pre-miRNA Information
pre-miRNA hsa-mir-4747   
Genomic Coordinates chr19: 4932687 - 4932740
Description Homo sapiens miR-4747 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4747-5p
Sequence 1| AGGGAAGGAGGCUUGGUCUUAG |22
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs560927363 4 dbSNP
rs1471226927 10 dbSNP
rs763137545 12 dbSNP
rs767337154 15 dbSNP
rs775298039 16 dbSNP
rs760472311 19 dbSNP
rs1207950315 21 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol LHFPL3   
Synonyms LHFPL4
Description LHFPL tetraspan subfamily member 3
Transcript NM_199000   
Expression
Putative miRNA Targets on LHFPL3
3'UTR of LHFPL3
(miRNA target sites are highlighted)
>LHFPL3|NM_199000|3'UTR
   1 GCACAAAACAAATCGAATAACAGCTAAACAAATCGAATAACAGCTAAACGAATCGAATAACAGCTTTTGTACATCAACAT
  81 CAAGAAGGAATACGCCTGAGAGAGATCAGAGTATATAGATGAATATGAACAAGAATGGAACATTCACTTGTCAACGCACT
 161 TTCTAAATCTAGATCAGCAGAGATGGGAGTGATTTTCTGGAAAGAGATGTGATCATGGATTAAACACCAGCTCATTGGAA
 241 ACTCATTGGATGAGATCAGAAAACGTTCATGAAAAATCATATTCAGGAAATAAGGAAGAGGAATATAAATGCTCTAGAGT
 321 TAACATGTAAAATATATACGTACTGAGGTTTGTAAACTGTCCTTTTTAAATCAAACTGAAAACAAAAAGCTTTAACCTTT
 401 CAACAGAATTTTTAAAAAGGCAGTTAGTTCTAAATTATTCCTATCTCAATAGCCAAGAGGCTGATCAAGCGTCATTTATT
 481 GAGGAAGCATCTTAGAAAATGCCTCTGAATGTTTTCATAGGAGCCGTGACCTTTGGTTCTTCATCTCTACCATTCATTTA
 561 CTTCACTGTGTAATTAGTTACAACCACTCAGTTATTAAGAGACGTAACGCTTCAAACTTTTTACCAAGTCTGTGTTCTGT
 641 TTAATCTGTCCATACAAGTTATTACTGAGAAAGTGTTTATGCCATATACTATTACTCCATCAAGCTGTATATTACAGGAA
 721 GTACATCTTTACATCATAGGTTCCCAAGCAACATAGATTTCCCTATCTTTCAGGAAACAGCATCAAGGAACTCTGAAAAA
 801 TATAGAAAAAGTTCATTTTCACCTTGGAAGCTCACGTGTAATATTATAGGCTACTATCAAATAAACACTTTTTTTCTAAT
 881 TCTCCCTAGTATATGCATAGGAATTTAATATACTTTATAAATAAGTATCTAAAATGTCTCCTACTTTTTTCCTATTTCTT
 961 TGCCATACATGTTATCAGAAATCCATGTCTTCTATTTCCCTTACTGATGGGCACTCATTTTTATTTTTTTAAAAATCATT
1041 CCATTAAACATATTTCTAAATAATAGTAAGTGGTACTAACAAAATAAATAATAATTTAATAGCCTTAGAAATAAATGACT
1121 GTATACTTATACAGGTTGAAAAAAACTCGGTAGGAATAAGTTACCTTTTTGTTTACTAATGTTGGTTTCAAAAATACTCA
1201 GATTCATTTTAGTTGGCTGACATCTGGAAGTAGTTAACAACTAACCAGTGGACTTCAACAATCATTTGCTCCCAGGCTTC
1281 CCCCATCATCACCCTCACCACATATCCTGCTAATATCCAACAACAAACAAATATTTAATATTGAAATAGCCCATTGCCTG
1361 AGAATGAACACAAGCTAAAATACATGCAAGGGTACTTAATGGAAGCCAAACCATGTTCTATACCTAAGGAGAAAACATGG
1441 ACATGTAGAATGCTTTTATTCATGTATTCAAAATCAGAACAAATCAGTGTATATCACTAGAACATCAGATGGAGGATAAC
1521 ACAAGAAGTGATACAGATCAGGGTTCACTTCTCTTACCCTCTCTCTGTTAGGACCACATTCCTATTTTAGCCAAATGTTT
1601 CTGGTACGGGCCATCTTTTCACCATAAATGGCATTATGTTTCAAATGGCTAAAAGCATATTATGGGTATGCTCAAAGGAG
1681 TAAAACCCAATTCACAGAGATGTGGCTTTTCTAAAGAACCAAATTAAGGGAATACTTAGTATCTACAACTAAAGTATTAG
1761 TCATTCTGAGGATTATTTGTTGCTTTAAGTATTAGCTCCCTACTACATCCATAACACCCTACTTACTAAATTTAATTACA
1841 CACAACTTTTCAAGAATTCGTATTTTATTTGAAGGGAGGTACCTGTCTACTTTATCTACAATAAAAACAAAGGGTATTGG
1921 CTTTCTCTAATCCATGCAAACTACAAATTCCATCGGGAGTCCTACATCACTAACAGTGGTATGAACAAAACTAAGAAAGT
2001 ACTTCCTATCCACATGTGAATGTTTTAAAAAAGTTTTTGCCATAAAACCTAAGTGTAATTTAGCATACCACAGTGCTCTG
2081 AAGATGGGTCATTGACGATGTACCATTTGTATATAGGTAATACACATGTAAATCACTAATTGTTAATTAAATATAAGAAG
2161 TAGGTTTTTATCTTTTTAAAAAAAAAACAAAAAAGGTGACTCCCTTTCTCATTCTGTTCTGTTGTATTGCGTCCAAAAGT
2241 TGTGTGTAATTTTTTTAAGGTCCAAGAAATGTAAAGAAATTTGTTGGAATACCTGAATTTCTGTAAAAAAATAAAAATAA
2321 AAATAAGATTTTGTTACTTAAAAAAAAAAAAAAAAA
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' gauUCUGGUUCGGAG-GAAGGGa 5'
             |||:||:| :|| ||||:| 
Target 5' tacAGATCAGGGTTCACTTCTCt 3'
