miRTarBase - #MIRT114143


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pre-miRNA Information
pre-miRNA hsa-mir-4282   
Genomic Coordinates chr6: 72967687 - 72967753
Description Homo sapiens miR-4282 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4282
Sequence 40| UAAAAUUUGCAUCCAGGA |57
Evidence Experimental
Experiments SOLiD
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN32074657 13 COSMIC
COSN6331413 18 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1195771339 5 dbSNP
rs755058572 6 dbSNP
rs1245753664 11 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol MZT1   
Synonyms C13orf37, MOZART1
Description mitotic spindle organizing protein 1
Transcript NM_001071775   
Expression
Putative miRNA Targets on MZT1
3'UTR of MZT1
(miRNA target sites are highlighted)		 
>MZT1|NM_001071775|3'UTR
   1 CTTTCTGGAGAAATTCTGATGAGATATGTCAAGCTCTGCAAGAGGGTTTGAAGATTGCATTGTAGTTGAGAATGTACAAT
  81 GAAATTACTGCATGCAGCAGTGTAGAAAAATTTTACTTTTTAAAAGAATTATAAAACCATAGCTTTATAAATCAGTGGAA
 161 AGTGGCTTACAGAGAGAACTATCAGATGTGTTTACATCACATCTTATTCACTTTTTTTAACAGCTCTAATGCTTTGGCAT
 241 TGCTATGTTCATATTTATGTATTCCTTATTTATAGCTCTGATAGCTTTAATTTTCTAAGCAGTCTGTCTATCAGATGTGC
 321 ACATCTGCTGTGCCAGGTTGAAGTATAGTGGAACCCATCAGTAGTAATGTGTAGTAGTTATGACTTGTTGACATTTCCAT
 401 TATAAACTTTAATTTTGAATTGTTTATGCATTATAACTGTGGATTTATATTGTATTGGGCTGAAAGTTGACAGGATTTCA
 481 GCCACCACTTGTGAATTTTTATTTAGATTCATTATGTATATCAGAATCTTGTTTTTTGAAATAAGAGCATGGAAAACATT
 561 TCTTGTAATCTACTCTTGAACAAAGAATATTTAGTTTTTCAAACAGTTTGTTGGGCAGCTAATAGTGTGAACCAGGTCAT
 641 TTTTGTATTGAGTAAAAAAATCAAACTTTGAGAAACTTGGATTTTAAAAGTAATGACAATGCTTAGGTTAGTATTATTTG
 721 TAATTTGAATCATTTACATCTAATGAGAATGTTAGTTGAGAATGTTTTCTTAAAGTTTTATATCCTATAAATAACGGAAT
 801 AAAAAAATTTGTAAAATGAAACAACAAACATGCAAAATTCCTATTTACTTTTATTACATAAAAGTAATTTTAGTGCTTAC
 881 CTAATAAATCTTGAATGGTTATTTAATAAATTATTAGATGGGTGATGTGTTTCAAAAGATACTTGCTATTTTTTGAAGAA
 961 ATAAGGATTTCCAGTCATTAAACAAAACTAAACAATCTTATTAGATGGGTGATGTGTTTCAAAGGATACTTGCTATTTTT
1041 TGAAGAAATAAGGATTTCCAGTCATTAAACAAAACTAAACAATCAAATGTTCTATATTAGGAATCTCAAGTATGGCTTTT
1121 TTTAAAAAACCTTTTTAACATCTTGATGTCAAGGATTATAAGTATGGCTTTTCAGAATTGTTTTGTTTGTCATTATTCTT
1201 GCCTTTAAAATTTTAACTCATCAAAGTGAAGATTAGAAATAAATTTTAGAAAATGTAGAATAGTATTGATTCTGTTCCTG
1281 TAATAGAATCTCAGTGGAGTTTTTTTGCAAAACTAATATGGATTTCATCTGATTTTATTATTTCTTAAATTTTAGATTTT
1361 ATTGAGTACCATTTATATGATTGTACAAGCATTCACTCTTTACTAGCATTTTTTGTTTTTCAGACAAGCTGAAGTGGTTT
1441 TATTAAGATTTGGTAATATTTAAATAGCAACCTTCTCTGCCTTTTTTTTTTTTTAATATAGAATTTTGACCATTTTGACT
1521 TTTTAAATGCCTGGCATCTTTACCAACCAAGTAAACTGGAAGATCTGTTACTGGTAGAACAGGTTGAGGAGACAGTAGGA
1601 ATTTGTAAAAAGTCATTTGATTTATAATCAACACTACAAATACTATGTGTTATTTATAAAATCATAAAGAACACTTTTGT
1681 CAGACTCCAAAATTTGTATATACTTCCAGGCCATAAGAGTTGATAGTATTATTTATGACTTTGTAGATTAAGTTATTTAT
1761 GTATGAAACAAAGCAGGAAAATATATTGAGAAGGGATCGTGTTTACAGAGGACTTCTTTAAAGTGTCACATTTTTAAAAT
1841 GTAAACATATTTTTAATGCATACTTAAGTAATATTTAAGAAACTAAACAAAATAATGATACAATTGCAGTGTTGTGCTTG
1921 TTGTCAATGACAAAAATAAAACCATTTTGGTGGTATTGGCCTGTA
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' aggaccuacgUUUAAAAu 5'
                    ||||||| 
Target 5' cttgcctttaAAATTTTa 3'
 1198 - 1215 140.00 -5.10
2 
miRNA  3' agGACCUACGUUUAAAAu 5'
            ||||| | ||||| | 
Target 5' ttCTGGA-G-AAATTCTg 3'
 3 - 18 122.00 -7.30
3 
miRNA  3' agGACCU-ACGUUUAAaau 5'
            :|||: || ||:||   
Target 5' taTTGGGCTGAAAGTTgac 3'
