pre-miRNA Information
pre-miRNA hsa-mir-4301   
Genomic Coordinates chr11: 113450023 - 113450088
Description Homo sapiens miR-4301 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4301
Sequence 11| UCCCACUACUUCACUUGUGA |30
Evidence Experimental
Experiments SOLiD
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs184176277 2 dbSNP
rs1191324913 13 dbSNP
rs1369198005 15 dbSNP
rs1036973189 16 dbSNP
rs944900541 18 dbSNP
Putative Targets

miRNA Expression profile
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol POP4   
Synonyms RPP29
Description POP4 homolog, ribonuclease P/MRP subunit
Transcript NM_006627   
Expression
Putative miRNA Targets on POP4
3'UTR of POP4
(miRNA target sites are highlighted)
>POP4|NM_006627|3'UTR
   1 ATTCTTTGCCGTCTAAGGCAGTTGTTTATGACAGCTGAAAACTGGACACTCCCTAAATGTCCACCTTTCAGTGAAGAGAT
  81 AGTTAAGCCAATTCCATTTATAGACCACCTCCAGCCAGTGACGCTCCGAGTTGAGGATGTTGAACAACATGGGAAGGTCG
 161 CAGCGTACTAAGTGAAGAAGTCAGAGGACAGAGGAATTTCTCTTTCTAGGAGATTTTCATTTTGTGTGACTCCCATGGGG
 241 AGGAACAGACTGGCAGGAAGCACACCGGGGTTAACACTGGTTGACTTGAATAGGATTATTCGATTTTTAAAAATACTTTT
 321 CCATGTTTTCTGAGTGCTCTATGATAAATCAGTTGCATCTGTGATAATACAGTACATATGTGGACATAAACAGGGATCAA
 401 ATAAAGGAGGTATTGCTGCAGTCCAGCCAGGTTGAAAGGGAAGGGGGGTCCCCAAAGGTCCATTGGATGGCAGGTGTCTA
 481 CAGAGGCTCGCCTTTGGGTGGAACTCTGACCCACCTAAGGTTTACTTTGCTATTTCAGGAAGGTTGAAGAGGATTGAAGG
 561 GTGAGTTGCTAAGTGACTTAGGGTTTATTCACTTCAGGAATCATAGCTGGGGTGGACCCCAGGAGCAGAGTACTGCATGC
 641 AGCTGTGCCCATGCATGGTTGCCCCAGCGTAGTGAGATGGGACCTGCCGCAGCATGCCCACTCCTGAGCTGCCAGGCTGA
 721 GCCATGGAGGACTGAAAGGAGGTCGCCCGGCATCACCTCCCGAGGTGAGACCTGCTGCAAAAGCCAAGCCAGCAGCATTG
 801 ACGCCCTTTGATATCTTCGCCATTTTTGCTGCTGAAAGACTTGGCTTTTCAGTCTGACCCTGGCCCTCTGTGACCATGTG
 881 TCTGTAAAGCCAGTGGGTCAGGCCCTTCCATGCAGGGCCAGAGGAAAAGCGGGCCCAGGGCTGCAGTGAGAGCGGGGCAG
 961 GGGACCAGCCTACCAGATGGGTTGGAAACATGGCTCAGAAGGACCAACTACCCCTTCCCTTTGAGGAGCAAGTCTCTGCC
1041 GATCAGCAAGGCAAGGCCAGGAGCCCTCCTGGCGAAAGGCAGGCCACAAATCTGTTCTCCCCCAGGAGAAGTAGCAGTGC
1121 CAGGGCTTTGCGTTTCTGGTAACTTCCACCCAAACCACACCAGAGAGAAACACCGTAGTGGAGAAGGGAAGTGGGAGCGC
1201 TGACTGCTGTGTGCCAGGAGAGTAGAAAGGCCCAGGTCTGTGCCACCACCCCTCCCCAAAGCTCAGTGCACCCAGAGTCT
1281 CACAGGGACCAACACGGTGCCTCGGTCCTGCTTCCATCCATGCAAGTGTCCTCCGCTCACCAGGGTGTTCTGAGGCAGCT
1361 CAAGTGCTCTCCCCCAAGCAGCACGCAGTCACCGCTGCCAGTGATGAACACACGCACGGGCTAGGCACATGGAGCCCAAG
1441 CACACTGCCACCTCGGACACGGGCCCCGGCCCAGCGACTGCCTTGTGGTGTGGCCGTCCTCATCTGCCACAGGAAGACAG
1521 ACTTCGAGGGACCTCTTGCCTAAGGCCTCGCTGACTCAAGGGTAGATTGAGATTTGGACCTAATAGGCTCCAGAACTGTG
1601 CTTTGAGCTACAGGGTGGCTGCAGGATGAGACGGATGCAGTTCAAAGTGCAGGATGTGCTGCCTTTATTACCTGCTTTCC
1681 CGCTGAGCAAATCCCTGTCTTGAGTGGGAAGTGGCATCTATTCCCCCAGCCATCTGAAAATGCTGTGTTCATAACCAAAT
1761 AGGTGCTGTAGCTTCCTAGCCATCCCGCTCTTACCCGCCCCTCTGCAATGTAAAAGGCGTCCACTGTTGTGTAAATACAC
