 dbSNP
rs1015453288 761 dbSNP
rs1021809854 763 dbSNP
rs968852593 764 dbSNP
rs963477530 773 dbSNP
rs979846174 776 dbSNP
rs1383629693 778 dbSNP
rs994648378 780 dbSNP
rs569886691 782 dbSNP
rs1446129564 799 dbSNP
rs953303909 810 dbSNP
rs535063283 811 dbSNP
rs1449830369 812 dbSNP
rs1243571749 819 dbSNP
rs911808704 819 dbSNP
rs1213563933 820 dbSNP
rs1033964311 825 dbSNP
rs1385281374 826 dbSNP
rs1283679861 827 dbSNP
rs7237593 833 dbSNP
rs573784202 835 dbSNP
rs987809073 837 dbSNP
rs1245778008 841 dbSNP
rs992700861 841 dbSNP
rs754636855 842 dbSNP
rs1272229484 845 dbSNP
rs61506158 851 dbSNP
rs780922074 857 dbSNP
rs1429259438 858 dbSNP
rs11877289 869 dbSNP
rs151283676 875 dbSNP
rs1316789792 877 dbSNP
rs1207232065 880 dbSNP
rs557614872 886 dbSNP
rs1363405715 889 dbSNP
rs1162544600 891 dbSNP
rs927407331 895 dbSNP
rs1462427491 911 dbSNP
rs931368314 913 dbSNP
rs1475065965 918 dbSNP
rs1049866331 923 dbSNP
rs1183805502 929 dbSNP
rs182360931 931 dbSNP
rs1289596082 935 dbSNP
rs773136450 945 dbSNP
rs1222037794 946 dbSNP
rs889782687 957 dbSNP
rs943982292 964 dbSNP
rs1159753455 966 dbSNP
rs937491216 971 dbSNP
rs1339377849 973 dbSNP
rs1284481128 975 dbSNP
rs1407226045 977 dbSNP
rs1343112909 978 dbSNP
rs1301938547 982 dbSNP
rs1410088536 985 dbSNP
rs1057513384 989 dbSNP
rs1355889250 994 dbSNP
rs1408658985 1000 dbSNP
rs896057609 1001 dbSNP
rs447982 1002 dbSNP
rs1425866344 1007 dbSNP
rs768591600 1014 dbSNP
rs56385005 1015 dbSNP
rs1266887555 1017 dbSNP
rs892016340 1017 dbSNP
rs1198730506 1018 dbSNP
rs1408028441 1027 dbSNP
rs1022192641 1040 dbSNP
rs1453730506 1040 dbSNP
rs1437618274 1041 dbSNP
rs1264083498 1043 dbSNP
rs1225911714 1048 dbSNP
rs904718447 1054 dbSNP
rs1001232479 1055 dbSNP
rs1223831019 1057 dbSNP
rs1034103207 1059 dbSNP
rs387462 1060 dbSNP
rs777674417 1065 dbSNP
rs1440934170 1081 dbSNP
rs1338396737 1088 dbSNP
rs1468192703 1095 dbSNP
rs899268634 1101 dbSNP
rs1175871012 1105 dbSNP
rs1419745753 1109 dbSNP
rs555341726 1110 dbSNP
rs1175716290 1111 dbSNP
rs1373250244 1115 dbSNP
rs866674874 1115 dbSNP
rs1028784771 1116 dbSNP
rs1205935966 1134 dbSNP
rs1460409041 1137 dbSNP
rs543010815 1142 dbSNP
rs1263046836 1162 dbSNP
rs559795406 1168 dbSNP
rs528547920 1169 dbSNP
rs1019306728 1170 dbSNP
rs1324689176 1173 dbSNP
rs956628818 1177 dbSNP
rs1316943797 1180 dbSNP
rs1450173399 1183 dbSNP
rs988228444 1185 dbSNP
rs867378667 1186 dbSNP
rs1405351338 1191 dbSNP
rs1203949386 1194 dbSNP
rs973364901 1195 dbSNP
rs1347062674 1197 dbSNP
rs186653381 1201 dbSNP
rs1418763357 1203 dbSNP
rs980557238 1221 dbSNP
rs1440292107 1224 dbSNP
rs1183374939 1225 dbSNP
rs74692024 1226 dbSNP
rs985537640 1235 dbSNP
rs911276306 1239 dbSNP
rs1472263911 1243 dbSNP
rs1487106844 1244 dbSNP
rs1258464222 1245 dbSNP
rs944119546 1246 dbSNP
rs191807591 1248 dbSNP
rs937522270 1250 dbSNP
rs377760755 1259 dbSNP
rs1295970179 1273 dbSNP
rs1383885761 1282 dbSNP
rs946278650 1283 dbSNP
rs1431230129 1284 dbSNP
rs920451556 1284 dbSNP
rs142659618 1285 dbSNP
rs917508077 1286 dbSNP
rs1165705537 1292 dbSNP
rs527358457 1295 dbSNP
rs940924325 1307 dbSNP
rs904688033 1312 dbSNP