 453 - 471 100.00 -5.42
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30464577 35 COSMIC
COSN18737552 49 COSMIC
COSN26602832 78 COSMIC
COSN1161511 96 COSMIC
COSN31538551 111 COSMIC
COSN31506383 115 COSMIC
COSN31506395 123 COSMIC
COSN31492714 157 COSMIC
COSN1161510 186 COSMIC
COSN31598374 187 COSMIC
COSN31480025 198 COSMIC
COSN31541870 211 COSMIC
COSN31559580 216 COSMIC
COSN30169502 251 COSMIC
COSN27749915 312 COSMIC
COSN23987487 433 COSMIC
COSN20781671 469 COSMIC
COSN15406931 594 COSMIC
COSN26239005 1116 COSMIC
COSN1161509 1277 COSMIC
COSN7416973 1321 COSMIC
COSN20110787 1482 COSMIC
COSN31529352 1660 COSMIC
COSN30172953 1710 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs753244239 5 dbSNP
rs765560555 6 dbSNP
rs1483341050 15 dbSNP
rs759924562 18 dbSNP
rs772763025 19 dbSNP
rs771814228 20 dbSNP
rs1409109424 22 dbSNP
rs1274517289 25 dbSNP
rs758862559 28 dbSNP
rs761415885 33 dbSNP
rs773943956 40 dbSNP
rs768264117 42 dbSNP
rs139369257 46 dbSNP
rs7931 49 dbSNP
rs1292591909 50 dbSNP
rs1364976209 55 dbSNP
rs1388029691 60 dbSNP
rs1301306758 61 dbSNP
rs531502324 76 dbSNP
rs1033550590 79 dbSNP
rs909006444 81 dbSNP
rs1291716765 84 dbSNP
rs1354143166 88 dbSNP
rs1458939271 97 dbSNP
rs980492142 99 dbSNP
rs1487605289 104 dbSNP
rs1349981414 116 dbSNP
rs1157861889 118 dbSNP
rs1193033124 126 dbSNP
rs1002099091 132 dbSNP
rs771956749 139 dbSNP
rs1268120355 142 dbSNP
rs969161419 146 dbSNP
rs1398633219 149 dbSNP
rs1024781466 160 dbSNP
rs887603276 162 dbSNP
rs1177312222 164 dbSNP
rs1382636307 172 dbSNP
rs560948080 174 dbSNP
rs1027912071 181 dbSNP
rs542836258 184 dbSNP
rs1161896938 186 dbSNP
rs527569190 196 dbSNP
rs11550968 202 dbSNP
rs1473126730 204 dbSNP
rs956677923 214 dbSNP
rs993570955 218 dbSNP
rs1293653492 220 dbSNP
rs1268729366 228 dbSNP
rs1444557367 237 dbSNP
rs1311378324 245 dbSNP
rs146911858 247 dbSNP
rs1227563580 248 dbSNP
rs1287432462 250 dbSNP
rs1040364962 262 dbSNP
rs1489483415 266 dbSNP
rs944680824 268 dbSNP
rs1224033282 276 dbSNP
rs1273966261 282 dbSNP
rs762904289 290 dbSNP
rs1457376688 291 dbSNP
rs544972433 297 dbSNP
rs1240592954 302 dbSNP
rs1215306474 310 dbSNP
rs1050649564 315 dbSNP
rs936280798 322 dbSNP
rs184381537 323 dbSNP
rs1039774861 332 dbSNP
rs1269784180 342 dbSNP
rs556189585 345 dbSNP
rs1463618237 354 dbSNP
rs377205625 357 dbSNP
rs1332746728 358 dbSNP
rs926114720 359 dbSNP
rs1447172810 360 dbSNP
rs1388476698 362 dbSNP
rs1367657333 370 dbSNP
rs543996554 372 dbSNP
rs1381071480 374 dbSNP
rs1228609909 380 dbSNP
rs1294154827 381 dbSNP
rs1287832227 387 dbSNP
rs1438946807 389 dbSNP
rs978011848 389 dbSNP
rs1210011515 402 dbSNP
rs1236152493 403 dbSNP
rs1432428644 410 dbSNP
rs945108805 417 dbSNP
rs1189024313 423 dbSNP
rs1422499194 426 dbSNP
rs913664243 430 dbSNP
rs991905683 433 dbSNP
rs1423707867 446 dbSNP
rs1413905199 452 dbSNP
rs763161617 454 dbSNP
rs1360770995 458 dbSNP
rs571068752 458 dbSNP
rs1448515789 459 dbSNP
rs918882019 460 dbSNP
rs1429066107 470 dbSNP
rs1033332947 473 dbSNP
rs1340167788 505 dbSNP
rs573704989 509 dbSNP
rs980683722 511 dbSNP
rs1280238831 514 dbSNP
rs1340147697 518 dbSNP
rs1036435828 521 dbSNP
rs952071624 530 dbSNP
rs554847195 542 dbSNP
rs1212097026 553 dbSNP
rs536486286 558 dbSNP
rs1425948735 559 dbSNP
rs1487138589 570 dbSNP
rs1186075877 574 dbSNP
rs1242274858 576 dbSNP
rs566028820 587 dbSNP
rs554049101 589 dbSNP
rs980460956 590 dbSNP