1841 AGTTGCTTTCCAGAAAAGTTGTAGGTACCACTTGCAAAAAAAAAAAAAAAAAA
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' aguGU-UCACUU-----CAUCACCcu 5'
             || || |||     |||||||  
Target 5' cacCAGAGAGAAACACCGTAGTGGag 3'
1158 - 1183 133.00 -12.61
2
miRNA  3' aguguuCACUUC-AUCACCCu 5'
                || |||  |||||| 
Target 5' gtgtctGTAAAGCCAGTGGGt 3'
878 - 898 122.00 -10.80
3
miRNA  3' aguguucacuucaUCACCCu 5'
                       |||||| 
Target 5' aatccctgtcttgAGTGGGa 3'
1690 - 1709 120.00 -11.60
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN26989923 5 COSMIC
COSN6552270 11 COSMIC
COSN30566702 20 COSMIC
COSN30512409 45 COSMIC
COSN30185987 49 COSMIC
COSN31555619 55 COSMIC
COSN30182724 63 COSMIC
COSN23015362 64 COSMIC
COSN20131422 129 COSMIC
COSN30513962 148 COSMIC
COSN22870401 231 COSMIC
COSN208807 259 COSMIC
COSN30137267 270 COSMIC
COSN20115681 429 COSMIC
COSN26514095 553 COSMIC
COSN21565919 621 COSMIC
COSN23632404 701 COSMIC
COSN15662901 706 COSMIC
COSN59881 910 COSMIC
COSN6141624 955 COSMIC
COSN505797 1199 COSMIC
COSN29209351 1387 COSMIC
COSN31652982 1566 COSMIC
COSN20115682 1567 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs779795933 2 dbSNP
rs201552591 4 dbSNP
rs116235956 11 dbSNP
rs189372850 12 dbSNP
rs1462892083 18 dbSNP
rs755803699 19 dbSNP
rs779656928 20 dbSNP
rs1456098930 21 dbSNP
rs1178410464 24 dbSNP
rs899777366 27 dbSNP
rs749101521 28 dbSNP
rs938880779 29 dbSNP
rs1405220214 30 dbSNP
rs768398213 33 dbSNP
rs1470109988 35 dbSNP
rs778911203 40 dbSNP
rs1321360002 42 dbSNP
rs747974592 43 dbSNP
rs772028611 44 dbSNP
rs776618371 49 dbSNP
rs992979010 52 dbSNP
rs561509755 60 dbSNP
rs1300949685 68 dbSNP
rs1317900983 76 dbSNP
rs1048088205 79 dbSNP
rs915647396 88 dbSNP
rs1455557692 90 dbSNP
rs530370053 108 dbSNP
rs546985925 111 dbSNP
rs1411381414 117 dbSNP
rs948505292 123 dbSNP
rs530336840 124 dbSNP
rs559266504 128 dbSNP
rs1376075747 129 dbSNP
rs1198602104 132 dbSNP
rs145599797 138 dbSNP
rs1024699153 148 dbSNP
rs1464814488 150 dbSNP
rs1267009608 154 dbSNP
rs1223534416 157 dbSNP
rs898832170 158 dbSNP
rs550990301 160 dbSNP
rs1270455108 161 dbSNP
rs1047655192 163 dbSNP
rs570994277 165 dbSNP
rs541511531 166 dbSNP
rs1250894145 172 dbSNP
rs1003071862 179 dbSNP
rs1432896055 183 dbSNP
rs1034999072 187 dbSNP
rs1008719151 190 dbSNP
rs1179468750 198 dbSNP
rs1470958423 201 dbSNP
rs959028472 203 dbSNP
rs990144046 205 dbSNP
rs1475849611 208 dbSNP
rs1375180015 209 dbSNP
rs1187058376 210 dbSNP
rs1449450292 212 dbSNP
rs1244218563 223 dbSNP
rs567092722 223 dbSNP
rs1367543298 224 dbSNP
rs780053868 225 dbSNP
rs899911920 227 dbSNP
rs1293153360 231 dbSNP
rs1339655166 236 dbSNP
rs1374401210 239 dbSNP
rs550315113 240 dbSNP
rs1364376720 243 dbSNP
