miRTarBase - #MIRT321168


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pre-miRNA Information
pre-miRNA hsa-mir-4271   
Genomic Coordinates chr3: 49274120 - 49274186
Description Homo sapiens miR-4271 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4271
Sequence 39| GGGGGAAGAAAAGGUGGGG |57
Evidence Experimental
Experiments SOLiD
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN30481495 1 COSMIC
COSN31532060 5 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs760829741 1 dbSNP
rs1277951968 2 dbSNP
rs189148716 3 dbSNP
rs757021935 4 dbSNP
rs1285201145 6 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol EIF4H   
Synonyms WBSCR1, WSCR1, eIF-4H
Description eukaryotic translation initiation factor 4H
Transcript NM_022170   
Other Transcripts NM_031992   
Expression
Putative miRNA Targets on EIF4H
3'UTR of EIF4H
(miRNA target sites are highlighted)		 
>EIF4H|NM_022170|3'UTR
   1 GCCTGCGGTTGGGAGGGAATGGGGCGTGGGGGGTTAGAGCAGGACCACAGCCTGGTGAGTCCCCGGGCAGCCGTCCTGCA
  81 GCCGCCACTCCTGCGCCTGCCATTGGCCTCCTCACAGCGGAAACACAGCTTGTGAGTGCATGTCAGCTGTTAACAAGTGG
 161 TTTTTAGTACATTCTGGGCTTTGCTGTATCTATCTAGTGCCTGTTTGTGCGTTTTTTTCTTTCTTCCGCTGCTTCCCCAT
 241 TTTCCTTCTGTCCTTTTTCTCCTGCTCCTTGTTTTCCCAGCAGCACATGGGGTTCCTCGGAGGAGCAGAGGTGGCCGCCG
 321 TGGGGGGGCGTTTGGGCTGCGGTGCTGCGTCATTTTTCCTTTGCTTTCTCTTTACTTTAGACACTGGCCCAACTCCAGGC
 401 GTTTCCTTTCATTCCCTCAGTGCTTCTCTTCTGACCTGCATGTTGAGTTCTGTATTGCTGGGGCTTCCAACAAAAACCAG
 481 AGTCACTGACAGAGGGAACAGCAGAGACCTTGTTGGTATTCAGCTGTGATGGATATAGAGAATCAGAGGCACCTTGTTTT
 561 CACAACTAGGATAAAAATATCTGCAGGGTCCTTTCCATTCCTATTTAGAGGGAGTCCTGGCTCCATGACCCCCTCCCGAG
 641 TGGACTGTCCAAGCAGATAGGCTCACACGAGAAACAGTGAGGCTGAAAGGGGGGGCTATGGAAGAGCGGTAGGGAGTCCA
 721 CGGAGAAGATGCAGTGAATGCTTGCATGCATTCACACGTGTGTGTGTCCCAGCTAGTTCACTCCTTTCGCCGTGCGTGGT
 801 GGAGGCTGGCCTCTCTGGCTGGGTGCAGTGAATGGCCAGCGGGTTTCTTTTCTGCTGGGCCAAGGCGCTTTGGGGGTGGA
 881 GGGGGTGGTGCTGGTGCTGCACTGGGCTGACTGCGGCGCTGACGCAGCGTTTCCCCCCATCCCTGTTGCCTGTGTGTTGT
 961 GTGGATCTGTTCCTAGTATAGGCAACATAATGAGATACTGTGCTTCCCACCTCCCCTTCAGTTCAGAGCCAAAATGGGTC
1041 TAGAATCTGGCACTTTACTCATTTCCTTTGATAAATTGTACTATGCAGAGCTGTCAGGAACCTTCAGATAGCAGTAGAGG
1121 ACTGCAGCTGTCTAGGTCTGCGGCCACATCTTGGGGACACACTGGACTGTTCCCATGTGCAGGGTTCAGCAGTTATGTGG
1201 GAGTGCTAGGGGTTAGGCTTTTGAGCTTGAACGCCTGCGTGTGAACAGATGAAAAATCCTTCAGTACCCAAGTCCCAGTC
1281 TGTCCTATGGGGAGCAGTTTGGGGGCGGCCGGCAGCAGGAGCCTGGGAAAGAGGCCCTCGCCAGGTGATGGCAGGGCCAG
1361 GGTGGCCTGGGGCACCCAGCGGAATGTGCTTAGTATTTGGTCACCAGCCGTCATCCTGGGCTTTTCCTACTGTGTCTTGT
1441 TACAAGGCCTCAGCAATCCACAGAACTCTCTCTCCTTCCTTCCACCTGTCAGCTTCTCTGCTTCTGAGATAAGAACCATT
1521 TGTGTAACACCAACACTTAACTTCAGAAAGACATGCATTATGTGGTGTAATCAAACCCGATGCTTTCAGATGACCTACTT
1601 ACATCTTCAATGTGGATAAGATAAAGAACAAAACACATGCATCTAAACTGCTGGGCAATCCAGTTGACTTTTAAATGTAA
1681 GAATGGAATTCCAAACACTTAACACATTCAGCTATATGACAGAAAGTAAATCTATGGATATGGTATTTTGTGAATGATCT
1761 TTTAAATAAAAGAAAACCTTACGTAATATTT
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' ggGGUGGAAAAGAAGGGGg 5'
            |: ||  | ||||||| 
Target 5' ttCTTCCGCTGCTTCCCCa 3'
 221 - 239 149.00 -20.40
2 
miRNA  3' gggguGGAAAAGAAGGGGg 5'
               ||||| |||:|:| 
Target 5' tttttCCTTTGCTTTCTCt 3'
 353 - 371 130.00 -13.10
3 
miRNA  3' ggggugGAAAAGAAGGGgg 5'
                || | ||||||  
Target 5' gagataCTGTGCTTCCCac 3'
 992 - 1010 129.00 -12.20
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30506350 8 COSMIC
COSN14300882 26 COSMIC
COSN30128096 30 COSMIC
COSN30495418 65 COSMIC
COSN31531541 66 COSMIC
COSN30499239 141 COSMIC