rs969132247 593 dbSNP
rs1427225778 601 dbSNP
rs917729306 602 dbSNP
rs1157874053 606 dbSNP
rs538609798 608 dbSNP
rs368553158 610 dbSNP
rs1019036939 612 dbSNP
rs571325212 613 dbSNP
rs1300282216 633 dbSNP
rs1327185315 636 dbSNP
rs1435877063 637 dbSNP
rs1273109488 638 dbSNP
rs1209616320 639 dbSNP
rs1347809458 645 dbSNP
rs1235649403 652 dbSNP
rs1285841658 657 dbSNP
rs1351969885 661 dbSNP
rs139032196 661 dbSNP
rs1460672818 661 dbSNP
rs1009010302 662 dbSNP
rs1219177132 664 dbSNP
rs889108387 706 dbSNP
rs1284552980 712 dbSNP
rs149214062 716 dbSNP
rs1030876736 719 dbSNP
rs936243818 727 dbSNP
rs1247921711 737 dbSNP
rs1454699906 740 dbSNP
rs1235295453 747 dbSNP
rs1421301827 754 dbSNP
rs904777986 756 dbSNP
rs1158879850 758 dbSNP
rs1385987221 758 dbSNP
rs1404964361 768 dbSNP
rs1321734541 772 dbSNP
rs1332905791 772 dbSNP
rs11550969 776 dbSNP
rs1041857565 779 dbSNP
rs1312759080 780 dbSNP
rs770964160 787 dbSNP
rs1001197540 791 dbSNP
rs537930895 795 dbSNP
rs191564101 796 dbSNP
rs1280476211 798 dbSNP
rs747137317 801 dbSNP
rs1207680509 807 dbSNP
rs189703850 808 dbSNP
rs527531007 813 dbSNP
rs560445876 816 dbSNP
rs1030238308 830 dbSNP
rs1401918773 833 dbSNP
rs994388389 847 dbSNP
rs1367664341 848 dbSNP
rs1472630941 848 dbSNP
rs1161686206 852 dbSNP
rs776378705 855 dbSNP
rs1462054501 864 dbSNP
rs1330720206 873 dbSNP
rs1038584115 876 dbSNP
rs1393628140 879 dbSNP
rs1308228558 883 dbSNP
rs1340240637 890 dbSNP
rs1242978788 893 dbSNP
rs1468028820 901 dbSNP
rs551712491 907 dbSNP
rs1285606708 908 dbSNP
rs1335020880 920 dbSNP
rs1217515177 922 dbSNP
rs768544672 924 dbSNP
rs1255569174 935 dbSNP
rs972044909 937 dbSNP
rs1360189330 942 dbSNP
rs184401412 948 dbSNP
rs1440500447 951 dbSNP
rs1189304225 974 dbSNP
rs1420338653 976 dbSNP
rs887421450 992 dbSNP
rs1170129082 1008 dbSNP
rs1464036077 1012 dbSNP
rs1392133497 1016 dbSNP
rs1299244617 1020 dbSNP
rs562322932 1024 dbSNP
rs1394673706 1025 dbSNP
rs1315126903 1035 dbSNP
rs1355740976 1047 dbSNP
rs775561978 1053 dbSNP
rs145215829 1058 dbSNP
rs149982267 1064 dbSNP
rs992318525 1074 dbSNP
rs41283992 1080 dbSNP
rs1250643776 1082 dbSNP
rs548587548 1084 dbSNP
rs1202009873 1087 dbSNP
rs1257943966 1089 dbSNP
rs1486157511 1090 dbSNP
rs369129426 1094 dbSNP
rs979318295 1095 dbSNP
rs1343643027 1107 dbSNP
rs904559799 1112 dbSNP
rs572315544 1123 dbSNP
rs1010513064 1124 dbSNP
rs1377587188 1124 dbSNP
rs55925056 1131 dbSNP
rs1376439934 1152 dbSNP
rs1419410893 1154 dbSNP
rs1314442239 1158 dbSNP
rs1018277372 1161 dbSNP
rs985494997 1164 dbSNP
rs1299955767 1172 dbSNP
rs895958179 1178 dbSNP
rs1236395862 1184 dbSNP
rs1280857591 1210 dbSNP
rs1057247018 1221 dbSNP
rs1398088641 1245 dbSNP
rs1380372559 1253 dbSNP
rs769304278 1255 dbSNP
rs374802734 1272 dbSNP
rs1187224731 1274 dbSNP
rs9543091 1276 dbSNP
rs926380816 1280 dbSNP
rs1169370393 1286 dbSNP
rs367887027 1287 dbSNP
rs1396151241 1290 dbSNP
rs868552931 1293 dbSNP
rs776197978 1295 dbSNP
rs1366869654 1300 dbSNP
rs367968036 1316 dbSNP
rs778662478 1319 dbSNP
rs1346637310 1337 dbSNP
rs930301755 1338 dbSNP
rs192481881 1340 dbSNP
rs556270549 1348 dbSNP
rs1292491079 1350 dbSNP
rs897293982 1352 dbSNP
rs1442386346 1353 dbSNP
rs1017539676 1356 dbSNP
rs1424136210 1361 dbSNP
rs1237733727 1362 dbSNP
rs1250855705 1364 dbSNP
rs1179899368 1371 dbSNP
rs1484030087 1375 dbSNP
rs972377528 1377 dbSNP
rs1005744378 1383 dbSNP
rs961970365 1387 dbSNP
rs1353666289 1396 dbSNP