rs996973673 252 dbSNP
rs1338822500 267 dbSNP
rs967372578 267 dbSNP
rs977478170 268 dbSNP
rs148905508 271 dbSNP
rs1376756214 275 dbSNP
rs1167106869 286 dbSNP
rs1429471768 291 dbSNP
rs968761472 302 dbSNP
rs536514122 303 dbSNP
rs553017209 306 dbSNP
rs1293254861 317 dbSNP
rs1186022854 324 dbSNP
rs943853474 326 dbSNP
rs1039563403 340 dbSNP
rs543747283 345 dbSNP
rs773517857 349 dbSNP
rs1202796875 350 dbSNP
rs1031903806 353 dbSNP
rs1048306541 361 dbSNP
rs762896788 371 dbSNP
rs7283 373 dbSNP
rs1337788941 375 dbSNP
rs992947666 377 dbSNP
rs1046118985 378 dbSNP
rs906306467 402 dbSNP
rs1003453244 406 dbSNP
rs1165861040 408 dbSNP
rs774656628 411 dbSNP
rs530386856 417 dbSNP
rs376142522 433 dbSNP
rs760153330 440 dbSNP
rs1021902060 443 dbSNP
rs1470161029 443 dbSNP
rs538644357 445 dbSNP
rs181663107 447 dbSNP
rs1179628484 448 dbSNP
rs1482506097 449 dbSNP
rs575803329 459 dbSNP
rs1319867314 474 dbSNP
rs1289013381 475 dbSNP
rs1224429970 480 dbSNP
rs544718228 482 dbSNP
rs386808534 488 dbSNP
rs2042968 489 dbSNP
rs45529438 490 dbSNP
rs1020098784 491 dbSNP
rs540892355 497 dbSNP
rs560599368 501 dbSNP
rs965529281 506 dbSNP
rs1349838846 507 dbSNP
rs1319499550 511 dbSNP
rs1400048530 550 dbSNP
rs1402925245 552 dbSNP
rs1453931483 554 dbSNP
rs369866406 561 dbSNP
rs1156310457 567 dbSNP
rs1472092947 573 dbSNP
rs1377704306 577 dbSNP
rs1227224147 582 dbSNP
rs45590931 587 dbSNP
rs1308854345 588 dbSNP
rs544594230 596 dbSNP
rs983974473 599 dbSNP
rs2115370 605 dbSNP
rs939671380 607 dbSNP
rs1208127271 611 dbSNP
rs763695308 621 dbSNP
rs1303621685 622 dbSNP
rs1217853455 623 dbSNP
rs753550781 628 dbSNP
rs530482038 636 dbSNP
rs756661921 646 dbSNP
rs150983678 648 dbSNP
rs567428062 649 dbSNP
rs1235640722 650 dbSNP
rs1433583192 652 dbSNP
rs865896255 668 dbSNP
rs548292731 670 dbSNP
rs1317972011 672 dbSNP
rs1234909057 678 dbSNP
rs1011012803 683 dbSNP
rs529830311 688 dbSNP
rs546809768 689 dbSNP
rs1456185836 693 dbSNP
rs998852257 699 dbSNP
rs1177855190 706 dbSNP
rs937743383 719 dbSNP
rs1424285052 733 dbSNP
rs1186879065 737 dbSNP
rs1451272832 738 dbSNP
rs1420340557 742 dbSNP
rs1430467142 745 dbSNP
rs1168803631 746 dbSNP
rs73927204 749 dbSNP
rs750316509 750 dbSNP
rs1014459290 752 dbSNP
rs1021107996 756 dbSNP
rs1311820568 757 dbSNP
rs1023052959 758 dbSNP
rs577546078 762 dbSNP
rs894622562 763 dbSNP
rs1011763066 765 dbSNP
rs1021869508 766 dbSNP
rs1288895446 772 dbSNP
rs1379316809 773 dbSNP
rs755691795 777 dbSNP
rs1363457616 779 dbSNP
rs1464283712 786 dbSNP
rs973104891 788 dbSNP
rs1170887099 796 dbSNP
rs538978430 799 dbSNP
rs1388270436 803 dbSNP
rs558942161 804 dbSNP
rs1445131202 807 dbSNP
rs879910265 813 dbSNP
rs758460222 814 dbSNP
rs569282427 815 dbSNP
rs1323876306 816 dbSNP
rs140852746 819 dbSNP
rs147058657 820 dbSNP