rs1194293434 1313 dbSNP
rs1001618049 1321 dbSNP
rs1055895462 1327 dbSNP
rs895540385 1330 dbSNP
rs1036779030 1333 dbSNP
rs1329696556 1339 dbSNP
rs1335231220 1349 dbSNP
rs563563268 1350 dbSNP
rs1270345032 1359 dbSNP
rs1408588067 1361 dbSNP
rs1285713065 1363 dbSNP
rs1014983712 1377 dbSNP
rs1346650414 1398 dbSNP
rs899132819 1403 dbSNP
rs961763703 1406 dbSNP
rs878991153 1408 dbSNP
rs115310714 1409 dbSNP
rs1342443188 1413 dbSNP
rs371274241 1420 dbSNP
rs1197180200 1423 dbSNP
rs1390244849 1423 dbSNP
rs953284628 1430 dbSNP
rs183989261 1434 dbSNP
rs985935023 1435 dbSNP
rs1481023822 1436 dbSNP
rs1009168534 1438 dbSNP
rs7229123 1441 dbSNP
rs1202991027 1443 dbSNP
rs892387690 1446 dbSNP
rs1480687119 1452 dbSNP
rs1197906894 1453 dbSNP
rs1250780456 1453 dbSNP
rs534356712 1470 dbSNP
rs1479538475 1474 dbSNP
rs1250491303 1480 dbSNP
rs1224070523 1483 dbSNP
rs1009449985 1484 dbSNP
rs965437261 1485 dbSNP
rs570806457 1487 dbSNP
rs1330796728 1489 dbSNP
rs1329800132 1494 dbSNP
rs1393306618 1495 dbSNP
rs75802730 1496 dbSNP
rs1470612763 1505 dbSNP
rs1432055912 1515 dbSNP
rs946109384 1524 dbSNP
rs967741872 1526 dbSNP
rs1477406424 1528 dbSNP
rs1363802566 1531 dbSNP
rs1183552734 1532 dbSNP
rs1427939544 1542 dbSNP
rs768722857 1544 dbSNP
rs776918562 1548 dbSNP
rs571281600 1558 dbSNP
rs926191405 1559 dbSNP
rs937606793 1568 dbSNP
rs1055865661 1569 dbSNP
rs1202885309 1571 dbSNP
rs762214670 1571 dbSNP
rs1033454185 1573 dbSNP
rs1344421513 1574 dbSNP
rs1404807068 1594 dbSNP
rs1241489152 1595 dbSNP
rs1280164808 1595 dbSNP
rs896012144 1609 dbSNP
rs189841534 1614 dbSNP
rs993418766 1630 dbSNP
rs917390591 1631 dbSNP
rs775588547 1645 dbSNP
rs972381844 1647 dbSNP
rs1385077543 1650 dbSNP
rs920836633 1668 dbSNP
rs1159751975 1670 dbSNP
rs371106320 1671 dbSNP
rs1050366566 1688 dbSNP
rs1184030223 1689 dbSNP
rs889215403 1692 dbSNP
rs1270384555 1699 dbSNP
rs1446219570 1703 dbSNP
rs1027748068 1711 dbSNP
rs1186783085 1718 dbSNP
rs1340977955 1719 dbSNP
rs1447474370 1723 dbSNP
rs1225558813 1726 dbSNP
rs557288530 1729 dbSNP
rs374442511 1733 dbSNP
rs892339257 1735 dbSNP
rs1246903205 1736 dbSNP
rs7243976 1736 dbSNP
rs1313310360 1740 dbSNP
rs574344173 1742 dbSNP
rs185233500 1743 dbSNP
rs1389807940 1750 dbSNP
rs536950326 1754 dbSNP
rs1001888802 1761 dbSNP
rs1165553561 1765 dbSNP
rs1033318338 1773 dbSNP
rs553750148 1778 dbSNP
rs967873870 1782 dbSNP
rs960745660 1783 dbSNP
rs1487352654 1784 dbSNP
rs140487684 1785 dbSNP
rs1223528983 1787 dbSNP
rs754166400 1793 dbSNP
rs1361805651 1797 dbSNP
rs1228081358 1807 dbSNP
rs1457896854 1809 dbSNP
rs1015756013 1816 dbSNP
rs763595571 1818 dbSNP
rs374533251 1824 dbSNP
rs1292272484 1827 dbSNP
rs1363311185 1828 dbSNP
rs1387649912 1830 dbSNP
rs1322717719 1842 dbSNP
rs1410318989 1842 dbSNP
rs962270956 1843 dbSNP
rs950256387 1849 dbSNP
rs1383161469 1853 dbSNP
rs1423043834 1856 dbSNP
rs1200195514 1857 dbSNP
rs1245184730 1864 dbSNP
rs1490915851 1864 dbSNP
rs972628496 1865 dbSNP
rs765893274 1866 dbSNP
rs1317817002 1867 dbSNP
rs952273167 1873 dbSNP
rs545108904 1876 dbSNP
rs1365130013 1878 dbSNP
rs1273888730 1882 dbSNP