rs9318114 1403 dbSNP
rs1254209866 1408 dbSNP
rs1439587112 1415 dbSNP
rs987306281 1421 dbSNP
rs1341411970 1430 dbSNP
rs1410598384 1436 dbSNP
rs953410659 1437 dbSNP
rs1029486849 1444 dbSNP
rs1000326468 1448 dbSNP
rs1366295538 1450 dbSNP
rs866120549 1453 dbSNP
rs1020295820 1461 dbSNP
rs1010419078 1467 dbSNP
rs1444452154 1471 dbSNP
rs1352935453 1475 dbSNP
rs1309178095 1477 dbSNP
rs1386234250 1481 dbSNP
rs1373781524 1482 dbSNP
rs201268168 1482 dbSNP
rs1227471949 1484 dbSNP
rs1388707848 1484 dbSNP
rs1165190883 1485 dbSNP
rs896147849 1489 dbSNP
rs896072648 1490 dbSNP
rs1057192377 1493 dbSNP
rs1273863916 1494 dbSNP
rs1235033759 1495 dbSNP
rs1253623963 1495 dbSNP
rs35899662 1495 dbSNP
rs539797231 1495 dbSNP
rs77819695 1495 dbSNP
rs796390698 1495 dbSNP
rs1156770635 1496 dbSNP
rs935093087 1498 dbSNP
rs1473455037 1499 dbSNP
rs1252381343 1500 dbSNP
rs1198099753 1501 dbSNP
rs923778494 1503 dbSNP
rs1001649340 1506 dbSNP
rs979290219 1507 dbSNP
rs1268889962 1508 dbSNP
rs567652698 1510 dbSNP
rs946608647 1530 dbSNP
rs906070485 1534 dbSNP
rs1045195434 1541 dbSNP
rs1464060315 1546 dbSNP
rs1172461118 1562 dbSNP
rs1354988066 1566 dbSNP
rs1447052637 1571 dbSNP
rs1300831707 1576 dbSNP
rs1349576308 1596 dbSNP
rs1267885743 1607 dbSNP
rs930437965 1613 dbSNP
rs535818178 1614 dbSNP
rs985377269 1617 dbSNP
rs1275752025 1621 dbSNP
rs1289481953 1631 dbSNP
rs1255825658 1636 dbSNP
rs898799072 1638 dbSNP
rs1036048469 1639 dbSNP
rs1486482612 1644 dbSNP
rs940549967 1646 dbSNP
rs911820869 1650 dbSNP
rs987421133 1658 dbSNP
rs371877584 1661 dbSNP
rs955370441 1663 dbSNP
rs1261934680 1664 dbSNP
rs1474153659 1669 dbSNP
rs1030091274 1673 dbSNP
rs1420187704 1685 dbSNP
rs568646329 1692 dbSNP
rs972821154 1696 dbSNP
rs931802664 1698 dbSNP
rs1173761893 1700 dbSNP
rs1377041194 1703 dbSNP
rs1233210071 1705 dbSNP
rs748993121 1713 dbSNP
rs1313726102 1719 dbSNP
rs1340069486 1720 dbSNP
rs4885028 1725 dbSNP
rs1325681531 1728 dbSNP
rs1363337855 1738 dbSNP
rs1017048502 1744 dbSNP
rs1005712015 1763 dbSNP
rs187881709 1772 dbSNP
rs1211982924 1773 dbSNP
rs1284904908 1775 dbSNP
rs1318796248 1777 dbSNP
rs183251604 1784 dbSNP
rs988777930 1786 dbSNP
rs960063164 1789 dbSNP
rs1035900229 1792 dbSNP
rs1242176012 1796 dbSNP
rs551626725 1798 dbSNP
rs531398330 1799 dbSNP
rs1191670132 1814 dbSNP
rs1396744013 1817 dbSNP
rs896129249 1835 dbSNP
rs1157790455 1836 dbSNP
rs1384577910 1844 dbSNP
rs1056555921 1851 dbSNP
rs1320438675 1857 dbSNP
rs1435765803 1868 dbSNP
rs999270657 1872 dbSNP
rs902296080 1873 dbSNP
rs1235528206 1874 dbSNP
rs1308958791 1895 dbSNP
rs1027167042 1901 dbSNP
rs533249206 1903 dbSNP
rs994973393 1908 dbSNP
rs1450548901 1910 dbSNP
rs192567564 1914 dbSNP
rs1210245401 1917 dbSNP
rs1468838350 1918 dbSNP
rs1466505900 1922 dbSNP
rs1177833624 1925 dbSNP
rs1035996200 1926 dbSNP
rs570569032 1927 dbSNP
rs1160518807 1938 dbSNP
rs1408915174 1950 dbSNP
rs890168313 1955 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 440145.0
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 GSM714644. RNA binding protein: AGO2. Condition:completeT1 ...

- Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' aggaccuacgUUUAAAAu 5'
                    ||||||| 
Target 5' cuugccuuuaAAAUUUUa 3'
 		9 - 26
Article - Kishore S; Jaskiewicz L; Burger L; Hausser et al.
- Nature methods, 2011
Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.