1532 - 1554 127.00 -22.40
2
miRNA  3' gaUUCUGGUUCGGA---GGAAGGga 5'
            || |  ||||:|   ||||:|  
Target 5' aaAACAAAAAGCTTTAACCTTTCaa 3'
379 - 403 124.00 -11.20
3
miRNA  3' gaUUCUGGUUCGGAGGAAGGGa 5'
            |||: ::| :| |:|||:| 
Target 5' aaAAGG-TGACTCCCTTTCTCa 3'
2191 - 2211 123.00 -10.90
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30136312 15 COSMIC
COSN31488230 16 COSMIC
COSN14249707 35 COSMIC
COSN31520447 35 COSMIC
COSN30136654 55 COSMIC
COSN20967418 58 COSMIC
COSN31511732 79 COSMIC
COSN31487428 85 COSMIC
COSN18722797 99 COSMIC
COSN2189876 126 COSMIC
COSN18722798 128 COSMIC
COSN30125293 131 COSMIC
COSN8515130 142 COSMIC
COSN31481807 150 COSMIC
COSN31606039 156 COSMIC
COSN31537496 174 COSMIC
COSN8515131 215 COSMIC
COSN31571656 245 COSMIC
COSN31577679 247 COSMIC
COSN31484148 300 COSMIC
COSN31529236 313 COSMIC
COSN31584610 412 COSMIC
COSN31549099 446 COSMIC
COSN20420683 526 COSMIC
COSN31482063 529 COSMIC
COSN31485508 556 COSMIC
COSN4930180 609 COSMIC
COSN31579261 767 COSMIC
COSN31590417 782 COSMIC
COSN29564208 908 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1390979397 3 dbSNP
rs1394785639 4 dbSNP
rs1167579494 5 dbSNP
rs758901902 6 dbSNP
rs1440334124 11 dbSNP
rs1323966141 14 dbSNP
rs368474937 15 dbSNP
rs773080259 16 dbSNP
rs1467122859 18 dbSNP
rs370934861 20 dbSNP
rs1180655073 21 dbSNP
rs762922734 22 dbSNP
rs1372288453 29 dbSNP
rs13307747 31 dbSNP
rs1388991867 31 dbSNP
rs778309233 31 dbSNP
rs1221825449 35 dbSNP
rs372641296 36 dbSNP
rs1335389816 38 dbSNP
rs1239801751 39 dbSNP
rs774085195 42 dbSNP
rs947761866 46 dbSNP
rs377263841 50 dbSNP
rs747338695 51 dbSNP
rs767023615 51 dbSNP
rs557833963 55 dbSNP
rs993127987 56 dbSNP
rs1256593106 60 dbSNP
rs1286542009 68 dbSNP
rs1053315508 69 dbSNP
rs577978343 71 dbSNP
rs1447985118 73 dbSNP
rs1264597722 74 dbSNP
rs1335338089 88 dbSNP
rs146703164 92 dbSNP
rs554288975 94 dbSNP
rs574268515 95 dbSNP
rs543271674 98 dbSNP
rs1381747484 101 dbSNP
rs775531217 103 dbSNP
rs74700377 104 dbSNP
rs764353262 119 dbSNP
rs1017222304 126 dbSNP
rs1240975974 131 dbSNP
rs1189537882 142 dbSNP
rs1442890952 145 dbSNP
rs1256975757 156 dbSNP
rs115201492 157 dbSNP
rs545723740 160 dbSNP
rs192129150 161 dbSNP
rs890095107 173 dbSNP
rs1472688593 185 dbSNP
rs532988136 207 dbSNP
rs1368229369 215 dbSNP
rs960548460 217 dbSNP
rs1450845448 219 dbSNP
rs992291069 227 dbSNP
rs1023394427 236 dbSNP
rs1397585029 237 dbSNP
rs1038992019 242 dbSNP
rs546366637 243 dbSNP
rs969421914 246 dbSNP
rs1298444331 247 dbSNP
rs560230596 249 dbSNP
rs979160446 265 dbSNP
rs527974383 266 dbSNP
rs994641821 271 dbSNP
rs770874923 272 dbSNP
rs1473111580 289 dbSNP
rs1027420761 291 dbSNP
rs1372394378 292 dbSNP
rs1192642838 294 dbSNP
rs1487359282 295 dbSNP
rs184677653 301 dbSNP
rs988958868 311 dbSNP
rs913379490 327 dbSNP
rs1004216872 337 dbSNP
rs1016084121 340 dbSNP
rs960106190 341 dbSNP
rs1410634821 342 dbSNP
rs934188989 345 dbSNP
rs1270114186 367 dbSNP
rs1217276662 369 dbSNP
rs1341838965 373 dbSNP
rs993220571 388 dbSNP
rs916195911 397 dbSNP
rs1403975305 415 dbSNP
rs1051582294 425 dbSNP
rs1325323333 431 dbSNP
rs1405731633 441 dbSNP
rs1395437244 447 dbSNP
rs549222350 451 dbSNP
rs1166095433 460 dbSNP
rs970271502 471 dbSNP
rs928533102 472 dbSNP
rs1194452586 473 dbSNP
rs926071780 480 dbSNP
rs1480255839 485 dbSNP
rs568729158 519 dbSNP
rs148849518 526 dbSNP
rs777696929 527 dbSNP
rs1483123404 547 dbSNP