COSN31523115 170 COSMIC
COSN23147096 286 COSMIC
COSN32073891 321 COSMIC
COSN30606725 329 COSMIC
COSN2234626 368 COSMIC
COSN19657016 401 COSMIC
COSN30703376 401 COSMIC
COSN26585833 458 COSMIC
COSN20344171 695 COSMIC
COSN15763972 817 COSMIC
COSN30545151 953 COSMIC
COSN31546031 976 COSMIC
COSN31486972 1048 COSMIC
COSN30545207 1086 COSMIC
COSN30158034 1089 COSMIC
COSN31549529 1748 COSMIC
COSN26279660 1780 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1447066597 4 dbSNP
rs1375628741 7 dbSNP
rs782454237 8 dbSNP
rs782576980 19 dbSNP
rs782302162 25 dbSNP
rs782192917 26 dbSNP
rs782406670 26 dbSNP
rs535742148 27 dbSNP
rs782449959 28 dbSNP
rs782220493 29 dbSNP
rs557645944 30 dbSNP
rs781929810 31 dbSNP
rs782045444 32 dbSNP
rs782422377 33 dbSNP
rs1403484370 35 dbSNP
rs1411755730 41 dbSNP
rs575700661 42 dbSNP
rs782127280 47 dbSNP
rs1180509928 48 dbSNP
rs1440564472 50 dbSNP
rs546032982 51 dbSNP
rs782667557 53 dbSNP
rs563827396 56 dbSNP
rs1489700851 65 dbSNP
rs1266354891 66 dbSNP
rs1320374895 67 dbSNP
rs1287564941 69 dbSNP
rs572635003 73 dbSNP
rs555278621 74 dbSNP
rs575358681 84 dbSNP
rs1368064384 85 dbSNP
rs1434212880 87 dbSNP
rs1346835243 90 dbSNP
rs1159166914 91 dbSNP
rs1420454180 94 dbSNP
rs1379734297 95 dbSNP
rs1157106019 96 dbSNP
rs1435089329 97 dbSNP
rs1268499263 98 dbSNP
rs1190917956 103 dbSNP
rs1487704403 104 dbSNP
rs1266061180 108 dbSNP
rs1217955211 109 dbSNP
rs1352406823 110 dbSNP
rs561497484 114 dbSNP
rs1234995896 117 dbSNP
rs1312340390 119 dbSNP
rs1300343611 123 dbSNP
rs1217321215 133 dbSNP
rs1342135094 140 dbSNP
rs1298774617 165 dbSNP
rs1399272300 172 dbSNP
rs1360020008 178 dbSNP
rs1287122881 187 dbSNP
rs1467788433 187 dbSNP
rs1378489390 191 dbSNP
rs1175626703 195 dbSNP
rs1426206354 202 dbSNP
rs1431844709 202 dbSNP
rs1195058778 206 dbSNP
rs1488225944 207 dbSNP
rs1260409416 210 dbSNP
rs1201612826 211 dbSNP
rs1255121889 212 dbSNP
rs1483283060 212 dbSNP
rs1230571985 221 dbSNP
rs528897220 228 dbSNP
rs1278564798 229 dbSNP
rs1217942859 233 dbSNP
rs1338260999 236 dbSNP
rs1314755497 237 dbSNP
rs1397932666 241 dbSNP
rs782705400 249 dbSNP
rs1302539923 257 dbSNP
rs1468389231 268 dbSNP
rs1171750800 270 dbSNP
rs1477786470 275 dbSNP
rs1422175355 276 dbSNP
rs1190215731 278 dbSNP
rs544136216 287 dbSNP
rs562848775 289 dbSNP
rs187036467 297 dbSNP
rs1458769107 299 dbSNP
rs1258481490 300 dbSNP
rs1197843498 306 dbSNP
rs1315836673 318 dbSNP
rs1267194745 319 dbSNP
rs1245402751 320 dbSNP
rs1312041115 321 dbSNP
rs1332276468 322 dbSNP
rs1379316417 322 dbSNP
rs1465493490 323 dbSNP
rs551636758 328 dbSNP
rs1367388245 329 dbSNP
rs1181152620 331 dbSNP
rs1440985551 334 dbSNP
rs1177595853 335 dbSNP
rs1456316503 336 dbSNP
rs537769003 337 dbSNP
rs1210394774 341 dbSNP
rs1355469633 342 dbSNP
rs1264949418 343 dbSNP
rs1243941495 349 dbSNP
rs1355939584 350 dbSNP
rs528571636 355 dbSNP
rs782521136 363 dbSNP
rs1446298528 371 dbSNP
rs1334373923 372 dbSNP
rs1325867254 373 dbSNP
rs547088922 375 dbSNP
rs1390718981 380 dbSNP
rs1162218501 382 dbSNP
rs1421034843 385 dbSNP
rs1380357944 390 dbSNP
rs55815268 394 dbSNP
rs1157704699 397 dbSNP
rs1248243222 400 dbSNP
rs1199227719 401 dbSNP
rs1265260458 403 dbSNP
rs568324188 405 dbSNP
rs1489339486 413 dbSNP
rs535843720 416 dbSNP
rs1239733056 421 dbSNP
rs557364764 424 dbSNP
rs1276815713 425 dbSNP
rs1234510830 432 dbSNP
rs1330854557 436 dbSNP
rs1301892873 441 dbSNP
rs782071929 441 dbSNP
rs1402348685 442 dbSNP
rs1360647858 444 dbSNP
rs1296972524 471 dbSNP
