miRTarBase - #MIRT453653


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pre-miRNA Information
pre-miRNA hsa-mir-5590   
Genomic Coordinates chr2: 134857820 - 134857873
Description Homo sapiens miR-5590 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-5590-5p
Sequence 1| UUGCCAUACAUAGACUUUAUU |21
Evidence Not_experimental
Experiments
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs553031425 1 dbSNP
rs1255264134 4 dbSNP
rs1205476379 9 dbSNP
rs1387316331 10 dbSNP
rs1031241138 11 dbSNP
rs1465409255 12 dbSNP
rs1227248415 18 dbSNP
rs1334861447 19 dbSNP
Putative Targets

Gene Information
Gene Symbol RAB6C   
Synonyms WTH3
Description RAB6C, member RAS oncogene family
Transcript NM_032144   
Expression
Putative miRNA Targets on RAB6C
3'UTR of RAB6C
(miRNA target sites are highlighted)		 
>RAB6C|NM_032144|3'UTR
   1 TCTATTAGCTTCACAAGCACAAAAAAAGTCAGCGTCTTCATTATTTATATTTTACAAAAAGCCAAATTATTTCAGCATAT
  81 TCCGGTGATAACTTTAAAAATTAGATACATTTTCTTAACATTTTTTTCTTTTTTAATGTTATGATAATGTACTTCAAAAT
 161 GATGGAAATCTCAACAGTATGAGTATGGCTTGGTTAACGAGCAGTATGTTCACAGCCTGCTTTATCTCTCCTTGCTCTTC
 241 TCACCTCTCCCTTACCCCGTTCCCTATTTCCGTGTTCTTACCTAGCCTCCCCCCACTTCCTCAAAACAAACAAGAGATGG
 321 CAAAGCAGCAGTCCGACCAAGCCCACTGGAATTATCCTTTAATTTTACAGATACCACTTGCTGTAGGCTGTGGACCAAGA
 401 TGTCCAGAATTATTCTTGAGCACTGATGTAAATTACTTAGATCTTCTTTGAGGTCAGAATTCAGCGATCACGGTAGGCAG
 481 TGCTTGAATGAGAAAAGCCTCCTGGTGCATCTTCAAAATGAGTCCTAAAGAACATACTGAGTACTTATAAGTAGCAGAAC
 561 ATAAAATGTATTTCTGACTAACACAAATGGTCCTTTCACATGTGCTTTATTAGACTCTGGGAGAGAAAAGTAACCAAGTG
 641 CTTCAGAACAGGTTTTTAGTATTTACTTCTTCATGGTAAGATAATGAAGTTCTAATGAACTATTTCTCCCAAGGTTTTAA
 721 AATTGTCAAGAGTTATTCTGTTTGTTTAAAAAGTAAGAAACCTCTGTAAGCAATAGATTTTGCTTGGGTTTTCTTTCTTA
 801 AAAAAATAATACTATGCAGGCAAGACACCATAAAAGTTTAATTCCTTACAGAAGAACCAGTGGAAGAATTTAAATTTGGC
 881 ACTACGATCAAAACTACTGAATTAGCAGAAATAACGATATCTAAAGCTTACCAGCAAAAGAACCCTCAGCAGAATAGCAA
 961 AAACTTTGCTCAGGACATTTGAGGTCAAATTGAAGACGGAAGACGGAAGACGGAAACCGGAAACCGTTTTCTTGTAAGCC
1041 CCTAGAGGCAGATCAGGTAAAGCATACATAGTAGAGGGAAAGGAGAGAATGGAAATAAAACTGAATATTATGCAGATTTA
1121 TGCCTTATTTTTTAGCATTTTTTAAGGTTGGGTCTTTCAGGCTGGTTTTGGTTTGTATTAGATCTGTATAGTTTAACTAG
1201 TGATTTAGTTTTATATTTAAGCTACGATTAATATTTTTTCTTTGGCGATATTTCTTTGCTTTTTTTTTTTTTAACAACTT
1281 TCCATTTTTAGATGTTTCGTTGAATCTATTTAGAGCTTCACCATGGCAATATGTATTTCCCTTAAAACACTGCAAACAAA
1361 TATACTAGGAGTGTGCCCTTTTAATCTTTACTAGTTATTGTGAGATTGCTGTGTAAGCTAATAAACACATTTGTAAATAC
1441 ATTGTTTGCAGGAAGAAAACTTCGAGTTACAGGTCAGGAAAAGCCTGCTGAATTTATGTTGTAAACGTTACTTAACACAG
1521 TATAAAGATGAAAAGACAACAAAAGTATCTTCATACTTCCTCATCCCCTCATTGCAACAAAACCTTAAACTGGGAGAACC
1601 TTAGTCCCCTCTCTTTCCTCTTCCTCCTCCACTTCCCACTTATTGTCACTTTGTAATATTCAGAGAGCACTTGGATTATG
1681 GATCTGAATAGAGAAATGCTTACAGATAATCATTAGCCCACATACCAGTAACTTATACTTAAAGATGGGATGGAGTTATA