rs986106121 1884 dbSNP
rs1356083397 1885 dbSNP
rs1048707762 1892 dbSNP
rs910515458 1899 dbSNP
rs1406702960 1904 dbSNP
rs1177311412 1920 dbSNP
rs1481454715 1921 dbSNP
rs1423066936 1923 dbSNP
rs1190839051 1924 dbSNP
rs1007474634 1925 dbSNP
rs1235003715 1930 dbSNP
rs1018912788 1949 dbSNP
rs7229926 1957 dbSNP
rs1263642559 1958 dbSNP
rs1009369463 1960 dbSNP
rs1021219680 1965 dbSNP
rs967464535 1977 dbSNP
rs1224022654 1982 dbSNP
rs575672245 1996 dbSNP
rs1040498942 1998 dbSNP
rs1445756098 2017 dbSNP
rs1205517821 2019 dbSNP
rs913964200 2020 dbSNP
rs945253721 2026 dbSNP
rs1463766427 2034 dbSNP
rs190498550 2038 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 GSM1462573. RNA binding protein: AGO2. Condition:TZM-bl 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' ugcAAAUUUAAAGUGGGGAAGa 5'
             |||   || | ||||||| 
Target 5' auuUUUUUUUUCCUCCCCUUCc 3'
1 - 22
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 GSM1462573
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl BaL
Location of target site ENST00000330513.5 | 3UTR | AUUUUUUUUUUCCUCCCCUUCCCUUUUUUUG
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
Click to see details
133 hsa-miR-3179 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT102087 GIGYF1 GRB10 interacting GYF protein 1 2 4
MIRT110061 OGT O-linked N-acetylglucosamine (GlcNAc) transferase 2 6
MIRT112198 BTG2 BTG anti-proliferation factor 2 2 2
MIRT117668 SCAMP4 secretory carrier membrane protein 4 2 2
MIRT146657 MINK1 misshapen like kinase 1 2 2
MIRT175505 ZBTB33 zinc finger and BTB domain containing 33 2 4
MIRT180535 TXNIP thioredoxin interacting protein 2 2
MIRT190624 BCL2L2-PABPN1 BCL2L2-PABPN1 readthrough 2 2
MIRT190650 PABPN1 poly(A) binding protein nuclear 1 2 2
MIRT366902 NONO non-POU domain containing octamer binding 2 2
MIRT443554 ZFP3 ZFP3 zinc finger protein 2 2
MIRT445953 MLLT11 MLLT11, transcription factor 7 cofactor 2 2
MIRT446042 HMCN1 hemicentin 1 2 2
MIRT447968 MSH6 mutS homolog 6 2 2
MIRT448634 ONECUT1 one cut homeobox 1 2 2
MIRT449316 MRO maestro 2 2
MIRT451380 C19orf43 telomerase RNA component interacting RNase 2 2
MIRT451547 CIAPIN1 cytokine induced apoptosis inhibitor 1 2 2
MIRT451807 CDCA3 cell division cycle associated 3 2 4
MIRT451916 ILK integrin linked kinase 2 2
MIRT451938 TMPRSS5 transmembrane protease, serine 5 2 2
MIRT452189 KIAA1456 KIAA1456 2 2
MIRT452498 HMGXB3 HMG-box containing 3 2 2
MIRT452548 ZNF467 zinc finger protein 467 2 2
MIRT453844 SDK1 sidekick cell adhesion molecule 1 2 2
MIRT454515 ZFYVE27 zinc finger FYVE-type containing 27 2 2
MIRT455363 KDM5C lysine demethylase 5C 2 2
MIRT455455 EPB41L4B erythrocyte membrane protein band 4.1 like 4B 2 2
MIRT455628 PABPC1L2B poly(A) binding protein cytoplasmic 1 like 2B 2 10
MIRT455639 PABPC1L2A poly(A) binding protein cytoplasmic 1 like 2A 2 10
MIRT455690 GLO1 glyoxalase I 2 2
MIRT456300 ASH1L ASH1 like histone lysine methyltransferase 2 2
MIRT456784 MTHFSD methenyltetrahydrofolate synthetase domain containing 2 2
MIRT456819 PIGP phosphatidylinositol glycan anchor biosynthesis class P 2 2