rs1398604509 477 dbSNP
rs1426897041 479 dbSNP
rs764267904 480 dbSNP
rs1477595969 488 dbSNP
rs1426913260 497 dbSNP
rs1195782458 517 dbSNP
rs569247953 520 dbSNP
rs1264003266 525 dbSNP
rs1445351033 527 dbSNP
rs774618863 534 dbSNP
rs1201229617 537 dbSNP
rs1344782144 538 dbSNP
rs1281733905 547 dbSNP
rs1221013395 548 dbSNP
rs1341611642 554 dbSNP
rs1428121081 559 dbSNP
rs1360355849 567 dbSNP
rs1334457500 578 dbSNP
rs1413503768 581 dbSNP
rs539625737 591 dbSNP
rs1172467941 602 dbSNP
rs1478019230 607 dbSNP
rs1184678043 617 dbSNP
rs1422913057 617 dbSNP
rs1474496851 621 dbSNP
rs1239237297 630 dbSNP
rs1188550062 633 dbSNP
rs557958107 634 dbSNP
rs1200976957 639 dbSNP
rs1319024880 648 dbSNP
rs1272971376 656 dbSNP
rs1213298787 663 dbSNP
rs1380737236 670 dbSNP
rs1284230954 675 dbSNP
rs1446841615 676 dbSNP
rs1380045636 678 dbSNP
rs1332946970 685 dbSNP
rs1491474929 688 dbSNP
rs1491427393 689 dbSNP
rs558005791 689 dbSNP
rs1406980624 690 dbSNP
rs1163858057 691 dbSNP
rs1180707358 692 dbSNP
rs573123037 693 dbSNP
rs1232614653 695 dbSNP
rs1203070817 697 dbSNP
rs35927562 698 dbSNP
rs539906540 708 dbSNP
rs1289985861 709 dbSNP
rs1244691063 711 dbSNP
rs1356603370 719 dbSNP
rs1311064994 722 dbSNP
rs555448696 723 dbSNP
rs1375922460 731 dbSNP
rs1296173012 736 dbSNP
rs1438545297 740 dbSNP
rs1350461572 742 dbSNP
rs1163981236 758 dbSNP
rs1383434432 758 dbSNP
rs1424138701 758 dbSNP
rs1160703246 760 dbSNP
rs573554269 765 dbSNP
rs1407719699 766 dbSNP
rs1175789431 767 dbSNP
rs1489663261 781 dbSNP
rs1247845569 785 dbSNP
rs544236987 789 dbSNP
rs562625826 790 dbSNP
rs1240432239 792 dbSNP
rs533293491 793 dbSNP
rs545347649 797 dbSNP
rs560357870 800 dbSNP
rs1304402390 811 dbSNP
rs1220799516 823 dbSNP
rs1367998214 828 dbSNP
rs34460100 834 dbSNP
rs115874427 840 dbSNP
rs868951948 841 dbSNP
rs1300039684 842 dbSNP
rs1420552200 850 dbSNP
rs1344888939 856 dbSNP
rs546733200 862 dbSNP
rs1435331108 863 dbSNP
rs1426254489 867 dbSNP
rs1199371558 868 dbSNP
rs34839061 874 dbSNP
rs1264725723 875 dbSNP
rs1216781120 877 dbSNP
rs1258623600 878 dbSNP
rs1485259234 878 dbSNP
rs1211767533 880 dbSNP
rs568584758 882 dbSNP
rs529260836 883 dbSNP
rs35864042 886 dbSNP
rs1282351198 887 dbSNP
rs1221614239 893 dbSNP
rs1278749150 895 dbSNP
rs1342230679 895 dbSNP
rs35689317 896 dbSNP
rs1382913653 899 dbSNP
rs1384319696 907 dbSNP
rs1287358590 910 dbSNP
rs1467739103 915 dbSNP
rs868917281 916 dbSNP
rs1176092941 918 dbSNP
rs1426499963 922 dbSNP
rs1427455111 924 dbSNP
rs35239215 925 dbSNP
rs1183266290 926 dbSNP
rs1483333803 927 dbSNP
rs577983075 929 dbSNP
rs1201597524 930 dbSNP
rs1319730995 933 dbSNP
rs550985054 937 dbSNP
rs1226542671 942 dbSNP
rs1325962496 949 dbSNP
rs1293443018 950 dbSNP
rs1398022853 955 dbSNP
rs1383881046 964 dbSNP
rs1336322518 970 dbSNP
rs569183773 975 dbSNP
rs1450971954 986 dbSNP
rs1402877720 993 dbSNP
rs1169017622 995 dbSNP
rs1461882754 1000 dbSNP
rs373695868 1011 dbSNP
rs1166213207 1012 dbSNP
rs1423874203 1014 dbSNP
rs1242219931 1017 dbSNP
rs1181336264 1031 dbSNP
rs1458943722 1033 dbSNP
rs1238519713 1035 dbSNP
rs1195163454 1037 dbSNP
rs1337304080 1039 dbSNP
rs1267134129 1040 dbSNP
rs1247171847 1043 dbSNP
rs1360223104 1054 dbSNP
rs1314686415 1057 dbSNP
rs1379610861 1062 dbSNP
rs1450654308 1062 dbSNP
rs558044327 1065 dbSNP
rs1329880897 1077 dbSNP
rs34251399 1084 dbSNP
rs1395038602 1088 dbSNP
rs1295796989 1092 dbSNP
rs1424790469 1107 dbSNP
rs1384025790 1114 dbSNP
rs1161317353 1116 dbSNP
rs34582986 1132 dbSNP
rs1441087074 1142 dbSNP