LinkOut: [PMID: 21572407]
Experimental Support 2 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' aggaccuacgUUUAAAAu 5'
                    ||||||| 
Target 5' cuugccuuuaAAAUUUUa 3'
 		7 - 24
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 GSM714644
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repA
Location of target site ENST00000377818.3 | 3UTR | UCAUUAUUCUUGCCUUUAAAAUUUUAACUCAUCAAAGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1462573
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl BaL
Location of target site ENST00000377818.3 | 3UTR | AUUAUUCUUGCCUUUAAAAUUUUAACUCAUCAAAG
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
280 hsa-miR-4282 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT057628 LCOR ligand dependent nuclear receptor corepressor 2 2
MIRT060732 RPS3 ribosomal protein S3 2 2
MIRT063371 ETNK1 ethanolamine kinase 1 2 2
MIRT066257 LRIG3 leucine rich repeats and immunoglobulin like domains 3 2 4
MIRT070774 HIF1A hypoxia inducible factor 1 alpha subunit 2 2
MIRT070871 EIF2S1 eukaryotic translation initiation factor 2 subunit alpha 2 4
MIRT078056 PCTP phosphatidylcholine transfer protein 2 2
MIRT078408 DCAF7 DDB1 and CUL4 associated factor 7 2 4
MIRT084059 PPP1R3D protein phosphatase 1 regulatory subunit 3D 2 2
MIRT093537 GALNT7 polypeptide N-acetylgalactosaminyltransferase 7 2 6
MIRT096072 SFXN1 sideroflexin 1 2 2
MIRT098316 REV3L REV3 like, DNA directed polymerase zeta catalytic subunit 2 2
MIRT100493 UHRF1BP1 UHRF1 binding protein 1 2 2
MIRT102254 HBP1 HMG-box transcription factor 1 2 4
MIRT105318 VPS37A VPS37A, ESCRT-I subunit 2 2
MIRT114143 MZT1 mitotic spindle organizing protein 1 2 4
MIRT114873 DICER1 dicer 1, ribonuclease III 2 2
MIRT134683 PNRC2 proline rich nuclear receptor coactivator 2 2 2
MIRT137640 RCOR1 REST corepressor 1 2 2
MIRT155449 CCNT2 cyclin T2 2 4
MIRT165656 DCTN4 dynactin subunit 4 2 2
MIRT177570 CSTF2T cleavage stimulation factor subunit 2 tau variant 2 4
MIRT188514 E2F7 E2F transcription factor 7 2 10
MIRT193019 TMOD3 tropomodulin 3 2 4
MIRT195823 GADD45A growth arrest and DNA damage inducible alpha 2 2
MIRT195885 DEPDC1 DEP domain containing 1 2 6
MIRT206029 NUP50 nucleoporin 50 2 6
MIRT212148 CLCN3 chloride voltage-gated channel 3 2 2
MIRT213999 DCP2 decapping mRNA 2 2 2
MIRT214650 HNRNPA0 heterogeneous nuclear ribonucleoprotein A0 2 2
MIRT221568 CBX3 chromobox 3 2 2
MIRT224544 ZNF623 zinc finger protein 623 2 2
MIRT227654 SET SET nuclear proto-oncogene 2 2
MIRT229992 CHIC1 cysteine rich hydrophobic domain 1 2 2
MIRT238968 QKI QKI, KH domain containing RNA binding 2 2
MIRT239825 ACTB actin beta 2 2
MIRT241084 ZXDA zinc finger, X-linked, duplicated A 2 4
MIRT244852 ZBTB5 zinc finger and BTB domain containing 5 2 2
MIRT264534 TARDBP TAR DNA binding protein 2 2
MIRT271438 SKI SKI proto-oncogene 2 2
MIRT271597 ENAH ENAH, actin regulator 2 2
MIRT294332 ZNF264 zinc finger protein 264 2 2
MIRT296341 PARD6B par-6 family cell polarity regulator beta 2 2
MIRT301715 TEF TEF, PAR bZIP transcription factor 2 2
MIRT308549 ZNF654 zinc finger protein 654 2 2
MIRT313866 DEPDC1B DEP domain containing 1B 2 2
MIRT315529 MARCKS myristoylated alanine rich protein kinase C substrate 2 2
MIRT321066 RABGEF1 RAB guanine nucleotide exchange factor 1 2 2
MIRT343777 NUTF2 nuclear transport factor 2 2 2
MIRT359109 MAP1B microtubule associated protein 1B 2 2
MIRT397393 GOLGA3 golgin A3 2 4
MIRT400822 CPEB2 cytoplasmic polyadenylation element binding protein 2 2 2
MIRT442171 DSEL dermatan sulfate epimerase-like 2 2
MIRT442777 JAG1 jagged 1 2 2
MIRT442862 SCARF1 scavenger receptor class F member 1 2 4
MIRT442919 PCBD2 pterin-4 alpha-carbinolamine dehydratase 2 2 2
MIRT444567 TRA2B transformer 2 beta homolog 2 2
MIRT444718 CMSS1 cms1 ribosomal small subunit homolog (yeast) 2 2
MIRT445018 RBMS3 RNA binding motif single stranded interacting protein 3 2 2
MIRT445853 LRRC1 leucine rich repeat containing 1 2 2
MIRT446242 HELZ helicase with zinc finger 2 2
MIRT446542 GOLGA8B golgin A8 family member B 2 2
MIRT446643 SPTY2D1 SPT2 chromatin protein domain containing 1 2 2