rs1276278761 821 dbSNP
rs911587538 822 dbSNP
rs944567793 827 dbSNP
rs1233598974 830 dbSNP
rs1207776855 835 dbSNP
rs1340547932 836 dbSNP
rs1311482323 841 dbSNP
rs369713872 845 dbSNP
rs1274328724 847 dbSNP
rs1216431726 848 dbSNP
rs1038977743 860 dbSNP
rs1242710557 863 dbSNP
rs921739279 864 dbSNP
rs1028840013 866 dbSNP
rs952535663 884 dbSNP
rs540453713 890 dbSNP
rs45589732 897 dbSNP
rs1167718830 898 dbSNP
rs45496800 898 dbSNP
rs1174639094 903 dbSNP
rs768598517 904 dbSNP
rs138416321 905 dbSNP
rs1053085437 906 dbSNP
rs982447269 911 dbSNP
rs1423275803 912 dbSNP
rs1160461703 914 dbSNP
rs895827338 915 dbSNP
rs1482195657 918 dbSNP
rs927614306 928 dbSNP
rs375627279 931 dbSNP
rs1489758887 934 dbSNP
rs1264167049 935 dbSNP
rs1242015050 944 dbSNP
rs1207667730 949 dbSNP
rs1023193750 954 dbSNP
rs970309959 955 dbSNP
rs995004775 957 dbSNP
rs1297083926 962 dbSNP
rs1348222981 963 dbSNP
rs1345701107 974 dbSNP
rs564507142 979 dbSNP
rs915020320 991 dbSNP
rs1387070624 995 dbSNP
rs1406413448 998 dbSNP
rs950495282 1012 dbSNP
rs1291664133 1015 dbSNP
rs1274564443 1019 dbSNP
rs1457317668 1036 dbSNP
rs983609857 1037 dbSNP
rs190269964 1041 dbSNP
rs965715013 1042 dbSNP
rs534358058 1044 dbSNP
rs10413641 1045 dbSNP
rs903428518 1057 dbSNP
rs780573541 1061 dbSNP
rs1435231190 1062 dbSNP
rs1286251302 1065 dbSNP
rs1209808278 1067 dbSNP
rs999081231 1070 dbSNP
rs560805826 1074 dbSNP
rs529841308 1075 dbSNP
rs1351488006 1077 dbSNP
rs546477192 1077 dbSNP
rs901145739 1081 dbSNP
rs1214504345 1083 dbSNP
rs560296047 1085 dbSNP
rs532403953 1089 dbSNP
rs1201300481 1093 dbSNP
rs923771480 1095 dbSNP
rs1322650419 1101 dbSNP
rs774543950 1103 dbSNP
rs747342859 1104 dbSNP
rs1455676467 1105 dbSNP
rs1053622921 1107 dbSNP
rs570647742 1112 dbSNP
rs950038751 1114 dbSNP
rs1376350225 1126 dbSNP
rs760011774 1132 dbSNP
rs1005335620 1133 dbSNP
rs8105791 1133 dbSNP
rs2042969 1136 dbSNP
rs1463123089 1140 dbSNP
rs760979004 1141 dbSNP
rs982029489 1142 dbSNP
rs1346671555 1147 dbSNP
rs927882077 1149 dbSNP
rs1027784418 1150 dbSNP
rs1365885965 1162 dbSNP
rs1299674019 1163 dbSNP
rs1432783350 1168 dbSNP
rs886615021 1170 dbSNP
rs1426095199 1172 dbSNP
rs1004607968 1175 dbSNP
rs1018686669 1176 dbSNP
rs1400261170 1182 dbSNP
rs990913072 1187 dbSNP
rs914989101 1193 dbSNP
rs1167315412 1199 dbSNP
rs1392591088 1199 dbSNP
rs1281111626 1200 dbSNP
rs1241075144 1210 dbSNP
rs965814540 1213 dbSNP
rs974396857 1214 dbSNP
rs946482426 1215 dbSNP
rs553077296 1217 dbSNP
rs1042168368 1221 dbSNP
rs1253596534 1221 dbSNP
rs1199688666 1223 dbSNP
rs1342675299 1241 dbSNP
rs1028702368 1244 dbSNP
rs924733387 1245 dbSNP
rs764455920 1247 dbSNP
rs1239365771 1253 dbSNP
rs538219918 1257 dbSNP
rs45462597 1260 dbSNP
rs1284863855 1264 dbSNP
rs935177986 1265 dbSNP