rs1180913780 548 dbSNP
rs1272657377 548 dbSNP
rs1320558473 571 dbSNP
rs1278330121 576 dbSNP
rs1222336193 578 dbSNP
rs1365126451 583 dbSNP
rs1253728231 584 dbSNP
rs551658503 593 dbSNP
rs1276266060 599 dbSNP
rs1436674102 602 dbSNP
rs944414774 604 dbSNP
rs1189986443 605 dbSNP
rs755713467 605 dbSNP
rs567545006 609 dbSNP
rs534240132 610 dbSNP
rs898404375 615 dbSNP
rs994023384 616 dbSNP
rs1167310174 631 dbSNP
rs1372461862 633 dbSNP
rs1462619952 640 dbSNP
rs1302336979 644 dbSNP
rs1478454996 647 dbSNP
rs1400264613 648 dbSNP
rs1046981205 650 dbSNP
rs867060756 651 dbSNP
rs779651679 664 dbSNP
rs947997488 687 dbSNP
rs1048886470 689 dbSNP
rs1309942228 710 dbSNP
rs553952223 711 dbSNP
rs1005119244 713 dbSNP
rs1398027672 719 dbSNP
rs1280084263 731 dbSNP
rs1219474087 732 dbSNP
rs574154312 733 dbSNP
rs1349479445 743 dbSNP
rs1313106543 748 dbSNP
rs1364236865 750 dbSNP
rs1013423366 751 dbSNP
rs1015700127 753 dbSNP
rs1377631984 758 dbSNP
rs1023803141 766 dbSNP
rs1445644022 773 dbSNP
rs960388744 774 dbSNP
rs749155074 782 dbSNP
rs1415303574 783 dbSNP
rs1023366205 801 dbSNP
rs970302765 802 dbSNP
rs1253758444 803 dbSNP
rs978974681 821 dbSNP
rs1183552359 824 dbSNP
rs1484001699 824 dbSNP
rs926185488 831 dbSNP
rs536757146 832 dbSNP
rs1032033488 836 dbSNP
rs142530941 837 dbSNP
rs1449296203 840 dbSNP
rs1187220254 847 dbSNP
rs576711103 859 dbSNP
rs989032189 861 dbSNP
rs956232638 867 dbSNP
rs1429642718 868 dbSNP
rs1381225211 869 dbSNP
rs989368469 876 dbSNP
rs1175387809 882 dbSNP
rs911656710 889 dbSNP
rs1304699371 890 dbSNP
rs944429583 895 dbSNP
rs955687942 896 dbSNP
rs1296594772 899 dbSNP
rs545373272 912 dbSNP
rs377023325 913 dbSNP
rs749027052 914 dbSNP
rs911287871 919 dbSNP
rs921567074 928 dbSNP
rs942826573 945 dbSNP
rs1416586205 946 dbSNP
rs1387615508 952 dbSNP
rs1432719975 953 dbSNP
rs1322307129 955 dbSNP
rs930301361 958 dbSNP
rs1362506389 959 dbSNP
rs1049005503 964 dbSNP
rs56007018 972 dbSNP
rs57770518 973 dbSNP
rs1260321998 981 dbSNP
rs1298508584 991 dbSNP
rs919899476 995 dbSNP
rs1367188913 1002 dbSNP
rs929987110 1007 dbSNP
rs940565730 1009 dbSNP
rs577552305 1012 dbSNP
rs1290824041 1014 dbSNP
rs1056674347 1015 dbSNP
rs1046925758 1017 dbSNP
rs1323497188 1017 dbSNP
rs1213858254 1025 dbSNP
rs895921802 1031 dbSNP
rs1014717691 1032 dbSNP
rs1250313883 1048 dbSNP
rs1486456291 1052 dbSNP
rs1402136176 1054 dbSNP
rs1022979870 1055 dbSNP
rs905897416 1072 dbSNP
rs1293378282 1074 dbSNP
rs1456703313 1076 dbSNP
rs1423120992 1077 dbSNP
rs1435036586 1083 dbSNP
rs1166117382 1085 dbSNP
rs1477757306 1092 dbSNP
rs778509903 1098 dbSNP
rs1177409769 1102 dbSNP
rs1411430174 1104 dbSNP
rs145958309 1109 dbSNP
rs1195181880 1116 dbSNP
rs904923934 1123 dbSNP
rs1266223006 1124 dbSNP
rs1345604586 1128 dbSNP
rs1000194989 1135 dbSNP
rs1000595695 1139 dbSNP
rs1435633713 1139 dbSNP
rs58052615 1147 dbSNP
rs371220571 1149 dbSNP
rs374395270 1150 dbSNP
rs528923755 1157 dbSNP
rs1315966184 1159 dbSNP
rs1256284424 1160 dbSNP
rs1404957496 1163 dbSNP
rs1220543237 1164 dbSNP
rs1341426348 1168 dbSNP
rs1287172312 1171 dbSNP
rs1300862118 1184 dbSNP
rs1385241401 1189 dbSNP
rs1370218580 1190 dbSNP
rs1294436041 1199 dbSNP
rs1009236365 1202 dbSNP
rs1229885103 1211 dbSNP
rs771095524 1228 dbSNP
rs1020545515 1233 dbSNP
rs1317944877 1239 dbSNP
rs1196307498 1249 dbSNP
rs1434498220 1251 dbSNP
rs1267859749 1263 dbSNP
rs189148435 1276 dbSNP
rs1456443917 1277 dbSNP
rs1239922438 1282 dbSNP
rs987360756 1284 dbSNP