MIRT446948 ZMAT3 zinc finger matrin-type 3 2 4
MIRT447061 KCNAB1 potassium voltage-gated channel subfamily A member regulatory beta subunit 1 2 2
MIRT447327 ZSCAN21 zinc finger and SCAN domain containing 21 2 2
MIRT447995 CDX1 caudal type homeobox 1 2 2
MIRT448543 RHEBP1 RHEB pseudogene 1 2 6
MIRT448752 HINT1 histidine triad nucleotide binding protein 1 2 2
MIRT448772 GOLGA8A golgin A8 family member A 2 2
MIRT449342 WDR26 WD repeat domain 26 2 2
MIRT450011 SLC16A6 solute carrier family 16 member 6 2 4
MIRT450229 PCNX pecanex homolog 1 2 2
MIRT450340 MRPL17 mitochondrial ribosomal protein L17 2 4
MIRT450381 MSI2 musashi RNA binding protein 2 2 2
MIRT450759 PGGT1B protein geranylgeranyltransferase type I subunit beta 2 2
MIRT450809 NRCAM neuronal cell adhesion molecule 2 2
MIRT450947 ATAD2 ATPase family, AAA domain containing 2 2 2
MIRT459095 CCPG1 cell cycle progression 1 2 2
MIRT462428 TWISTNB TWIST neighbor 2 2
MIRT465200 TROVE2 TROVE domain family member 2 2 4
MIRT467382 SON SON DNA binding protein 2 4
MIRT468546 SERP1 stress associated endoplasmic reticulum protein 1 2 2
MIRT471506 PDE4D phosphodiesterase 4D 2 2
MIRT471981 NR3C1 nuclear receptor subfamily 3 group C member 1 2 2
MIRT474478 KLHL11 kelch like family member 11 2 8
MIRT475011 KANSL1 KAT8 regulatory NSL complex subunit 1 2 8
MIRT480341 C5orf51 chromosome 5 open reading frame 51 2 2
MIRT482696 TEX9 testis expressed 9 2 6
MIRT483462 YTHDF1 YTH N6-methyladenosine RNA binding protein 1 2 6
MIRT485623 FAM217B family with sequence similarity 217 member B 2 2
MIRT485714 CASP16 caspase 16, pseudogene 2 8
MIRT486279 SEC23A Sec23 homolog A, coat complex II component 2 2
MIRT491000 PEBP1 phosphatidylethanolamine binding protein 1 2 4
MIRT492594 PPIL4 peptidylprolyl isomerase like 4 2 2
MIRT493365 KIF5B kinesin family member 5B 2 2
MIRT494316 CDKN1B cyclin dependent kinase inhibitor 1B 2 2
MIRT495208 EDN3 endothelin 3 2 2
MIRT497011 TCF15 transcription factor 15 2 2
MIRT498512 FRK fyn related Src family tyrosine kinase 2 2
MIRT498778 PARP15 poly(ADP-ribose) polymerase family member 15 2 2
MIRT501045 SMG1 SMG1, nonsense mediated mRNA decay associated PI3K related kinase 2 6
MIRT502939 CDC37L1 cell division cycle 37 like 1 2 8
MIRT504806 VHL von Hippel-Lindau tumor suppressor 2 6
MIRT505656 SHMT1 serine hydroxymethyltransferase 1 2 6
MIRT505964 RAB5C RAB5C, member RAS oncogene family 2 6
MIRT506322 OTUD4 OTU deubiquitinase 4 2 4
MIRT506803 KLHL15 kelch like family member 15 2 6
MIRT506917 KBTBD8 kelch repeat and BTB domain containing 8 2 4
MIRT507400 EMC7 ER membrane protein complex subunit 7 2 8
MIRT507471 EDEM3 ER degradation enhancing alpha-mannosidase like protein 3 2 6
MIRT508058 ATP13A3 ATPase 13A3 2 4
MIRT508135 AMD1 adenosylmethionine decarboxylase 1 2 2
MIRT509895 RPS23 ribosomal protein S23 2 4
MIRT510881 RAN RAN, member RAS oncogene family 2 8
MIRT513766 PEX5L peroxisomal biogenesis factor 5 like 2 4
MIRT516898 COPS8 COP9 signalosome subunit 8 2 2
MIRT518703 TIMD4 T-cell immunoglobulin and mucin domain containing 4 2 4
MIRT520429 TTPAL alpha tocopherol transfer protein like 2 6
MIRT521843 PNISR PNN interacting serine and arginine rich protein 2 4
MIRT522116 NUDT3 nudix hydrolase 3 2 4
MIRT525467 TMPRSS12 transmembrane protease, serine 12 2 2
MIRT525583 MTRNR2L7 MT-RNR2-like 7 2 2
MIRT525906 BUB1 BUB1 mitotic checkpoint serine/threonine kinase 2 2
MIRT526072 C11orf54 chromosome 11 open reading frame 54 2 2
MIRT526232 MTRNR2L5 MT-RNR2-like 5 2 4
MIRT526455 FAM71F2 family with sequence similarity 71 member F2 2 4
MIRT526515 POU5F1B POU class 5 homeobox 1B 2 2
MIRT528032 FEZ2 fasciculation and elongation protein zeta 2 2 2
MIRT528422 MRPS16 mitochondrial ribosomal protein S16 2 2
MIRT528995 ISLR2 immunoglobulin superfamily containing leucine rich repeat 2 2 4
MIRT529311 ATRNL1 attractin like 1 2 2
MIRT529376 SKP1 S-phase kinase associated protein 1 2 4
MIRT530015 SRRM1 serine and arginine repetitive matrix 1 2 2
MIRT530089 FMN2 formin 2 2 2
MIRT530942 ENPP6 ectonucleotide pyrophosphatase/phosphodiesterase 6 2 2
MIRT531229 HIST1H2BD histone cluster 1 H2B family member d 2 2