rs568453042 1267 dbSNP
rs992030514 1268 dbSNP
rs996855078 1272 dbSNP
rs1333696794 1273 dbSNP
rs1410640376 1283 dbSNP
rs1372837189 1292 dbSNP
rs1306548230 1294 dbSNP
rs572855942 1296 dbSNP
rs1211771391 1297 dbSNP
rs534349099 1299 dbSNP
rs45518039 1304 dbSNP
rs577039858 1305 dbSNP
rs1005556278 1309 dbSNP
rs143804286 1332 dbSNP
rs2042970 1335 dbSNP
rs886586474 1346 dbSNP
rs1003813358 1350 dbSNP
rs1473487833 1359 dbSNP
rs1034923619 1367 dbSNP
rs1161004986 1370 dbSNP
rs146387340 1375 dbSNP
rs1019158368 1380 dbSNP
rs901590052 1381 dbSNP
rs990492786 1382 dbSNP
rs138921553 1385 dbSNP
rs1028627471 1386 dbSNP
rs968129253 1388 dbSNP
rs758013969 1394 dbSNP
rs1031319040 1395 dbSNP
rs1388038332 1407 dbSNP
rs1337295580 1410 dbSNP
rs956681122 1412 dbSNP
rs1163570250 1413 dbSNP
rs923715205 1414 dbSNP
rs773233524 1415 dbSNP
rs1282531389 1418 dbSNP
rs934829082 1419 dbSNP
rs1247043241 1420 dbSNP
rs1215391556 1429 dbSNP
rs977364491 1430 dbSNP
rs1449788659 1431 dbSNP
rs1272643845 1441 dbSNP
rs922872148 1449 dbSNP
rs1331531092 1452 dbSNP
rs1286633670 1457 dbSNP
rs1456716120 1457 dbSNP
rs1368800434 1460 dbSNP
rs1276973762 1462 dbSNP
rs991946630 1469 dbSNP
rs560988194 1476 dbSNP
rs1244272239 1477 dbSNP
rs537013687 1484 dbSNP
rs1444679462 1485 dbSNP
rs1457271294 1495 dbSNP
rs1184728545 1496 dbSNP
rs1367407352 1497 dbSNP
rs1475505497 1499 dbSNP
rs932865132 1502 dbSNP
rs1421095537 1508 dbSNP
rs1477003073 1510 dbSNP
rs574400624 1523 dbSNP
rs575242704 1526 dbSNP
rs1266285308 1527 dbSNP
rs1215424374 1531 dbSNP
rs888425400 1536 dbSNP
rs1281190230 1537 dbSNP
rs1217762328 1540 dbSNP
rs941379936 1545 dbSNP
rs751560795 1546 dbSNP
rs754755798 1550 dbSNP
rs1337193728 1551 dbSNP
rs781111937 1552 dbSNP
rs370610750 1558 dbSNP
rs927268605 1561 dbSNP
rs374809540 1565 dbSNP
rs3214564 1566 dbSNP
rs397726866 1566 dbSNP
rs1359311761 1568 dbSNP
rs1178004321 1575 dbSNP
rs1412495778 1580 dbSNP
rs1003372825 1585 dbSNP
rs1169189072 1601 dbSNP
rs1451250941 1609 dbSNP
rs930658163 1613 dbSNP
rs1035296575 1623 dbSNP
rs1394239096 1633 dbSNP
rs1049089132 1634 dbSNP
rs1012132265 1643 dbSNP
rs1239387935 1644 dbSNP
rs1208486982 1649 dbSNP
rs1347671868 1654 dbSNP
rs908111857 1659 dbSNP
rs1231339593 1667 dbSNP
rs1340642063 1669 dbSNP
rs967676594 1670 dbSNP
rs1213436932 1671 dbSNP
rs977777124 1672 dbSNP
rs1304280227 1675 dbSNP
rs940991202 1676 dbSNP
rs1040525437 1678 dbSNP
rs902018733 1682 dbSNP
rs377736586 1683 dbSNP
rs1316351496 1698 dbSNP
rs966221700 1700 dbSNP
rs975865494 1707 dbSNP
rs182796540 1715 dbSNP
rs1424418738 1718 dbSNP
rs61731815 1721 dbSNP
rs1347696169 1723 dbSNP
rs1050188300 1726 dbSNP
rs1199259305 1728 dbSNP
rs903623381 1735 dbSNP
rs1253059392 1746 dbSNP
rs1207667255 1752 dbSNP
rs1000928579 1761 dbSNP