rs965830593 1287 dbSNP
rs79039929 1294 dbSNP
rs1200167627 1298 dbSNP
rs1251208119 1299 dbSNP
rs1314139578 1322 dbSNP
rs1302458379 1343 dbSNP
rs1446501310 1366 dbSNP
rs1375400017 1369 dbSNP
rs1333961842 1378 dbSNP
rs964574861 1381 dbSNP
rs1400906525 1390 dbSNP
rs1471713189 1390 dbSNP
rs1467298872 1391 dbSNP
rs1377843587 1392 dbSNP
rs1157891872 1394 dbSNP
rs1437610291 1397 dbSNP
rs1184661683 1412 dbSNP
rs1408416962 1415 dbSNP
rs1404612316 1422 dbSNP
rs1441722007 1425 dbSNP
rs974095610 1428 dbSNP
rs1198771908 1430 dbSNP
rs1484398020 1437 dbSNP
rs921681841 1444 dbSNP
rs1281287931 1446 dbSNP
rs920014296 1460 dbSNP
rs1351964222 1462 dbSNP
rs1351487416 1465 dbSNP
rs929978891 1468 dbSNP
rs1240452751 1474 dbSNP
rs1340365658 1477 dbSNP
rs1331709986 1483 dbSNP
rs531448805 1487 dbSNP
rs551378006 1488 dbSNP
rs571545728 1496 dbSNP
rs533865532 1500 dbSNP
rs1279826800 1505 dbSNP
rs547734486 1524 dbSNP
rs567671975 1544 dbSNP
rs1289748736 1545 dbSNP
rs536696399 1547 dbSNP
rs1045403823 1557 dbSNP
rs769741679 1558 dbSNP
rs936495502 1559 dbSNP
rs1425644681 1560 dbSNP
rs1288187407 1576 dbSNP
rs1258227105 1579 dbSNP
rs1216200336 1589 dbSNP
rs556740422 1598 dbSNP
rs10253341 1605 dbSNP
rs1273977175 1606 dbSNP
rs537148026 1609 dbSNP
rs1056305420 1611 dbSNP
rs896277008 1622 dbSNP
rs146199017 1623 dbSNP
rs1355577893 1626 dbSNP
rs1276968510 1631 dbSNP
rs1397806159 1648 dbSNP
rs17706864 1658 dbSNP
rs1298652187 1659 dbSNP
rs1472598712 1660 dbSNP
rs1388232688 1669 dbSNP
rs1179850862 1682 dbSNP
rs1044538760 1696 dbSNP
rs1458308394 1707 dbSNP
rs1418689849 1711 dbSNP
rs905929979 1721 dbSNP
rs191656562 1725 dbSNP
rs541378806 1752 dbSNP
rs1265599520 1754 dbSNP
rs1194102675 1763 dbSNP
rs1018951212 1766 dbSNP
rs1445135522 1767 dbSNP
rs553313382 1773 dbSNP
rs964206766 1780 dbSNP
rs1212177463 1792 dbSNP
rs567511632 1807 dbSNP
rs1032987300 1808 dbSNP
rs1431171483 1811 dbSNP
rs1342051484 1812 dbSNP
rs974250912 1812 dbSNP
rs573306958 1818 dbSNP
rs892050152 1819 dbSNP
rs951497103 1821 dbSNP
rs1399456209 1830 dbSNP
rs982730773 1839 dbSNP
rs542312202 1841 dbSNP
rs1010870842 1844 dbSNP
rs917903509 1860 dbSNP
rs548267161 1861 dbSNP
rs949426119 1865 dbSNP
rs1019184882 1875 dbSNP
rs966648534 1885 dbSNP
rs1201423902 1888 dbSNP
rs138891337 1897 dbSNP
rs1238089448 1903 dbSNP
rs1028727289 1913 dbSNP
rs936484220 1927 dbSNP
rs1273045150 1928 dbSNP
rs951768778 1935 dbSNP
rs984442036 1936 dbSNP
rs907512003 1938 dbSNP
rs1218299155 1941 dbSNP
rs1197562708 1954 dbSNP
rs1273828284 1955 dbSNP
rs940628156 1956 dbSNP
rs992520147 1958 dbSNP
rs535355460 1962 dbSNP
rs2430483 1971 dbSNP
rs1383572979 1974 dbSNP
rs1356376555 1978 dbSNP
rs1244723320 1980 dbSNP
rs1414162028 1981 dbSNP
rs545160160 1983 dbSNP
rs1044908598 1987 dbSNP
rs184798368 1997 dbSNP
rs1454991835 1998 dbSNP
rs1380001332 2024 dbSNP
rs1177343816 2029 dbSNP
rs141366167 2030 dbSNP
rs547377930 2031 dbSNP
rs1459440623 2035 dbSNP
rs1451265717 2044 dbSNP
rs936031190 2051 dbSNP
rs1208773720 2053 dbSNP
rs578245857 2055 dbSNP
rs1167943313 2064 dbSNP
rs1054467735 2067 dbSNP
rs1423898182 2069 dbSNP
rs1352760549 2073 dbSNP
rs891824836 2085 dbSNP
rs1412373353 2097 dbSNP
rs762288475 2100 dbSNP
rs772023737 2101 dbSNP
rs1007640742 2106 dbSNP
rs1041047075 2122 dbSNP
rs902078329 2124 dbSNP
rs767235545 2141 dbSNP
rs995621367 2143 dbSNP
rs1435524154 2166 dbSNP
rs1029095544 2167 dbSNP
rs951801215 2175 dbSNP
rs567659997 2176 dbSNP