1761 AAGTGCTTTTATAATACAATATAATTGCTAAAGGCAAGGGTTGACTCTTTGTTTTATTTTGACATGGCATGTCCTGAAAT
1841 AAATATTGATTCACTATG
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' uuaUUUCAGAUACAUACCGuu 5'
             | ||| |: |||||||  
Target 5' tcaACAGTATGAGTATGGCtt 3'
 171 - 191 142.00 -10.60
2 
miRNA  3' uuAUUUCAGAUACAUACCGUu 5'
            ||:|| :|    |||||| 
Target 5' ttTAGAGCTTCACCATGGCAa 3'
 1309 - 1329 123.00 -9.70
3 
miRNA  3' uuauuucagauacaUACCGUu 5'
                        |||||| 
Target 5' aaaacaaacaagagATGGCAa 3'
 303 - 323 120.00 -7.70
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN15626057 13 COSMIC
COSN30504367 17 COSMIC
COSN30126140 35 COSMIC
COSN30513114 85 COSMIC
COSN31551157 86 COSMIC
COSN30470266 88 COSMIC
COSN31507320 90 COSMIC
COSN31495736 91 COSMIC
COSN30456964 99 COSMIC
COSN510303 116 COSMIC
COSN31580533 123 COSMIC
COSN31534853 129 COSMIC
COSN30172526 162 COSMIC
COSN26650146 198 COSMIC
COSN31522226 252 COSMIC
COSN31600758 272 COSMIC
COSN30534488 275 COSMIC
COSN26396536 335 COSMIC
COSN31547346 416 COSMIC
COSN31571035 444 COSMIC
COSN30131016 447 COSMIC
COSN28830364 467 COSMIC
COSN26558151 472 COSMIC
COSN30142901 484 COSMIC
COSN14884236 493 COSMIC
COSN8607237 544 COSMIC
COSN31537699 599 COSMIC
COSN31585391 734 COSMIC
COSN15626058 739 COSMIC
COSN23987833 758 COSMIC
COSN30535028 813 COSMIC
COSN30132696 886 COSMIC
COSN8607238 898 COSMIC
COSN7337285 916 COSMIC
COSN31483989 936 COSMIC
COSN9080183 940 COSMIC
COSN31514836 964 COSMIC
COSN30533847 968 COSMIC
COSN30533858 969 COSMIC
COSN30307043 976 COSMIC
COSN30142846 979 COSMIC
COSN22513034 987 COSMIC
COSN30119275 1006 COSMIC
COSN8607239 1010 COSMIC
COSN8607240 1011 COSMIC
COSN31513144 1012 COSMIC
COSN26669843 1027 COSMIC
COSN31529422 1030 COSMIC
COSN9858934 1045 COSMIC
COSN20097147 1080 COSMIC
COSN30113813 1155 COSMIC
COSN31530523 1155 COSMIC
COSN20097148 1197 COSMIC
COSN20097149 1197 COSMIC
COSN30133887 1226 COSMIC
COSN15626060 1227 COSMIC
COSN31530524 1241 COSMIC
COSN30120393 1243 COSMIC
COSN31548963 1247 COSMIC
COSN31585823 1255 COSMIC
COSN26647280 1259 COSMIC
COSN15626061 1267 COSMIC
COSN20097152 1272 COSMIC
COSN30173572 1273 COSMIC
COSN31520622 1299 COSMIC
COSN30129397 1380 COSMIC
COSN30142046 1394 COSMIC
COSN30538554 1449 COSMIC
COSN8267923 1454 COSMIC
COSN25964939 1462 COSMIC
COSN5480864 1499 COSMIC
COSN30117299 1520 COSMIC
COSN8607241 1531 COSMIC
COSN31588174 1532 COSMIC
COSN31547748 1536 COSMIC
COSN15626062 1555 COSMIC
COSN31479896 1607 COSMIC
COSN15626063 1618 COSMIC
COSN15626064 1637 COSMIC
COSN15297808 1690 COSMIC
COSN28648573 1692 COSMIC
COSN31535301 1694 COSMIC
COSN8607242 1704 COSMIC
COSN9858935 1724 COSMIC
COSN26668140 1759 COSMIC
COSN26668423 1788 COSMIC