rs1030703229 1766 dbSNP
rs1251196705 1769 dbSNP
rs552428310 1770 dbSNP
rs1254784544 1771 dbSNP
rs1321839869 1775 dbSNP
rs1314249369 1776 dbSNP
rs562754552 1787 dbSNP
rs956833466 1788 dbSNP
rs1288759171 1789 dbSNP
rs2241609 1791 dbSNP
rs757372462 1794 dbSNP
rs941345457 1795 dbSNP
rs186545962 1797 dbSNP
rs1351754276 1798 dbSNP
rs1458317261 1798 dbSNP
rs568451704 1810 dbSNP
rs1024730445 1811 dbSNP
rs1037031425 1814 dbSNP
rs534003490 1819 dbSNP
rs939396152 1820 dbSNP
rs1471843566 1825 dbSNP
rs1056554632 1827 dbSNP
rs980132661 1829 dbSNP
rs927352332 1830 dbSNP
rs1379163965 1833 dbSNP
rs1012099466 1839 dbSNP
rs952196864 1851 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HEK293S
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... HITS-CLIP data was present in GSM1084065. RNA binding protein: AGO2. Condition:CLIP_emetine_AbnovaAb ...

- Karginov FV; Hannon GJ, 2013, Genes & development.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' agUGUUCACUUCAUCACCCu 5'
            | ||| ||   |||||| 
Target 5' -gAGAAGGGA---AGUGGGa 3'
1 - 16
Article - Karginov FV; Hannon GJ
- Genes & development, 2013
When adapting to environmental stress, cells attenuate and reprogram their translational output. In part, these altered translation profiles are established through changes in the interactions between RNA-binding proteins and mRNAs. The Argonaute 2 (Ago2)/microRNA (miRNA) machinery has been shown to participate in stress-induced translational up-regulation of a particular mRNA, CAT-1; however, a detailed, transcriptome-wide understanding of the involvement of Ago2 in the process has been lacking. Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by cross-linking immunoprecipitation (CLIP) followed by high-throughput sequencing (CLIP-seq). Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3' untranslated region (UTR) and coding sequence (CDS) sites exhibiting stronger interaction. Interestingly, target sites that were destined for release from Ago2 upon stress were depleted in miRNA complementarity signatures, suggesting an alternative mode of interaction. To compare the changes in Ago2-binding patterns across transcripts with changes in their translational states, we measured mRNA profiles on ribosome/polysome gradients by RNA sequencing (RNA-seq). Increased Ago2 occupancy correlated with stronger repression of translation for those mRNAs, as evidenced by a shift toward lighter gradient fractions upon stress, while release of Ago2 was associated with the limited number of transcripts that remained translated. Taken together, these data point to a role for Ago2 and the mammalian miRNAs in mediating the translational component of the stress response.