rs1364179646 1143 dbSNP
rs1180896780 1152 dbSNP
rs1435865845 1157 dbSNP
rs149967248 1159 dbSNP
rs534407152 1162 dbSNP
rs35628518 1168 dbSNP
rs1210341406 1172 dbSNP
rs1490539560 1173 dbSNP
rs1291077336 1185 dbSNP
rs35529759 1189 dbSNP
rs1356049504 1191 dbSNP
rs35668946 1197 dbSNP
rs1238867343 1205 dbSNP
rs1334318476 1215 dbSNP
rs1304115018 1221 dbSNP
rs1406048467 1223 dbSNP
rs1364413245 1227 dbSNP
rs555162045 1234 dbSNP
rs11557834 1236 dbSNP
rs573715163 1239 dbSNP
rs1468450699 1240 dbSNP
rs1379108284 1270 dbSNP
rs1200105490 1278 dbSNP
rs1480033133 1279 dbSNP
rs1220431167 1288 dbSNP
rs1489310879 1295 dbSNP
rs1285269969 1306 dbSNP
rs1204750730 1307 dbSNP
rs1349024133 1308 dbSNP
rs1276906790 1310 dbSNP
rs1224674104 1311 dbSNP
rs537422603 1312 dbSNP
rs1281923101 1324 dbSNP
rs1401347639 1326 dbSNP
rs1326479463 1328 dbSNP
rs1317222094 1329 dbSNP
rs1398556967 1330 dbSNP
rs1404096013 1331 dbSNP
rs1176818985 1336 dbSNP
rs1469091333 1337 dbSNP
rs1427200721 1339 dbSNP
rs1195716042 1340 dbSNP
rs556167786 1341 dbSNP
rs1192752738 1346 dbSNP
rs1445437011 1349 dbSNP
rs1265216578 1361 dbSNP
rs577730616 1363 dbSNP
rs1323234445 1367 dbSNP
rs13244093 1371 dbSNP
rs1220943937 1374 dbSNP
rs1339524704 1381 dbSNP
rs879977642 1382 dbSNP
rs1341957722 1383 dbSNP
rs1336978544 1386 dbSNP
rs1451702501 1407 dbSNP
rs1403606448 1410 dbSNP
rs1172759440 1411 dbSNP
rs545285956 1414 dbSNP
rs1420331809 1432 dbSNP
rs1167466129 1440 dbSNP
rs1474463648 1441 dbSNP
rs1245241045 1444 dbSNP
rs1461160436 1449 dbSNP
rs1241637668 1464 dbSNP
rs1207256141 1466 dbSNP
rs1438844702 1466 dbSNP
rs1272911262 1468 dbSNP
rs1212361318 1469 dbSNP
rs1360939704 1470 dbSNP
rs1315369175 1471 dbSNP
rs1244727035 1473 dbSNP
rs1380347265 1478 dbSNP
rs1333050219 1484 dbSNP
rs1442644807 1491 dbSNP
rs1353930201 1499 dbSNP
rs1326732784 1525 dbSNP
rs1408325105 1531 dbSNP
rs781847009 1531 dbSNP
rs1164481996 1535 dbSNP
rs1444170634 1537 dbSNP
rs1383796324 1554 dbSNP
rs1179382369 1557 dbSNP
rs1481163567 1561 dbSNP
rs1203010628 1566 dbSNP
rs1490703773 1567 dbSNP
rs1221297209 1568 dbSNP
rs1356900721 1576 dbSNP
rs560466954 1579 dbSNP
rs1224167141 1583 dbSNP
rs11557832 1585 dbSNP
rs1372313148 1590 dbSNP
rs1277722183 1594 dbSNP
rs1438466905 1594 dbSNP
rs1367531812 1601 dbSNP
rs1303780084 1603 dbSNP
rs1424088272 1604 dbSNP
rs782690308 1606 dbSNP
rs78099872 1611 dbSNP
rs1161517493 1612 dbSNP
rs1420106578 1613 dbSNP
rs1407656852 1617 dbSNP
rs1176018145 1622 dbSNP
rs1481667491 1623 dbSNP
rs542846380 1627 dbSNP
rs1270215312 1628 dbSNP
rs1198146341 1630 dbSNP
rs1489619420 1632 dbSNP
rs1262174551 1633 dbSNP
rs183678176 1637 dbSNP
rs1316150382 1638 dbSNP
rs1281796276 1641 dbSNP
rs1346141932 1659 dbSNP
rs201082008 1663 dbSNP
rs1404457590 1678 dbSNP
rs1365551186 1684 dbSNP
rs1290879839 1694 dbSNP
rs1454467085 1694 dbSNP
rs1344979502 1696 dbSNP
rs1157450219 1700 dbSNP
rs1471158348 1702 dbSNP
rs1430660557 1716 dbSNP
rs1199301397 1717 dbSNP
rs762221385 1721 dbSNP
rs1479181292 1726 dbSNP
rs1263168970 1729 dbSNP
rs367939007 1735 dbSNP
rs1186743411 1739 dbSNP
rs1485305789 1741 dbSNP
rs1239994544 1742 dbSNP
rs1205406023 1746 dbSNP
rs1323955260 1755 dbSNP
rs1262489051 1756 dbSNP
rs1221560955 1768 dbSNP
rs190525159 1772 dbSNP
rs1297729474 1783 dbSNP
rs1361606405 1784 dbSNP
rs1318749569 1787 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' ggGGUGGAAAAGAAGGGGg 5'
            |: ||  | ||||||| 
Target 5' uuCUUCCGCUGCUUCCCCa 3'
 		10 - 28
2 
miRNA  3' gggguggAAAAGAAggggg 5'