COSN15626065 1835 COSMIC
COSN217035 1849 COSMIC
COSN26667966 1858 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs535568191 5 dbSNP
rs771589595 6 dbSNP
rs774959506 7 dbSNP
rs1421609572 13 dbSNP
rs1316819414 14 dbSNP
rs1416571518 15 dbSNP
rs1160642495 16 dbSNP
rs1407293846 19 dbSNP
rs752243244 21 dbSNP
rs760138408 21 dbSNP
rs200163845 23 dbSNP
rs772545001 24 dbSNP
rs1433324872 31 dbSNP
rs775713705 32 dbSNP
rs761565605 33 dbSNP
rs1187140286 34 dbSNP
rs764773732 37 dbSNP
rs749954911 39 dbSNP
rs762405886 44 dbSNP
rs766304499 48 dbSNP
rs751444809 50 dbSNP
rs181121537 53 dbSNP
rs1190924963 56 dbSNP
rs568771728 66 dbSNP
rs1315084996 68 dbSNP
rs894164273 82 dbSNP
rs1340889527 84 dbSNP
rs995403280 96 dbSNP
rs1274542484 105 dbSNP
rs1026930563 106 dbSNP
rs866996080 108 dbSNP
rs185972652 109 dbSNP
rs1454985595 115 dbSNP
rs1384000923 119 dbSNP
rs1209208427 120 dbSNP
rs191016775 121 dbSNP
rs1484578664 123 dbSNP
rs1402777116 124 dbSNP
rs1201869796 129 dbSNP
rs1171373777 130 dbSNP
rs1256383801 131 dbSNP
rs112652268 135 dbSNP
rs1424827432 136 dbSNP
rs1187656932 137 dbSNP
rs1019445991 139 dbSNP
rs966489283 144 dbSNP
rs976204580 145 dbSNP
rs1459790587 148 dbSNP
rs1234310328 164 dbSNP
rs1204768809 175 dbSNP
rs1306418899 177 dbSNP
rs1270200630 182 dbSNP
rs1248827195 188 dbSNP
rs1360740798 189 dbSNP
rs573121904 200 dbSNP
rs540025314 204 dbSNP
rs932013369 208 dbSNP
rs1441666741 209 dbSNP
rs1352851486 220 dbSNP
rs1304981397 232 dbSNP
rs990355356 235 dbSNP
rs914865551 243 dbSNP
rs1162835761 251 dbSNP
rs1363350595 257 dbSNP
rs1442615868 258 dbSNP
rs1409803748 259 dbSNP
rs555159796 260 dbSNP
rs1177437118 265 dbSNP
rs1480077012 268 dbSNP
rs946306693 272 dbSNP
rs573770969 273 dbSNP
rs1042247201 283 dbSNP
rs1291767019 289 dbSNP
rs1244420936 290 dbSNP
rs200908298 295 dbSNP
rs1223452793 296 dbSNP
rs1403169434 299 dbSNP
rs938409104 308 dbSNP
rs1285398123 312 dbSNP
rs1055570295 321 dbSNP
rs1414336330 327 dbSNP
rs1310851063 344 dbSNP
rs1456275953 348 dbSNP
rs1346768272 364 dbSNP
rs894131696 371 dbSNP
rs1418252339 372 dbSNP
rs562362099 375 dbSNP
rs1201121653 376 dbSNP
rs1480518169 394 dbSNP
rs1267478097 396 dbSNP
rs1228954127 398 dbSNP
rs1306174787 399 dbSNP
rs1048337021 417 dbSNP
rs1261713080 429 dbSNP
rs886985540 436 dbSNP
rs1234776869 441 dbSNP
rs1354194405 442 dbSNP
rs1256284584 445 dbSNP
rs1004141129 457 dbSNP
rs1485146308 463 dbSNP
rs1281400598 464 dbSNP
rs1208194415 466 dbSNP
rs1019837380 467 dbSNP
rs1364033873 469 dbSNP
rs1289351374 470 dbSNP
rs1452861446 471 dbSNP
rs1386179556 472 dbSNP
rs1178152492 485 dbSNP
rs1469948194 486 dbSNP
rs965258505 495 dbSNP
rs1196080323 503 dbSNP
rs997997216 510 dbSNP
rs1255883483 514 dbSNP
rs533164970 523 dbSNP
rs1186434039 525 dbSNP
rs1245287688 526 dbSNP