MIRT533088 YTHDF3 YTH N6-methyladenosine RNA binding protein 3 2 2
MIRT533299 USP46 ubiquitin specific peptidase 46 2 2
MIRT533318 UNKL unkempt family like zinc finger 2 2
MIRT533721 TMEM30A transmembrane protein 30A 2 2
MIRT534096 AZF1 azoospermia factor 1 2 2
MIRT534188 SLC7A11 solute carrier family 7 member 11 2 2
MIRT534493 SAR1B secretion associated Ras related GTPase 1B 2 2
MIRT536077 MBOAT2 membrane bound O-acyltransferase domain containing 2 2 2
MIRT536242 LRIG2 leucine rich repeats and immunoglobulin like domains 2 2 2
MIRT537524 FAM104A family with sequence similarity 104 member A 2 2
MIRT538088 DGKH diacylglycerol kinase eta 2 2
MIRT538475 CNBP CCHC-type zinc finger nucleic acid binding protein 2 2
MIRT538853 BTG1 BTG anti-proliferation factor 1 2 4
MIRT539075 GDNF glial cell derived neurotrophic factor 2 2
MIRT539480 ACVR2B activin A receptor type 2B 2 4
MIRT540210 ARHGAP18 Rho GTPase activating protein 18 2 2
MIRT541940 TSPAN2 tetraspanin 2 2 2
MIRT543812 COCH cochlin 2 2
MIRT545120 PDZRN4 PDZ domain containing ring finger 4 2 2
MIRT545571 GIMAP4 GTPase, IMAP family member 4 2 2
MIRT545989 XKR4 XK related 4 2 2
MIRT547213 PANK3 pantothenate kinase 3 2 4
MIRT547740 KIAA1468 KIAA1468 2 2
MIRT548022 GRB2 growth factor receptor bound protein 2 2 4
MIRT548032 GOLIM4 golgi integral membrane protein 4 2 2
MIRT548102 GFPT1 glutamine--fructose-6-phosphate transaminase 1 2 4
MIRT548217 FKBP1A FK506 binding protein 1A 2 2
MIRT548588 DDX3X DEAD-box helicase 3, X-linked 2 4
MIRT548953 CDC27 cell division cycle 27 2 2
MIRT549072 CACUL1 CDK2 associated cullin domain 1 2 2
MIRT550368 INCENP inner centromere protein 2 6
MIRT550546 MYZAP myocardial zonula adherens protein 2 2
MIRT551491 TMEM192 transmembrane protein 192 2 4
MIRT553078 UEVLD UEV and lactate/malate dehyrogenase domains 2 2
MIRT554104 SMU1 DNA replication regulator and spliceosomal factor 2 2
MIRT555127 PTPRG protein tyrosine phosphatase, receptor type G 2 2
MIRT555477 POC1B-GALNT4 POC1B-GALNT4 readthrough 2 2
MIRT555978 NPTN neuroplastin 2 2
MIRT557011 HPRT1 hypoxanthine phosphoribosyltransferase 1 2 2
MIRT557706 GALNT4 polypeptide N-acetylgalactosaminyltransferase 4 2 2
MIRT558333 DNAJC28 DnaJ heat shock protein family (Hsp40) member C28 2 4
MIRT558488 DBN1 drebrin 1 2 2
MIRT559942 ZNF567 zinc finger protein 567 2 2
MIRT561127 ATP2B1 ATPase plasma membrane Ca2+ transporting 1 2 2
MIRT561791 PAWR pro-apoptotic WT1 regulator 2 2
MIRT562438 EEF2 eukaryotic translation elongation factor 2 2 2
MIRT563102 PABPC4L poly(A) binding protein cytoplasmic 4 like 2 2
MIRT563212 ZNF813 zinc finger protein 813 2 2
MIRT563426 KIF3A kinesin family member 3A 2 2
MIRT563473 SPIN4 spindlin family member 4 2 2
MIRT564015 HSPA4 heat shock protein family A (Hsp70) member 4 2 4
MIRT564117 ZYG11B zyg-11 family member B, cell cycle regulator 2 2
MIRT564223 SDE2 SDE2 telomere maintenance homolog 2 2
MIRT564503 CACNG1 calcium voltage-gated channel auxiliary subunit gamma 1 2 2
MIRT564515 DUSP3 dual specificity phosphatase 3 2 2
MIRT564811 ZBTB21 zinc finger and BTB domain containing 21 2 2
MIRT565265 TPD52 tumor protein D52 2 2
MIRT566012 RHOB ras homolog family member B 2 2
MIRT566216 PTMA prothymosin, alpha 2 2
MIRT566638 NFYA nuclear transcription factor Y subunit alpha 2 2
MIRT566821 MAPK8 mitogen-activated protein kinase 8 2 2
MIRT566948 LEPROT leptin receptor overlapping transcript 2 2
MIRT567290 HNRNPAB heterogeneous nuclear ribonucleoprotein A/B 2 2
MIRT567895 CSTF2 cleavage stimulation factor subunit 2 2 2
MIRT568731 MTRNR2L3 MT-RNR2-like 3 2 2
MIRT571263 ZNF239 zinc finger protein 239 2 2
MIRT572593 EIF2AK4 eukaryotic translation initiation factor 2 alpha kinase 4 2 2
MIRT573827 TGOLN2 trans-golgi network protein 2 2 2
MIRT576391 Fhl2 four and a half LIM domains 2 2 2
MIRT609901 SMS spermine synthase 2 2
MIRT613710 ELMSAN1 ELM2 and Myb/SANT domain containing 1 2 2
MIRT614406 ADAT1 adenosine deaminase, tRNA specific 1 2 2
MIRT615042 DCX doublecortin 2 2
MIRT617514 C5orf45 MRN complex interacting protein 2 2
MIRT619476 PRDM10 PR/SET domain 10 2 2