                 ||||:||     
Target 5' -------UUUUUUUcuuuc 3'
 		1 - 12
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 GSM4903833
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_a
Location of target site NM_031992 | 3UTR | GUUUUUUUCUUUCUUCCGCUGCUUCCCCAUUUUCCUUCUGUCCUUUUUCUCCUGCUCCUUGUUUUCCCAGCAGCACAUGGGGUUCCUCGGAGGAGCAGAGGUGGCCGCCGUGGGGGGGCGUUUGGGCUGCGGUGCU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM4903836
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_a
Location of target site NM_031992 | 3UTR | GCGUUUUUUUCUUUCUUCCGCUGCUUCCCCAUUUUCCUUCUGUCCUUUUUCUCCUGCUCCUUGUUUUCCCAGCAGCACAUGGGGUUCCUCGGAGGAGCAGAGGUGGCCGCCGUGGGGGGGCGUUUGGGCUGCGGUGCU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM4903837
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_b
Location of target site NM_031992 | 3UTR | CCGCUGCUUCCCCAUUUUCCUUCUGUCCUUUUUCUCCUGCUCCUUGUUUUCCCAGCAGCACAUGGGGUUCCUCGGAGGAGCAGAGGUGGCCGCCGUGGGGGGGCGUUUGGGCUGCGGUGCU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM4903838
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_c
Location of target site NM_031992 | 3UTR | CUUCCGCUGCUUCCCCAUUUUCCUUCUGUCCUUUUUCUCCUGCUCCUUGUUUUCCCAGCAGCACAUGGGGUUCCUCGGAGGAGCAGAGGUGGCCGCCGUGGGGGGGCGUUUGGGCUGCGGUGCU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000265753.8 | 3UTR | UUUUUUUCUUUCUUCCGCUGCUUCCCCAUUUUCCUUCUG
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
181 hsa-miR-4271 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT066209 MARCH9 membrane associated ring-CH-type finger 9 2 2
MIRT079367 CCDC137 coiled-coil domain containing 137 2 2
MIRT081183 MIDN midnolin 2 4
MIRT083278 ZCCHC3 zinc finger CCHC-type containing 3 2 6
MIRT086207 HOXD13 homeobox D13 2 2
MIRT133713 SKI SKI proto-oncogene 2 4
MIRT150653 SLC27A1 solute carrier family 27 member 1 2 2
MIRT159166 NRBP1 nuclear receptor binding protein 1 2 2
MIRT160059 TET3 tet methylcytosine dioxygenase 3 2 4
MIRT180856 RPRD2 regulation of nuclear pre-mRNA domain containing 2 2 2
MIRT181931 MARK2 microtubule affinity regulating kinase 2 2 2
MIRT190628 BCL2L2-PABPN1 BCL2L2-PABPN1 readthrough 2 2
MIRT190654 PABPN1 poly(A) binding protein nuclear 1 2 2
MIRT196107 MPRIP myosin phosphatase Rho interacting protein 2 2
MIRT263248 SGPL1 sphingosine-1-phosphate lyase 1 2 2
MIRT321168 EIF4H eukaryotic translation initiation factor 4H 2 2
MIRT338624 SHMT2 serine hydroxymethyltransferase 2 2 2
MIRT366301 GDI1 GDP dissociation inhibitor 1 2 4
MIRT375172 ARIH1 ariadne RBR E3 ubiquitin protein ligase 1 2 2
MIRT441488 NCEH1 neutral cholesterol ester hydrolase 1 2 2
MIRT442333 WNT9B Wnt family member 9B 2 2
MIRT443889 CNKSR3 CNKSR family member 3 2 2
MIRT445880 WBP1L WW domain binding protein 1 like 2 2
MIRT449312 MRO maestro 2 2
MIRT449844 BCL2L13 BCL2 like 13 2 2
MIRT450304 DRAXIN dorsal inhibitory axon guidance protein 2 2
MIRT450515 EMX1 empty spiracles homeobox 1 2 2
MIRT451243 ZNF444 zinc finger protein 444 2 2
MIRT451713 OLR1 oxidized low density lipoprotein receptor 1 2 2
MIRT451792 TLR5 toll like receptor 5 2 2
MIRT451823 ALDH3B1 aldehyde dehydrogenase 3 family member B1 2 2
MIRT451906 ILK integrin linked kinase 2 2
MIRT452181 KIAA1456 KIAA1456 2 4
MIRT452242 TRAM1 translocation associated membrane protein 1 2 2
MIRT452544 ZNF467 zinc finger protein 467 2 2
MIRT452605 REPIN1 replication initiator 1 2 2
MIRT454505 ZFYVE27 zinc finger FYVE-type containing 27 2 2