LinkOut: [PMID: 23824327]
CLIP-seq Support 1 for dataset GSM1084065
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_emetine_AbnovaAb
Location of target site ENST00000221770.3 | 3UTR | GAGAAGGGAAGUGGGAGC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
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
83 hsa-miR-4301 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT081134 LDLR low density lipoprotein receptor 2 4
MIRT090911 ARHGEF26 Rho guanine nucleotide exchange factor 26 2 2
MIRT229436 MECP2 methyl-CpG binding protein 2 2 2
MIRT274717 CPSF6 cleavage and polyadenylation specific factor 6 2 2
MIRT350957 BACH1 BTB domain and CNC homolog 1 2 2
MIRT386722 NUFIP2 NUFIP2, FMR1 interacting protein 2 2 2
MIRT446022 PEX3 peroxisomal biogenesis factor 3 2 2
MIRT481303 ATP5G3 ATP synthase, H+ transporting, mitochondrial Fo complex subunit C3 (subunit 9) 2 14
MIRT483959 ZNF354B zinc finger protein 354B 2 6
MIRT495667 TUBAL3 tubulin alpha like 3 2 2
MIRT496554 TBX15 T-box 15 2 2
MIRT497702 ARL6IP6 ADP ribosylation factor like GTPase 6 interacting protein 6 2 2
MIRT498105 RMND5A required for meiotic nuclear division 5 homolog A 2 2
MIRT512535 SEMA4D semaphorin 4D 2 2
MIRT512556 MFN2 mitofusin 2 2 6
MIRT521465 RABGAP1 RAB GTPase activating protein 1 2 6
MIRT526236 C2orf15 chromosome 2 open reading frame 15 2 2
MIRT526743 HLA-DOB major histocompatibility complex, class II, DO beta 2 2
MIRT527578 BRD7 bromodomain containing 7 2 4
MIRT528038 WT1 Wilms tumor 1 2 2
MIRT528267 GPRIN2 G protein regulated inducer of neurite outgrowth 2 2 2
MIRT528505 HTR7 5-hydroxytryptamine receptor 7 2 4
MIRT528758 RPS27 ribosomal protein S27 2 6
MIRT528999 IPO9 importin 9 2 2
MIRT529701 MRPL30 mitochondrial ribosomal protein L30 2 2
MIRT529781 C17orf82 chromosome 17 open reading frame 82 2 2
MIRT533797 TMEM119 transmembrane protein 119 2 6
MIRT535308 PHF12 PHD finger protein 12 2 2
MIRT535917 MKL2 MKL1/myocardin like 2 2 2
MIRT544892 OSBPL1A oxysterol binding protein like 1A 2 2
MIRT555423 PPIC peptidylprolyl isomerase C 2 2
MIRT562068 KLHL15 kelch like family member 15 2 2
MIRT565623 SLC31A1 solute carrier family 31 member 1 2 2
MIRT565661 SIX1 SIX homeobox 1 2 2
MIRT570138 IL1RL2 interleukin 1 receptor like 2 2 2
MIRT571045 YRDC yrdC N6-threonylcarbamoyltransferase domain containing 2 2
MIRT621232 LMAN1 lectin, mannose binding 1 2 2
MIRT622272 SH3TC2 SH3 domain and tetratricopeptide repeats 2 2 2
MIRT623844 GAN gigaxonin 2 2
MIRT626158 NFYA nuclear transcription factor Y subunit alpha 2 2
MIRT626464 CMKLR1 chemerin chemokine-like receptor 1 2 2
MIRT632087 ALDH1A2 aldehyde dehydrogenase 1 family member A2 2 2
MIRT637243 FAM26E calcium homeostasis modulator family member 5 2 2
MIRT642710 FGFR1OP2 FGFR1 oncogene partner 2 2 2
MIRT643611 KANSL3 KAT8 regulatory NSL complex subunit 3 2 2
MIRT644270 PAFAH1B1 platelet activating factor acetylhydrolase 1b regulatory subunit 1 2 2