rs1248212908 2178 dbSNP
rs139211927 2178 dbSNP
rs530155493 2178 dbSNP
rs550279684 2179 dbSNP
rs1238666019 2189 dbSNP
rs962056681 2189 dbSNP
rs1211184011 2194 dbSNP
rs991822916 2197 dbSNP
rs1344463296 2219 dbSNP
rs1487745614 2224 dbSNP
rs146983550 2225 dbSNP
rs372536670 2226 dbSNP
rs538782272 2232 dbSNP
rs1317504804 2245 dbSNP
rs1311938149 2260 dbSNP
rs980601309 2261 dbSNP
rs1226469801 2266 dbSNP
rs981217218 2271 dbSNP
rs1295146654 2273 dbSNP
rs1207813789 2274 dbSNP
rs926552663 2280 dbSNP
rs1340080338 2282 dbSNP
rs1296805180 2284 dbSNP
rs1455689016 2290 dbSNP
rs957970016 2291 dbSNP
rs989293827 2300 dbSNP
rs765789573 2304 dbSNP
rs189265042 2306 dbSNP
rs1193865962 2307 dbSNP
rs1245607642 2312 dbSNP
rs199900896 2313 dbSNP
rs936479250 2324 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions C8166
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 GSM1462572. RNA binding protein: AGO2. Condition:C8166 NL4-3 ...

- 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' gauucUGGUUCGGAGGAAGGGa 5'
               :||  | | ||||||| 
Target 5' uccccGCC--GGCGCCUUCCCg 3'
1 - 20
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 GSM1462572
Method / RBP PAR-CLIP / AGO2
Cell line / Condition C8166 / C8166 NL4-3
Location of target site ENST00000287585.6 | 3UTR | UCCCCGCCGGCGCCUUCCCGGAC
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
215 hsa-miR-4747-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT061689 BTG2 BTG anti-proliferation factor 2 2 2
MIRT062834 BCL7A BCL tumor suppressor 7A 2 2
MIRT079371 CCDC137 coiled-coil domain containing 137 2 2
MIRT081190 MIDN midnolin 2 4
MIRT081724 ZNF507 zinc finger protein 507 2 2
MIRT110565 ZMYND11 zinc finger MYND-type containing 11 2 2
MIRT133724 SKI SKI proto-oncogene 2 4
MIRT146689 MINK1 misshapen like kinase 1 2 2
MIRT150676 SLC27A1 solute carrier family 27 member 1 2 2
MIRT159196 NRBP1 nuclear receptor binding protein 1 2 2
MIRT180865 RPRD2 regulation of nuclear pre-mRNA domain containing 2 2 2
MIRT190659 PABPN1 poly(A) binding protein nuclear 1 2 2
MIRT196111 MPRIP myosin phosphatase Rho interacting protein 2 2
MIRT232390 SP1 Sp1 transcription factor 2 2
MIRT331070 EIF5AL1 eukaryotic translation initiation factor 5A-like 1 2 4
MIRT338632 SHMT2 serine hydroxymethyltransferase 2 2 2
MIRT407441 CTDSP1 CTD small phosphatase 1 2 2
MIRT444276 NKX6-1 NK6 homeobox 1 2 2
MIRT444834 PDE6D phosphodiesterase 6D 2 2
MIRT445452 EXT1 exostosin glycosyltransferase 1 2 2
MIRT445644 NPY4R neuropeptide Y receptor Y4 2 2
MIRT446157 RPL12 ribosomal protein L12 2 2
MIRT446608 HIP1 huntingtin interacting protein 1 2 2
MIRT447108 CLPX caseinolytic mitochondrial matrix peptidase chaperone subunit 2 2
MIRT449314 MRO maestro 2 2
MIRT450305 DRAXIN dorsal inhibitory axon guidance protein 2 2
MIRT451245 ZNF444 zinc finger protein 444 2 2
MIRT451714 OLR1 oxidized low density lipoprotein receptor 1 2 2
MIRT451908 ILK integrin linked kinase 2 2
MIRT452183 KIAA1456 KIAA1456 2 2
MIRT452610 REPIN1 replication initiator 1 2 2
MIRT453422 GLG1 golgi glycoprotein 1 2 2
MIRT454006 ALKBH5 alkB homolog 5, RNA demethylase 2 2
MIRT455072 ARHGAP39 Rho GTPase activating protein 39 2 2
MIRT455319 TTLL9 tubulin tyrosine ligase like 9 2 2
MIRT455357 KDM5C lysine demethylase 5C 2 2
MIRT455589 TAF12 TATA-box binding protein associated factor 12 2 2
MIRT455711 EIF4EBP2 eukaryotic translation initiation factor 4E binding protein 2 2 2