rs1204571475 535 dbSNP
rs1323044029 541 dbSNP
rs780520844 543 dbSNP
rs776311411 549 dbSNP
rs1229762666 560 dbSNP
rs1308135329 562 dbSNP
rs1183589524 567 dbSNP
rs545431691 575 dbSNP
rs560601136 576 dbSNP
rs1362790480 585 dbSNP
rs1338405635 592 dbSNP
rs964007993 594 dbSNP
rs528024637 601 dbSNP
rs1404954002 610 dbSNP
rs1170424933 614 dbSNP
rs1378208441 617 dbSNP
rs1373084734 628 dbSNP
rs1434373364 631 dbSNP
rs1170374292 632 dbSNP
rs549563977 635 dbSNP
rs1171959913 636 dbSNP
rs1245388991 639 dbSNP
rs1184631984 645 dbSNP
rs1461127666 650 dbSNP
rs201766390 659 dbSNP
rs1254401509 669 dbSNP
rs1372229848 674 dbSNP
rs1197769640 678 dbSNP
rs1410172020 700 dbSNP
rs1297606705 703 dbSNP
rs1371076011 709 dbSNP
rs11903479 712 dbSNP
rs369003700 715 dbSNP
rs1246506102 725 dbSNP
rs1346464335 729 dbSNP
rs914584312 730 dbSNP
rs1392711316 732 dbSNP
rs967575606 735 dbSNP
rs1297066633 740 dbSNP
rs1427227493 748 dbSNP
rs769299540 756 dbSNP
rs1164754362 762 dbSNP
rs928776686 773 dbSNP
rs1367014483 779 dbSNP
rs547964323 788 dbSNP
rs766511963 798 dbSNP
rs773116651 800 dbSNP
rs1205651267 803 dbSNP
rs1203160327 805 dbSNP
rs1490854874 807 dbSNP
rs371246716 811 dbSNP
rs1223131251 813 dbSNP
rs184069403 814 dbSNP
rs1479946939 829 dbSNP
rs1193390600 834 dbSNP
rs1240781819 834 dbSNP
rs568972166 836 dbSNP
rs1268176730 841 dbSNP
rs1453849520 842 dbSNP
rs1055940826 856 dbSNP
rs1192029431 857 dbSNP
rs915701060 864 dbSNP
rs111531418 867 dbSNP
rs1304282615 878 dbSNP
rs1424522067 887 dbSNP
rs1389056376 889 dbSNP
rs1048056823 892 dbSNP
rs886786458 904 dbSNP
rs749108547 916 dbSNP
rs1040996879 922 dbSNP
rs539044950 927 dbSNP
rs1481499339 934 dbSNP
rs1269617497 935 dbSNP
rs1200086113 936 dbSNP
rs1450921268 936 dbSNP
rs1287603975 938 dbSNP
rs1352473356 947 dbSNP
rs1351109132 950 dbSNP
rs1267172041 951 dbSNP
rs1226116810 953 dbSNP
rs557772118 956 dbSNP
rs1404918739 957 dbSNP
rs1329903962 960 dbSNP
rs1320824037 965 dbSNP
rs900994109 965 dbSNP
rs566396645 972 dbSNP
rs533858977 977 dbSNP
rs1471049409 979 dbSNP
rs112677904 992 dbSNP
rs559122050 992 dbSNP
rs953432420 992 dbSNP
rs1438074250 998 dbSNP
rs1299442823 1001 dbSNP
rs1365493649 1002 dbSNP
rs1213560233 1004 dbSNP
rs555098050 1004 dbSNP
rs1272782062 1005 dbSNP
rs1011632452 1006 dbSNP
rs1306079147 1008 dbSNP
rs1244969319 1009 dbSNP
rs67910912 1010 dbSNP
rs72863817 1011 dbSNP
rs1247118801 1012 dbSNP
rs1206464396 1014 dbSNP
rs1325197385 1021 dbSNP
rs1263345178 1022 dbSNP
rs1218182915 1026 dbSNP
rs1021559363 1030 dbSNP
rs1272500931 1034 dbSNP
rs1432027635 1035 dbSNP
rs1224493981 1038 dbSNP
rs564445582 1043 dbSNP
rs978062517 1045 dbSNP
rs1175953514 1047 dbSNP
rs1412904879 1050 dbSNP
rs1468144379 1053 dbSNP
rs13430313 1056 dbSNP
rs1249915796 1057 dbSNP