MIRT457566 ZNF34 zinc finger protein 34 2 2
MIRT457604 IDS iduronate 2-sulfatase 2 2
MIRT458236 NXPH3 neurexophilin 3 2 2
MIRT458313 TNFAIP8L3 TNF alpha induced protein 8 like 3 2 2
MIRT458350 NOC2L NOC2 like nucleolar associated transcriptional repressor 2 2
MIRT458670 GPR35 G protein-coupled receptor 35 2 2
MIRT459675 VPS37C VPS37C, ESCRT-I subunit 2 2
MIRT461126 RAB36 RAB36, member RAS oncogene family 2 2
MIRT461918 NECAB3 N-terminal EF-hand calcium binding protein 3 2 2
MIRT462301 PPM1H protein phosphatase, Mg2+/Mn2+ dependent 1H 2 2
MIRT463520 ZBTB7B zinc finger and BTB domain containing 7B 2 2
MIRT464378 URM1 ubiquitin related modifier 1 2 2
MIRT464614 UBE4B ubiquitination factor E4B 2 2
MIRT464711 UBE2V1 ubiquitin conjugating enzyme E2 V1 2 2
MIRT465520 PRICKLE4 prickle planar cell polarity protein 4 2 2
MIRT465974 TMEM189-UBE2V1 TMEM189-UBE2V1 readthrough 2 2
MIRT466058 TMEM189 transmembrane protein 189 2 2
MIRT466548 TBL1XR1 transducin beta like 1 X-linked receptor 1 2 2
MIRT466647 TAGLN2 transgelin 2 2 2
MIRT467357 SP2 Sp2 transcription factor 2 2
MIRT468744 SDC2 syndecan 2 2 2
MIRT470244 PRRC2A proline rich coiled-coil 2A 2 2
MIRT471426 PDIA6 protein disulfide isomerase family A member 6 2 2
MIRT471732 OTUB1 OTU deubiquitinase, ubiquitin aldehyde binding 1 2 2
MIRT472190 NHP2L1 small nuclear ribonucleoprotein 13 2 2
MIRT472450 NAV2 neuron navigator 2 2 6
MIRT474563 KLHDC3 kelch domain containing 3 2 2
MIRT474936 KCTD15 potassium channel tetramerization domain containing 15 2 2
MIRT475165 IP6K1 inositol hexakisphosphate kinase 1 2 2
MIRT475399 ICMT isoprenylcysteine carboxyl methyltransferase 2 4
MIRT475426 ICK intestinal cell kinase 2 2
MIRT477090 FAM168A family with sequence similarity 168 member A 2 2
MIRT478458 DAB2 DAB2, clathrin adaptor protein 2 2
MIRT478953 COX15 COX15, cytochrome c oxidase assembly homolog 2 2
MIRT480096 CALR calreticulin 2 2
MIRT481924 ANKRD33B ankyrin repeat domain 33B 2 2
MIRT483217 APOA1 apolipoprotein A1 2 6
MIRT483882 TGIF1 TGFB induced factor homeobox 1 2 2
MIRT483923 SPSB1 splA/ryanodine receptor domain and SOCS box containing 1 2 2
MIRT483942 LENG8 leukocyte receptor cluster member 8 2 4
MIRT484209 SUMO1 small ubiquitin-like modifier 1 2 2
MIRT484512 SYT7 synaptotagmin 7 2 2
MIRT484709 RNF11 ring finger protein 11 2 2
MIRT485356 MYO1C myosin IC 2 4
MIRT485615 FOSL1 FOS like 1, AP-1 transcription factor subunit 2 4
MIRT486584 ZNF619 zinc finger protein 619 2 2
MIRT487013 C2orf82 chromosome 2 open reading frame 82 2 2
MIRT487621 C20orf96 chromosome 20 open reading frame 96 2 2
MIRT487801 GPR20 G protein-coupled receptor 20 2 4
MIRT488134 GPR107 G protein-coupled receptor 107 2 2
MIRT488773 FXYD1 FXYD domain containing ion transport regulator 1 2 2
MIRT488854 UBTF upstream binding transcription factor, RNA polymerase I 2 2
MIRT489783 GRINA glutamate ionotropic receptor NMDA type subunit associated protein 1 2 2
MIRT490102 FN3K fructosamine 3 kinase 2 2
MIRT490389 LHFPL3 LHFPL tetraspan subfamily member 3 2 2
MIRT490434 MYL9 myosin light chain 9 2 2