MIRT455860 TMEM254 transmembrane protein 254 2 2
MIRT455919 RAPGEF1 Rap guanine nucleotide exchange factor 1 2 2
MIRT455946 CYP4A22 cytochrome P450 family 4 subfamily A member 22 2 2
MIRT456935 LRP10 LDL receptor related protein 10 2 2
MIRT457223 AP3D1 adaptor related protein complex 3 delta 1 subunit 2 2
MIRT457431 NOL10 nucleolar protein 10 2 2
MIRT457470 SLC35F6 solute carrier family 35 member F6 2 2
MIRT457907 ZNF212 zinc finger protein 212 2 2
MIRT458046 TSEN54 tRNA splicing endonuclease subunit 54 2 2
MIRT458073 RNLS renalase, FAD dependent amine oxidase 2 2
MIRT458234 NXPH3 neurexophilin 3 2 2
MIRT458307 TNFAIP8L3 TNF alpha induced protein 8 like 3 2 2
MIRT458378 ITM2C integral membrane protein 2C 2 2
MIRT458967 ZNF436 zinc finger protein 436 2 2
MIRT459099 CYP4A11 cytochrome P450 family 4 subfamily A member 11 2 2
MIRT459446 TMEM37 transmembrane protein 37 2 2
MIRT459671 VPS37C VPS37C, ESCRT-I subunit 2 2
MIRT460727 ASXL3 additional sex combs like 3, transcriptional regulator 2 2
MIRT460744 SRP14 signal recognition particle 14 2 2
MIRT461531 C14orf1 ergosterol biosynthesis 28 homolog 2 2
MIRT461752 DDX11 DEAD/H-box helicase 11 2 2
MIRT461837 F2RL3 F2R like thrombin or trypsin receptor 3 2 2
MIRT462019 RIF1 replication timing regulatory factor 1 2 2
MIRT462631 PHF5A PHD finger protein 5A 2 2
MIRT462772 ZNF8 zinc finger protein 8 2 2
MIRT463032 ZNF689 zinc finger protein 689 2 2
MIRT463886 WNT7B Wnt family member 7B 2 2
MIRT463995 WDTC1 WD and tetratricopeptide repeats 1 2 2
MIRT464371 URM1 ubiquitin related modifier 1 2 2
MIRT465342 TPM3 tropomyosin 3 2 4
MIRT465515 PRICKLE4 prickle planar cell polarity protein 4 2 2
MIRT465602 TNRC6A trinucleotide repeat containing 6A 2 2
MIRT465697 TNPO2 transportin 2 2 10
MIRT466988 SSRP1 structure specific recognition protein 1 2 4
MIRT467630 SLC7A5 solute carrier family 7 member 5 2 2
MIRT468132 SH3PXD2A SH3 and PX domains 2A 2 2
MIRT468322 SF3B3 splicing factor 3b subunit 3 2 2
MIRT468502 SESN2 sestrin 2 2 2
MIRT468881 RREB1 ras responsive element binding protein 1 2 2
MIRT469322 RGP1 RGP1 homolog, RAB6A GEF complex partner 1 2 2
MIRT469562 RARA retinoic acid receptor alpha 2 2
MIRT469898 PTRF caveolae associated protein 1 2 2
MIRT470045 PTGFRN prostaglandin F2 receptor inhibitor 2 2
MIRT470068 PTGES2 prostaglandin E synthase 2 2 2
MIRT470238 PRRC2A proline rich coiled-coil 2A 2 2
MIRT470390 PPP1R16B protein phosphatase 1 regulatory subunit 16B 2 2
MIRT470500 PPP1R11 protein phosphatase 1 regulatory inhibitor subunit 11 2 2
MIRT470689 POLR2D RNA polymerase II subunit D 2 2
MIRT470704 POGK pogo transposable element derived with KRAB domain 2 2
MIRT471083 PIK3C2B phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 beta 2 2
MIRT472482 NACC2 NACC family member 2 2 2
MIRT473583 MAT2A methionine adenosyltransferase 2A 2 2
MIRT474554 KLHDC3 kelch domain containing 3 2 2
MIRT474651 KLF13 Kruppel like factor 13 2 2
MIRT474843 KHSRP KH-type splicing regulatory protein 2 2
MIRT474934 KCTD15 potassium channel tetramerization domain containing 15 2 2
MIRT475573 HNRNPC heterogeneous nuclear ribonucleoprotein C (C1/C2) 2 2
MIRT476045 GRSF1 G-rich RNA sequence binding factor 1 2 2
MIRT476080 GRB2 growth factor receptor bound protein 2 2 2
MIRT476440 GBA2 glucosylceramidase beta 2 2 2
MIRT476764 FOSL2 FOS like 2, AP-1 transcription factor subunit 2 2