rs1475671553 1059 dbSNP
rs1389357674 1064 dbSNP
rs1186486961 1066 dbSNP
rs200526289 1068 dbSNP
rs1462470369 1070 dbSNP
rs1243441275 1073 dbSNP
rs368278778 1074 dbSNP
rs377315741 1074 dbSNP
rs1440203275 1086 dbSNP
rs141261108 1090 dbSNP
rs1215698587 1097 dbSNP
rs1342121619 1104 dbSNP
rs1296013007 1117 dbSNP
rs189003079 1119 dbSNP
rs578069031 1124 dbSNP
rs1417152946 1125 dbSNP
rs1425310693 1126 dbSNP
rs991630762 1128 dbSNP
rs916088921 1129 dbSNP
rs931021148 1138 dbSNP
rs1329580616 1143 dbSNP
rs1409422398 1148 dbSNP
rs1048190008 1176 dbSNP
rs1166626910 1178 dbSNP
rs1393627487 1192 dbSNP
rs200162908 1193 dbSNP
rs61481137 1193 dbSNP
rs762552408 1193 dbSNP
rs146061248 1194 dbSNP
rs55993213 1194 dbSNP
rs760390729 1194 dbSNP
rs202119748 1197 dbSNP
rs200435489 1198 dbSNP
rs1471578908 1199 dbSNP
rs545057690 1200 dbSNP
rs1429618134 1201 dbSNP
rs1234224317 1204 dbSNP
rs560550377 1211 dbSNP
rs908189301 1226 dbSNP
rs939737999 1227 dbSNP
rs1041357600 1228 dbSNP
rs901050781 1240 dbSNP
rs1226851804 1241 dbSNP
rs932570875 1246 dbSNP
rs1280339155 1247 dbSNP
rs1409351725 1249 dbSNP
rs1368783542 1255 dbSNP
rs1163856944 1260 dbSNP
rs1306116813 1260 dbSNP
rs1350278348 1260 dbSNP
rs1409779392 1260 dbSNP
rs201901688 1260 dbSNP
rs55715552 1260 dbSNP
rs1334781234 1268 dbSNP
rs1231926516 1273 dbSNP
rs1471980865 1273 dbSNP
rs1270123955 1278 dbSNP
rs1248909962 1284 dbSNP
rs1447602001 1292 dbSNP
rs546153161 1292 dbSNP
rs1490644226 1299 dbSNP
rs572747980 1309 dbSNP
rs893660251 1326 dbSNP
rs1240541820 1328 dbSNP
rs1285300013 1337 dbSNP
rs1484147344 1345 dbSNP
rs190620162 1350 dbSNP
rs1348727481 1369 dbSNP
rs1285222468 1376 dbSNP
rs1406732921 1379 dbSNP
rs1368274651 1385 dbSNP
rs561425245 1390 dbSNP
rs1434110562 1393 dbSNP
rs1346670720 1399 dbSNP
rs182966748 1407 dbSNP
rs1456335073 1413 dbSNP
rs1409167166 1418 dbSNP
rs998904320 1433 dbSNP
rs1036101245 1436 dbSNP
rs11674996 1439 dbSNP
rs1189979909 1441 dbSNP
rs1487057121 1442 dbSNP
rs1243004520 1450 dbSNP
rs1208372869 1453 dbSNP
rs991753742 1471 dbSNP
rs1265205936 1474 dbSNP
rs1023114123 1480 dbSNP
rs952880692 1485 dbSNP
rs1300504485 1489 dbSNP
rs1315864504 1492 dbSNP
rs983864400 1498 dbSNP
rs1320930942 1499 dbSNP
rs1434046390 1507 dbSNP
rs1386062831 1508 dbSNP
rs1338280882 1517 dbSNP
rs1448226811 1521 dbSNP
rs1313874456 1523 dbSNP
rs1376510906 1535 dbSNP
rs908328010 1538 dbSNP
rs56994843 1542 dbSNP
rs976412245 1543 dbSNP
rs750588680 1546 dbSNP
rs1245268762 1547 dbSNP
rs1204470795 1556 dbSNP
rs1290728096 1563 dbSNP
rs1482972496 1566 dbSNP
rs1049657425 1570 dbSNP
rs893629107 1574 dbSNP
rs946584683 1585 dbSNP
rs1298212660 1588 dbSNP
rs1043118200 1595 dbSNP
rs1362765981 1597 dbSNP
rs529713034 1605 dbSNP
rs187263385 1606 dbSNP