MIRT454657 FBXL18 F-box and leucine rich repeat protein 18 2 2
MIRT455354 KDM5C lysine demethylase 5C 2 2
MIRT455452 EPB41L4B erythrocyte membrane protein band 4.1 like 4B 2 2
MIRT455587 TAF12 TATA-box binding protein associated factor 12 2 2
MIRT456501 PFKFB2 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 2 2
MIRT456815 PIGP phosphatidylinositol glycan anchor biosynthesis class P 2 2
MIRT457425 NOL10 nucleolar protein 10 2 2
MIRT457468 SLC35F6 solute carrier family 35 member F6 2 2
MIRT457660 SERINC1 serine incorporator 1 2 2
MIRT458231 NXPH3 neurexophilin 3 2 2
MIRT458374 ITM2C integral membrane protein 2C 2 2
MIRT458667 GPR35 G protein-coupled receptor 35 2 2
MIRT459665 VPS37C VPS37C, ESCRT-I subunit 2 2
MIRT459825 TPP1 tripeptidyl peptidase 1 2 2
MIRT460564 FEM1A fem-1 homolog A 2 2
MIRT460725 ASXL3 additional sex combs like 3, transcriptional regulator 2 2
MIRT461121 RAB36 RAB36, member RAS oncogene family 2 2
MIRT461529 C14orf1 ergosterol biosynthesis 28 homolog 2 2
MIRT461750 DDX11 DEAD/H-box helicase 11 2 2
MIRT462570 STS steroid sulfatase 2 2
MIRT462798 NTN1 netrin 1 2 2
MIRT463030 ZNF689 zinc finger protein 689 2 2
MIRT463991 WDTC1 WD and tetratricopeptide repeats 1 2 2
MIRT464684 UBE2V1 ubiquitin conjugating enzyme E2 V1 2 2
MIRT465439 TP53 tumor protein p53 2 2
MIRT465512 PRICKLE4 prickle planar cell polarity protein 4 2 2
MIRT465649 TNPO2 transportin 2 2 10
MIRT465947 TMEM189-UBE2V1 TMEM189-UBE2V1 readthrough 2 2
MIRT466028 TMEM189 transmembrane protein 189 2 2
MIRT468076 SHOC2 SHOC2, leucine rich repeat scaffold protein 2 6
MIRT468131 SH3PXD2A SH3 and PX domains 2A 2 2
MIRT468498 SESN2 sestrin 2 2 2
MIRT468879 RREB1 ras responsive element binding protein 1 2 2
MIRT469318 RGP1 RGP1 homolog, RAB6A GEF complex partner 1 2 2
MIRT469558 RARA retinoic acid receptor alpha 2 2
MIRT469793 RAB15 RAB15, member RAS oncogene family 2 2
MIRT469896 PTRF caveolae associated protein 1 2 2
MIRT470235 PRRC2A proline rich coiled-coil 2A 2 2
MIRT470808 PLXND1 plexin D1 2 2
MIRT471597 PAQR5 progestin and adipoQ receptor family member 5 2 10
MIRT471710 OTUB1 OTU deubiquitinase, ubiquitin aldehyde binding 1 2 2
MIRT471752 OGT O-linked N-acetylglucosamine (GlcNAc) transferase 2 2
MIRT472978 MRRF mitochondrial ribosome recycling factor 2 2
MIRT473538 MAX MYC associated factor X 2 2
MIRT473581 MAT2A methionine adenosyltransferase 2A 2 2
MIRT473970 LRRC58 leucine rich repeat containing 58 2 2
MIRT474223 LCOR ligand dependent nuclear receptor corepressor 2 4
MIRT474553 KLHDC3 kelch domain containing 3 2 2
MIRT474777 KIAA0895L KIAA0895 like 2 2
MIRT476042 GRSF1 G-rich RNA sequence binding factor 1 2 2
MIRT476438 GBA2 glucosylceramidase beta 2 2 2
MIRT477773 E2F3 E2F transcription factor 3 2 4
MIRT477946 DPM2 dolichyl-phosphate mannosyltransferase subunit 2, regulatory 2 2
MIRT478782 CRTC2 CREB regulated transcription coactivator 2 2 2
MIRT479320 VPS72 vacuolar protein sorting 72 homolog 2 2
MIRT480405 C19orf47 chromosome 19 open reading frame 47 2 2
MIRT480593 BTRC beta-transducin repeat containing E3 ubiquitin protein ligase 2 2
MIRT480963 BBC3 BCL2 binding component 3 2 2
MIRT481127 AZIN1 antizyme inhibitor 1 2 4
MIRT481444 ARRB2 arrestin beta 2 2 2
MIRT481687 AR androgen receptor 2 2
MIRT481730 APH1A aph-1 homolog A, gamma-secretase subunit 2 2
MIRT482386 AEN apoptosis enhancing nuclease 2 2
MIRT482564 ABHD2 abhydrolase domain containing 2 2 2
MIRT482605 ABHD14B abhydrolase domain containing 14B 2 2