MIRT478785 CRTC2 CREB regulated transcription coactivator 2 2 2
MIRT479287 CHAC1 ChaC glutathione specific gamma-glutamylcyclotransferase 1 2 2
MIRT479505 CDH6 cadherin 6 2 2
MIRT479732 CCND1 cyclin D1 2 6
MIRT480352 C5orf24 chromosome 5 open reading frame 24 2 2
MIRT480407 C19orf47 chromosome 19 open reading frame 47 2 2
MIRT480859 BHLHB9 basic helix-loop-helix family member b9 2 2
MIRT481445 ARRB2 arrestin beta 2 2 2
MIRT481732 APH1A aph-1 homolog A, gamma-secretase subunit 2 2
MIRT481824 AP2M1 adaptor related protein complex 2 mu 1 subunit 2 2
MIRT482566 ABHD2 abhydrolase domain containing 2 2 2
MIRT482607 ABHD14B abhydrolase domain containing 14B 2 2
MIRT483144 SYCE1L synaptonemal complex central element protein 1 like 2 2
MIRT483214 APOA1 apolipoprotein A1 2 6
MIRT483878 TGIF1 TGFB induced factor homeobox 1 2 2
MIRT483917 SPSB1 splA/ryanodine receptor domain and SOCS box containing 1 2 2
MIRT483939 LENG8 leukocyte receptor cluster member 8 2 4
MIRT484420 SNX19 sorting nexin 19 2 2
MIRT484489 SLC9A1 solute carrier family 9 member A1 2 2
MIRT484612 SIX3 SIX homeobox 3 2 6
MIRT484705 RNF11 ring finger protein 11 2 2
MIRT485107 SHISA6 shisa family member 6 2 2
MIRT485354 MYO1C myosin IC 2 4
MIRT485609 FOSL1 FOS like 1, AP-1 transcription factor subunit 2 4
MIRT487311 GLTSCR1 BRD4 interacting chromatin remodeling complex associated protein 2 2
MIRT487417 CACNB1 calcium voltage-gated channel auxiliary subunit beta 1 2 2
MIRT487695 CDK14 cyclin dependent kinase 14 2 2
MIRT487791 GPR20 G protein-coupled receptor 20 2 4
MIRT488042 PABPC1L2B poly(A) binding protein cytoplasmic 1 like 2B 2 2
MIRT488058 PABPC1L2A poly(A) binding protein cytoplasmic 1 like 2A 2 2
MIRT488237 DNLZ DNL-type zinc finger 2 4
MIRT488764 FXYD1 FXYD domain containing ion transport regulator 1 2 2
MIRT489401 TUBB2A tubulin beta 2A class IIa 2 2
MIRT489777 GRINA glutamate ionotropic receptor NMDA type subunit associated protein 1 2 2
MIRT490099 FN3K fructosamine 3 kinase 2 2
MIRT490290 ISL2 ISL LIM homeobox 2 2 2
MIRT490378 LHFPL3 LHFPL tetraspan subfamily member 3 2 2
MIRT491329 GFER growth factor, augmenter of liver regeneration 2 2
MIRT491435 MSX2 msh homeobox 2 2 2
MIRT491769 ZNF385A zinc finger protein 385A 2 2
MIRT491922 WNK2 WNK lysine deficient protein kinase 2 2 2
MIRT491983 UNK unkempt family zinc finger 2 2
MIRT492228 SLC48A1 solute carrier family 48 member 1 2 2
MIRT492404 SDK1 sidekick cell adhesion molecule 1 2 2
MIRT492767 PDGFB platelet derived growth factor subunit B 2 2
MIRT492966 NCS1 neuronal calcium sensor 1 2 2
MIRT493295 LLGL2 LLGL2, scribble cell polarity complex component 2 2
MIRT493650 HDLBP high density lipoprotein binding protein 2 2
MIRT493913 FAM127B retrotransposon Gag like 8A 2 4
MIRT495601 NKX2-5 NK2 homeobox 5 2 2
MIRT496875 AHCYL2 adenosylhomocysteinase like 2 2 2
MIRT498514 MYH14 myosin heavy chain 14 2 2
MIRT499178 RBPJL recombination signal binding protein for immunoglobulin kappa J region like 2 2
MIRT502143 KIF5B kinesin family member 5B 2 8
MIRT502692 CSNK1G1 casein kinase 1 gamma 1 2 4
MIRT508460 HOXB6 homeobox B6 2 4
MIRT510430 ZNF207 zinc finger protein 207 2 6
MIRT511837 GPATCH8 G-patch domain containing 8 2 4
MIRT512368 CPM carboxypeptidase M 2 2
MIRT512506 BTBD19 BTB domain containing 19 2 2
MIRT513065 ANKRD45 ankyrin repeat domain 45 2 2
MIRT513267 SCUBE1 signal peptide, CUB domain and EGF like domain containing 1 2 4