rs1314172272 1607 dbSNP
rs1300530688 1612 dbSNP
rs1211821272 1625 dbSNP
rs1035666201 1631 dbSNP
rs200310879 1637 dbSNP
rs895823589 1640 dbSNP
rs201484535 1651 dbSNP
rs1448046124 1652 dbSNP
rs1387402713 1668 dbSNP
rs1188533785 1686 dbSNP
rs1013155561 1689 dbSNP
rs551063433 1690 dbSNP
rs191684706 1692 dbSNP
rs952854856 1696 dbSNP
rs1408638749 1698 dbSNP
rs1453592206 1699 dbSNP
rs1197678379 1704 dbSNP
rs1483416544 1710 dbSNP
rs984250449 1716 dbSNP
rs1016185077 1724 dbSNP
rs961125150 1737 dbSNP
rs1293615819 1739 dbSNP
rs1245111966 1747 dbSNP
rs183257820 1755 dbSNP
rs976929602 1757 dbSNP
rs1434981812 1761 dbSNP
rs1392690774 1766 dbSNP
rs1350493496 1771 dbSNP
rs1307971344 1772 dbSNP
rs1428322837 1776 dbSNP
rs150485930 1778 dbSNP
rs548857681 1779 dbSNP
rs1413286686 1782 dbSNP
rs985334246 1784 dbSNP
rs915197061 1786 dbSNP
rs1442032289 1789 dbSNP
rs1251099118 1790 dbSNP
rs1277887001 1805 dbSNP
rs1369756888 1806 dbSNP
rs1229540992 1808 dbSNP
rs765101182 1808 dbSNP
rs1355367233 1818 dbSNP
rs1263316216 1822 dbSNP
rs187724214 1825 dbSNP
rs1329258630 1837 dbSNP
rs946635533 1854 dbSNP
rs1287114455 1857 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' uuauuucagauacaUACCGUu 5'
                        |||||| 
Target 5' -------cuucaccAUGGCAa 3'
 		1 - 14
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 ENST00000410061.2 | 3UTR | CUUCACCAUGGCAAUAUG
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
69 hsa-miR-5590-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT056313 WAC WW domain containing adaptor with coiled-coil 2 6
MIRT066181 PIP4K2C phosphatidylinositol-5-phosphate 4-kinase type 2 gamma 2 2
MIRT095612 NR3C1 nuclear receptor subfamily 3 group C member 1 2 2
MIRT099166 MYLIP myosin regulatory light chain interacting protein 2 2
MIRT107578 VLDLR very low density lipoprotein receptor 2 2
MIRT179602 CAPZA1 capping actin protein of muscle Z-line alpha subunit 1 2 8
MIRT241303 ZC3H12C zinc finger CCCH-type containing 12C 2 8
MIRT244620 MCM4 minichromosome maintenance complex component 4 2 2
MIRT270705 SBNO1 strawberry notch homolog 1 2 4
MIRT453616 SNRPE small nuclear ribonucleoprotein polypeptide E 2 4
MIRT453653 RAB6C RAB6C, member RAS oncogene family 2 2
MIRT464159 VMP1 vacuole membrane protein 1 2 15
MIRT477720 EEF1A1 eukaryotic translation elongation factor 1 alpha 1 2 2
MIRT484301 ENDOD1 endonuclease domain containing 1 2 4
MIRT496069 GLCCI1 glucocorticoid induced 1 2 2
MIRT496338 TMEM81 transmembrane protein 81 2 2
MIRT496653 PITPNM3 PITPNM family member 3 2 2
MIRT499098 DENND4C DENN domain containing 4C 2 8
MIRT499862 SVOP SV2 related protein 2 12
MIRT504913 CD38 CD38 molecule 2 4
MIRT515401 WDR72 WD repeat domain 72 2 4
MIRT518156 TMEM133 transmembrane protein 133 2 2