MIRT483256 CITED4 Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 4 2 4
MIRT483531 TAGLN2 transgelin 2 2 2
MIRT483840 UNC5B unc-5 netrin receptor B 2 4
MIRT483935 LENG8 leukocyte receptor cluster member 8 2 4
MIRT484414 SNX19 sorting nexin 19 2 2
MIRT484487 SLC9A1 solute carrier family 9 member A1 2 2
MIRT484609 SIX3 SIX homeobox 3 2 6
MIRT484703 RNF11 ring finger protein 11 2 2
MIRT485244 POGZ pogo transposable element derived with ZNF domain 2 2
MIRT485607 FOSL1 FOS like 1, AP-1 transcription factor subunit 2 4
MIRT485965 RTBDN retbindin 2 2
MIRT487308 GLTSCR1 BRD4 interacting chromatin remodeling complex associated protein 2 2
MIRT487329 SREBF1 sterol regulatory element binding transcription factor 1 2 4
MIRT487410 CACNB1 calcium voltage-gated channel auxiliary subunit beta 1 2 2
MIRT487607 C20orf96 chromosome 20 open reading frame 96 2 2
MIRT487689 CDK14 cyclin dependent kinase 14 2 2
MIRT487787 GPR20 G protein-coupled receptor 20 2 4
MIRT488026 ADO 2-aminoethanethiol dioxygenase 2 2
MIRT488476 B3GALNT2 beta-1,3-N-acetylgalactosaminyltransferase 2 2 2
MIRT488761 FXYD1 FXYD domain containing ion transport regulator 1 2 2
MIRT489161 MRPL12 mitochondrial ribosomal protein L12 2 4
MIRT489529 MRE11A MRE11 homolog, double strand break repair nuclease 2 8
MIRT489774 GRINA glutamate ionotropic receptor NMDA type subunit associated protein 1 2 2
MIRT489878 MPLKIP M-phase specific PLK1 interacting protein 2 2
MIRT490094 FN3K fructosamine 3 kinase 2 2
MIRT490202 PKNOX2 PBX/knotted 1 homeobox 2 2 2
MIRT490283 ISL2 ISL LIM homeobox 2 2 2
MIRT490377 LHFPL3 LHFPL tetraspan subfamily member 3 2 2
MIRT491035 ALPK3 alpha kinase 3 2 2
MIRT491186 JUND JunD proto-oncogene, AP-1 transcription factor subunit 2 4
MIRT491766 ZNF385A zinc finger protein 385A 2 2
MIRT491888 YWHAE tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon 2 2
MIRT491981 UNK unkempt family zinc finger 2 2
MIRT492400 SDK1 sidekick cell adhesion molecule 1 2 2
MIRT493647 HDLBP high density lipoprotein binding protein 2 2
MIRT494010 DUSP9 dual specificity phosphatase 9 2 2
MIRT494167 CNOT6L CCR4-NOT transcription complex subunit 6 like 2 2
MIRT495712 PADI1 peptidyl arginine deiminase 1 2 2
MIRT496873 AHCYL2 adenosylhomocysteinase like 2 2 2
MIRT499175 RBPJL recombination signal binding protein for immunoglobulin kappa J region like 2 2
MIRT501652 PHLDA3 pleckstrin homology like domain family A member 3 2 2
MIRT506645 MAPK1 mitogen-activated protein kinase 1 2 4
MIRT510590 TUBB2A tubulin beta 2A class IIa 2 6
MIRT511907 FKBP1A FK506 binding protein 1A 2 2
MIRT513063 ANKRD45 ankyrin repeat domain 45 2 2
MIRT513104 DYNAP dynactin associated protein 2 2
MIRT521804 POM121C POM121 transmembrane nucleoporin C 2 2
MIRT523520 GLUL glutamate-ammonia ligase 2 2
MIRT525085 FRK fyn related Src family tyrosine kinase 2 2
MIRT530930 SCIN scinderin 2 2
MIRT533501 TRIM71 tripartite motif containing 71 2 2
MIRT538560 CECR2 CECR2, histone acetyl-lysine reader 2 2
MIRT544556 CSNK2A1 casein kinase 2 alpha 1 2 2
MIRT555912 ORMDL3 ORMDL sphingolipid biosynthesis regulator 3 2 2
MIRT560405 TMEM69 transmembrane protein 69 2 2
MIRT560664 RTN3 reticulon 3 2 2
MIRT564061 CDT1 chromatin licensing and DNA replication factor 1 2 2
MIRT565504 SP1 Sp1 transcription factor 2 2
MIRT570014 COL1A2 collagen type I alpha 2 chain 2 2
MIRT572321 HSPB6 heat shock protein family B (small) member 6 2 2
MIRT573229 TRIM21 tripartite motif containing 21 2 2