MIRT620349 TLN1 talin 1 2 2
MIRT620910 PLA2G7 phospholipase A2 group VII 2 2
MIRT622131 SP4 Sp4 transcription factor 2 2
MIRT622955 OTUD7B OTU deubiquitinase 7B 2 2
MIRT623351 MAGI3 membrane associated guanylate kinase, WW and PDZ domain containing 3 2 2
MIRT623619 INTU inturned planar cell polarity protein 2 2
MIRT624409 CCDC171 coiled-coil domain containing 171 2 2
MIRT625171 CCS copper chaperone for superoxide dismutase 2 2
MIRT625685 RPP40 ribonuclease P/MRP subunit p40 2 2
MIRT625875 ALDH18A1 aldehyde dehydrogenase 18 family member A1 2 2
MIRT626002 FAM107A family with sequence similarity 107 member A 2 2
MIRT626872 HRH4 histamine receptor H4 2 4
MIRT628220 FKBP9 FK506 binding protein 9 2 2
MIRT628265 DIO2 iodothyronine deiodinase 2 2 2
MIRT628402 C8orf37 chromosome 8 open reading frame 37 2 2
MIRT630564 C3orf36 chromosome 3 open reading frame 36 2 4
MIRT631577 RASSF9 Ras association domain family member 9 2 2
MIRT635730 CCDC58 coiled-coil domain containing 58 2 2
MIRT636224 SLC8A1 solute carrier family 8 member A1 2 2
MIRT636613 CLIC5 chloride intracellular channel 5 2 2
MIRT638899 CDK9 cyclin dependent kinase 9 2 2
MIRT640167 ATXN7L1 ataxin 7 like 1 2 2
MIRT642070 GTDC1 glycosyltransferase like domain containing 1 2 2
MIRT643034 CHCHD7 coiled-coil-helix-coiled-coil-helix domain containing 7 2 2
MIRT644572 SPOP speckle type BTB/POZ protein 2 2
MIRT644954 IFNB1 interferon beta 1 2 2
MIRT645948 TTF2 transcription termination factor 2 2 2
MIRT646440 XRCC2 X-ray repair cross complementing 2 2 2
MIRT647896 EPN2 epsin 2 2 2
MIRT648276 ZNF582 zinc finger protein 582 2 2
MIRT649381 NEDD1 neural precursor cell expressed, developmentally down-regulated 1 2 2
MIRT650254 CD68 CD68 molecule 2 2
MIRT650333 ATP5S ATP synthase, H+ transporting, mitochondrial Fo complex subunit s (factor B) 2 2
MIRT651707 VMP1 vacuole membrane protein 1 2 2
MIRT651774 VASP vasodilator stimulated phosphoprotein 2 2
MIRT653144 SRPK2 SRSF protein kinase 2 2 2
MIRT654112 RPS6KA5 ribosomal protein S6 kinase A5 2 2
MIRT654161 RORB RAR related orphan receptor B 2 2
MIRT655716 MLF2 myeloid leukemia factor 2 2 2
MIRT657476 HDAC4 histone deacetylase 4 2 2
MIRT658095 FOXO1 forkhead box O1 2 2
MIRT658860 DTX3L deltex E3 ubiquitin ligase 3L 2 2
MIRT658988 DNAJA1 DnaJ heat shock protein family (Hsp40) member A1 2 2
MIRT660767 ALDH6A1 aldehyde dehydrogenase 6 family member A1 2 2
MIRT661622 C2orf15 chromosome 2 open reading frame 15 2 2
MIRT661694 TFDP2 transcription factor Dp-2 2 2
MIRT662208 PLA2G4E phospholipase A2 group IVE 2 2
MIRT662443 RALGAPA1 Ral GTPase activating protein catalytic alpha subunit 1 2 2
MIRT664422 ADH5 alcohol dehydrogenase 5 (class III), chi polypeptide 2 2
MIRT687505 NECAB1 N-terminal EF-hand calcium binding protein 1 2 2
MIRT689910 SOD2 superoxide dismutase 2 2 2
MIRT690781 PLA2G2C phospholipase A2 group IIC 2 2
MIRT698488 TIAL1 TIA1 cytotoxic granule associated RNA binding protein like 1 2 2
MIRT699685 SFMBT2 Scm like with four mbt domains 2 2 2
MIRT700926 PDS5A PDS5 cohesin associated factor A 2 2
MIRT702258 LMNB1 lamin B1 2 2
MIRT703166 GPR137C G protein-coupled receptor 137C 2 2
MIRT703242 GNS glucosamine (N-acetyl)-6-sulfatase 2 2
MIRT704737 CENPQ centromere protein Q 2 2
MIRT707310 GLRX2 glutaredoxin 2 2 2
MIRT710021 KCNQ5 potassium voltage-gated channel subfamily Q member 5 2 2
MIRT712212 SCOC short coiled-coil protein 2 2
MIRT714742 SETBP1 SET binding protein 1 2 2
MIRT718268 ZNF749 zinc finger protein 749 2 2
MIRT720553 DYRK4 dual specificity tyrosine phosphorylation regulated kinase 4 2 2
MIRT722248 RBM41 RNA binding motif protein 41 2 2
MIRT723767 MPLKIP M-phase specific PLK1 interacting protein 2 2
MIRT723977 KIAA0146 scaffolding protein involved in DNA repair 1 1
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
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-4282 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4282 Neoadjuvant chemotherapy sensitive tissue (breast cancer)
hsa-miR-4282 Neoadjuvant chemotherapy sensitive tissue (breast cancer)

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