MIRT518558 GDPD1 glycerophosphodiester phosphodiesterase domain containing 1 2 2
MIRT518636 NOM1 nucleolar protein with MIF4G domain 1 2 2
MIRT518724 ABCG8 ATP binding cassette subfamily G member 8 2 2
MIRT524301 CTC1 CST telomere replication complex component 1 2 4
MIRT524472 CHRM3 cholinergic receptor muscarinic 3 2 4
MIRT527562 ADCY7 adenylate cyclase 7 2 2
MIRT532694 TCN2 transcobalamin 2 2 4
MIRT534640 RNF6 ring finger protein 6 2 2
MIRT537163 GGCX gamma-glutamyl carboxylase 2 2
MIRT539360 AFF4 AF4/FMR2 family member 4 2 2
MIRT547023 PPP1CB protein phosphatase 1 catalytic subunit beta 2 2
MIRT548155 FRAT2 FRAT2, WNT signaling pathway regulator 2 2
MIRT550127 ZNF138 zinc finger protein 138 2 2
MIRT558473 DBN1 drebrin 1 2 2
MIRT566862 LRRC58 leucine rich repeat containing 58 2 2
MIRT567246 HSP90AA1 heat shock protein 90 alpha family class A member 1 2 2
MIRT572848 BRPF3 bromodomain and PHD finger containing 3 2 2
MIRT574914 Vmp1 vacuole membrane protein 1 2 9
MIRT606849 RAB7A RAB7A, member RAS oncogene family 2 2
MIRT611274 RBMXL1 RNA binding motif protein, X-linked like 1 2 2
MIRT612328 TRPS1 transcriptional repressor GATA binding 1 2 2
MIRT612415 SP1 Sp1 transcription factor 2 2
MIRT614791 RRAGC Ras related GTP binding C 2 2
MIRT618449 SERPINA3 serpin family A member 3 2 2
MIRT621154 MICALCL MICAL C-terminal like 2 2
MIRT622141 SOX4 SRY-box 4 2 2
MIRT623504 KCNK5 potassium two pore domain channel subfamily K member 5 2 2
MIRT623598 IPO9 importin 9 2 2
MIRT624075 EBF1 early B-cell factor 1 2 2
MIRT639792 MVK mevalonate kinase 2 2
MIRT641109 ZNF274 zinc finger protein 274 2 2
MIRT641579 RFX1 regulatory factor X1 2 2
MIRT643095 NDUFB5 NADH:ubiquinone oxidoreductase subunit B5 2 2
MIRT645141 CUBN cubilin 2 2
MIRT646461 PRDM10 PR/SET domain 10 2 2
MIRT650815 HMOX1 heme oxygenase 1 2 2
MIRT653073 ST8SIA4 ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4 2 2
MIRT657675 GPR26 G protein-coupled receptor 26 2 2
MIRT665824 TIMM8B translocase of inner mitochondrial membrane 8 homolog B 2 2
MIRT695592 TMEM199 transmembrane protein 199 2 2
MIRT698039 TRPM7 transient receptor potential cation channel subfamily M member 7 2 2
MIRT701015 PCGF5 polycomb group ring finger 5 2 2
MIRT701357 NR4A3 nuclear receptor subfamily 4 group A member 3 2 2
MIRT707114 NWD1 NACHT and WD repeat domain containing 1 2 2
MIRT718661 HNF4A hepatocyte nuclear factor 4 alpha 2 2
MIRT719901 SERP1 stress associated endoplasmic reticulum protein 1 2 2
MIRT720564 C1RL complement C1r subcomponent like 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-5590-5p Gefitinib 123631 NSC715055 approved resistant cell line (HCC827)

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