MIRT573487 IQSEC3 IQ motif and Sec7 domain 3 2 2
MIRT574137 MARVELD1 MARVEL domain containing 1 2 2
MIRT574323 ZNF703 zinc finger protein 703 2 2
MIRT620939 OSMR oncostatin M receptor 2 2
MIRT650080 MTL5 testis expressed metallothionein like protein 2 2
MIRT684553 ZNF708 zinc finger protein 708 2 2
MIRT685841 ANGEL1 angel homolog 1 2 2
MIRT688551 DCAF16 DDB1 and CUL4 associated factor 16 2 2
MIRT701985 MIER3 MIER family member 3 2 2
MIRT703899 EPT1 selenoprotein I 2 2
MIRT706388 MC2R melanocortin 2 receptor 2 2
MIRT707487 UGT2B4 UDP glucuronosyltransferase family 2 member B4 2 2
MIRT711885 INSIG2 insulin induced gene 2 2 2
MIRT719164 KIF6 kinesin family member 6 2 2
MIRT721294 C3orf36 chromosome 3 open reading frame 36 2 2
MIRT721775 ARL6IP4 ADP ribosylation factor like GTPase 6 interacting protein 4 2 2
MIRT723763 NKIRAS2 NFKB inhibitor interacting Ras like 2 2 2
MIRT725485 GPR26 G protein-coupled receptor 26 2 2
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-4 Dexamethasone approved 5743 Microarray primary rat thymocytes 20847043 2010 up-regulated
miR-4271 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-4271 Cisplatin 5460033 NSC119875 approved sensitive High Gastric Cancer cell line (BGC823)
hsa-miR-4271 Platinum-based doublet chemotherapy sensitive High Lung Adenocarcinoma tissue
hsa-miR-4271 Platinum 23939 sensitive High Ovarian Cancer tissue
hsa-miR-4271 Fluorouracil 3385 NSC19893 approved sensitive High Pancreatic Cancer cell line (PATU8988)
hsa-miR-4271 Cisplatin 5460033 NSC119875 approved resistant Low Tongue Squamous Cell Carcinoma cell line (CAL-27, SCC-9)
hsa-miR-4271 Paclitaxel 36314 NSC125973 approved resistant High Non-Small Cell Lung Cancer cell line (H460)
hsa-miR-4271 Anlotinib 25017411 NSC832523 sensitive Low Non-Small Cell Lung Cancer cell line (A549, PDC, H460)
hsa-miR-4271 Gefitinib 123631 NSC715055 approved sensitive Low Non-Small Cell Lung Cancer cell line (A549, PDC, H460)
hsa-miR-4271 Icotinib 22024915 NSC800770 sensitive Low Non-Small Cell Lung Cancer cell line (A549, PDC, H460)
hsa-miR-4271 Erlotinib 176870 NSC718781 approved sensitive Low Non-Small Cell Lung Cancer cell line (A549, PDC, H460)
hsa-mir-4271 Cisplatin 5460033 NSC119875 approved resistant cell line (W1)
hsa-mir-4271 Cisplatin 5460033 NSC119875 approved sensitive cell line (A2780)
hsa-mir-4271 Androstenedione+Anastrozole resistant cell line (MCF-7)
hsa-mir-4271 Androstenedione+Letrozole resistant cell line (MCF-7)
hsa-mir-4271 Cisplatin 5460033 NSC119875 approved resistant cell line (BxPC3)
hsa-mir-4271 Cisplatin 5460033 NSC119875 approved sensitive cell line (BGC-823)
hsa-miR-4271 Cisplatin 5460033 NSC119875 approved resistant cell line (CAL-27) (cytosolic RNA)
hsa-miR-4271 Cisplatin 5460033 NSC119875 approved resistant cell line (CAL-27) (total RNA)
hsa-miR-4271 Osimertinib 71496458 NSC779217 approved resistant cell line (H1975)
hsa-miR-4271 Platinum-based doublet chemotherapy sensitive tissue (lung adenocarcinoma)
hsa-miR-4271 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4271 Vemurafenib 42611257 NSC761431 approved sensitive cell line (LM16)
hsa-miR-4271 Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (1500 ng/ml)
hsa-miR-4271 Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (100 ng/ml)
hsa-miR-4271 Paclitaxel/Docetaxel/Vinorelbine/Doxorubicin/Etoposide resistant cell line (Bads-200)

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