MIRT490451 GLUD1 glutamate dehydrogenase 1 2 2
MIRT490880 OSBP oxysterol binding protein 2 2
MIRT491037 ALPK3 alpha kinase 3 2 2
MIRT491250 HCN2 hyperpolarization activated cyclic nucleotide gated potassium and sodium channel 2 2 2
MIRT491748 SEMA3F semaphorin 3F 2 2
MIRT492235 SLC48A1 solute carrier family 48 member 1 2 2
MIRT492490 RAPGEF1 Rap guanine nucleotide exchange factor 1 2 2
MIRT492505 RANBP10 RAN binding protein 10 2 4
MIRT492773 PDGFB platelet derived growth factor subunit B 2 2
MIRT492922 NFAT5 nuclear factor of activated T-cells 5 2 2
MIRT493459 ITFG3 family with sequence similarity 234 member A 2 2
MIRT493654 HDLBP high density lipoprotein binding protein 2 2
MIRT494011 DUSP9 dual specificity phosphatase 9 2 2
MIRT499412 PLCG2 phospholipase C gamma 2 2 4
MIRT499552 C15orf43 telomere repeat binding bouquet formation protein 2 2 2
MIRT501836 NCOA2 nuclear receptor coactivator 2 2 2
MIRT501950 MAT2A methionine adenosyltransferase 2A 2 10
MIRT504066 KCTD12 potassium channel tetramerization domain containing 12 2 4
MIRT504509 PPP1R9B protein phosphatase 1 regulatory subunit 9B 2 2
MIRT508466 HOXB6 homeobox B6 2 4
MIRT512373 CPM carboxypeptidase M 2 2
MIRT513578 EVX1 even-skipped homeobox 1 2 2
MIRT517763 ZNF366 zinc finger protein 366 2 4
MIRT519773 ZNF354B zinc finger protein 354B 2 8
MIRT523568 GGCX gamma-glutamyl carboxylase 2 4
MIRT532802 CLDN11 claudin 11 2 2
MIRT544299 TSPYL1 TSPY like 1 2 2
MIRT544862 MYH2 myosin heavy chain 2 2 4
MIRT556731 KLHL15 kelch like family member 15 2 4
MIRT564347 AKR1B10 aldo-keto reductase family 1 member B10 2 2
MIRT568924 SMCR8 Smith-Magenis syndrome chromosome region, candidate 8 2 2
MIRT569012 CXorf36 chromosome X open reading frame 36 2 2
MIRT569256 FAM129B family with sequence similarity 129 member B 2 2
MIRT569591 PRELP proline and arginine rich end leucine rich repeat protein 2 2
MIRT569779 SAMD14 sterile alpha motif domain containing 14 2 2
MIRT570034 FAM228A family with sequence similarity 228 member A 2 2
MIRT573803 FRMPD4 FERM and PDZ domain containing 4 2 2
MIRT574190 ZNF264 zinc finger protein 264 2 2
MIRT576153 Hmox1 heme oxygenase 1 2 2
MIRT611311 CA8 carbonic anhydrase 8 2 4
MIRT673429 APAF1 apoptotic peptidase activating factor 1 2 2
MIRT674976 SH3BP2 SH3 domain binding protein 2 2 2
MIRT692712 MEAF6 MYST/Esa1 associated factor 6 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-3179 Gemcitabine 60750 NSC613327 approved resistant High Pancreatic Cancer cell line (AsPC-1)
hsa-miR-3179 Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-3179 Gefitinib 123631 NSC715055 approved sensitive cell line (PC9)
hsa-miR-3179 Osimertinib 71496458 NSC779217 approved sensitive cell line (HCC827)
hsa-miR-3179 Osimertinib 71496458 NSC779217 approved sensitive cell line (PC9)
hsa-miR-3179 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-3179 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (100 ng/ml)
hsa-miR-3179 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)

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