MIRT645470 SPIN3 spindlin family member 3 2 2
MIRT649193 DNPEP aspartyl aminopeptidase 2 2
MIRT650776 POP4 POP4 homolog, ribonuclease P/MRP subunit 2 2
MIRT651345 ZC2HC1C zinc finger C2HC-type containing 1C 2 2
MIRT652237 TRAPPC3L trafficking protein particle complex 3 like 2 2
MIRT652587 TIMM8A translocase of inner mitochondrial membrane 8A 2 2
MIRT654591 PURA purine rich element binding protein A 2 2
MIRT654649 PTAFR platelet activating factor receptor 2 2
MIRT656842 KLF7 Kruppel like factor 7 2 2
MIRT657209 IKZF2 IKAROS family zinc finger 2 2 2
MIRT658513 ETV3 ETS variant 3 2 2
MIRT659448 CNNM2 cyclin and CBS domain divalent metal cation transport mediator 2 2 2
MIRT668816 CYLD CYLD lysine 63 deubiquitinase 2 2
MIRT669067 CELSR3 cadherin EGF LAG seven-pass G-type receptor 3 2 2
MIRT677711 ELOF1 elongation factor 1 homolog 2 4
MIRT687146 PTPN12 protein tyrosine phosphatase, non-receptor type 12 2 2
MIRT698498 THOC2 THO complex 2 2 2
MIRT707930 PPP1R3D protein phosphatase 1 regulatory subunit 3D 4 2
MIRT708737 FAM71F2 family with sequence similarity 71 member F2 2 2
MIRT710031 POLL DNA polymerase lambda 2 2
MIRT712175 STK4 serine/threonine kinase 4 2 2
MIRT715297 MAPK1 mitogen-activated protein kinase 1 2 2
MIRT716892 AGPAT6 glycerol-3-phosphate acyltransferase 4 2 2
MIRT717378 RBM41 RNA binding motif protein 41 2 2
MIRT718082 CLIC5 chloride intracellular channel 5 2 2
MIRT718721 ANKRD18A ankyrin repeat domain 18A 2 2
MIRT719152 DPYSL5 dihydropyrimidinase like 5 2 2
MIRT719224 CAMK4 calcium/calmodulin dependent protein kinase IV 2 2
MIRT719528 SRCIN1 SRC kinase signaling inhibitor 1 2 2
MIRT719861 KLF2 Kruppel like factor 2 2 2
MIRT720326 CAMK2G calcium/calmodulin dependent protein kinase II gamma 2 2
MIRT721596 SREBF1 sterol regulatory element binding transcription factor 1 2 2
MIRT722020 NEBL nebulette 2 2
MIRT722484 QSOX1 quiescin sulfhydryl oxidase 1 2 2
MIRT722614 TEAD1 TEA domain transcription factor 1 2 2
MIRT723664 RPTN repetin 2 2
MIRT723939 SVOP SV2 related protein 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
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-4301 Cisplatin 5460033 NSC119875 approved sensitive High Hepatocellular Carcinoma cell line (Hep3B, 97L)
hsa-miR-4301 Imatinib 5291 NSC743414 approved resistant High Chronic Myelogenous Leukemia cell line (K562)
hsa-mir-4301 Paclitaxel 36314 NSC125973 approved resistant cell line (BAS)
hsa-mir-4301 Paclitaxel 36314 NSC125973 approved sensitive cell line (W1)
hsa-mir-4301 Doxorubicin 31703 NSC123127 approved sensitive cell line (W1)
hsa-mir-4301 Methotrexate 126941 NSC740 approved sensitive cell line (W1)
hsa-mir-4301 Topotecan 60699 NSC609699 approved sensitive cell line (W1)
hsa-miR-4301 Gefitinib 123631 NSC715055 approved resistant cell line (PC9)
hsa-miR-4301 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)

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