MIRT513575 EVX1 even-skipped homeobox 1 2 2
MIRT515051 EBNA1BP2 EBNA1 binding protein 2 2 2
MIRT515790 COL4A3BP collagen type IV alpha 3 binding protein 2 2
MIRT521657 PRKD3 protein kinase D3 2 2
MIRT522679 LUZP1 leucine zipper protein 1 2 6
MIRT528845 RAB32 RAB32, member RAS oncogene family 2 2
MIRT533569 TOR1AIP1 torsin 1A interacting protein 1 2 2
MIRT543738 DHCR7 7-dehydrocholesterol reductase 2 2
MIRT544295 TSPYL1 TSPY like 1 2 2
MIRT544857 MYH2 myosin heavy chain 2 2 4
MIRT557323 HIATL1 major facilitator superfamily domain containing 14B 2 4
MIRT560522 TMEM98 transmembrane protein 98 2 2
MIRT561565 SLC6A9 solute carrier family 6 member 9 2 2
MIRT562374 ERI2 ERI1 exoribonuclease family member 2 2 2
MIRT565780 SEMA6D semaphorin 6D 2 2
MIRT569548 UNC119B unc-119 lipid binding chaperone B 2 2
MIRT569944 PRRT2 proline rich transmembrane protein 2 2 2
MIRT570016 COL1A2 collagen type I alpha 2 chain 2 2
MIRT572163 CRK CRK proto-oncogene, adaptor protein 2 2
MIRT572322 HSPB6 heat shock protein family B (small) member 6 2 2
MIRT573495 IQSEC3 IQ motif and Sec7 domain 3 2 2
MIRT574139 MARVELD1 MARVEL domain containing 1 2 2
MIRT609449 CCDC149 coiled-coil domain containing 149 2 2
MIRT610619 ARHGAP18 Rho GTPase activating protein 18 2 2
MIRT623355 LZIC leucine zipper and CTNNBIP1 domain containing 2 2
MIRT629854 ACOX1 acyl-CoA oxidase 1 2 2
MIRT630516 CDC73 cell division cycle 73 2 2
MIRT632535 PSMB2 proteasome subunit beta 2 2 2
MIRT633975 SLC35E2 solute carrier family 35 member E2 2 2
MIRT636408 MTHFD2 methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase 2 2
MIRT641722 LTBR lymphotoxin beta receptor 2 2
MIRT642661 RGS6 regulator of G protein signaling 6 2 2
MIRT649649 MAST3 microtubule associated serine/threonine kinase 3 2 2
MIRT650367 MOCS3 molybdenum cofactor synthesis 3 2 2
MIRT651355 ZBTB40 zinc finger and BTB domain containing 40 2 2
MIRT664840 HUS1 HUS1 checkpoint clamp component 2 2
MIRT667322 MYH9 myosin heavy chain 9 2 2
MIRT670680 SUGT1 SGT1 homolog, MIS12 kinetochore complex assembly cochaperone 2 2
MIRT674922 TRPM6 transient receptor potential cation channel subfamily M member 6 2 2
MIRT675919 CYP51A1 cytochrome P450 family 51 subfamily A member 1 2 2
MIRT676493 GJD3 gap junction protein delta 3 2 2
MIRT680162 ZDHHC20 zinc finger DHHC-type containing 20 2 2
MIRT688008 GSN gelsolin 2 2
MIRT688997 ATP6AP1 ATPase H+ transporting accessory protein 1 2 2
MIRT700337 RAB4A RAB4A, member RAS oncogene family 2 2
MIRT701344 NR4A3 nuclear receptor subfamily 4 group A member 3 2 2
MIRT703519 FKBP15 FK506 binding protein 15 2 2
MIRT703901 EPT1 selenoprotein I 2 2
MIRT705565 ARHGEF18 Rho/Rac guanine nucleotide exchange factor 18 2 2
MIRT709709 DNAJC11 DnaJ heat shock protein family (Hsp40) member C11 2 2
MIRT713108 TMBIM4 transmembrane BAX inhibitor motif containing 4 2 2
MIRT718426 ZNF85 zinc finger protein 85 2 2
MIRT719236 CYSLTR2 cysteinyl leukotriene receptor 2 2 2
MIRT719326 STAC SH3 and cysteine rich domain 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-4747 Paclitaxel 36314 NSC125973 approved resistant cell line (A2780)
hsa-miR-4747-5p Temozolomide 5394 NSC362856 approved sensitive cell line (U251)
hsa-miR-4747-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4747-5p Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)

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