pre-miRNA Information
pre-miRNA hsa-mir-3179-1   
Genomic Coordinates chr16: 14901508 - 14901591
Description Homo sapiens miR-3179-1 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases
pre-miRNA hsa-mir-3179-2   
Genomic Coordinates chr16: 16300159 - 16300242
Description Homo sapiens miR-3179-2 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases
pre-miRNA hsa-mir-3179-3   
Genomic Coordinates chr16: 18411894 - 18411977
Description Homo sapiens miR-3179-3 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases
pre-miRNA hsa-mir-3179-4   
Genomic Coordinates chr16: 18494493 - 18494576
Description Homo sapiens miR-3179-4 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-3179
Sequence 52| AGAAGGGGUGAAAUUUAAACGU |73
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1351100204 1 dbSNP
rs1398613616 4 dbSNP
rs1340262765 20 dbSNP
rs1229893475 21 dbSNP
Putative Targets

miRNA Expression profile
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol MYO1C   
Synonyms MMI-beta, MMIb, NMI, myr2
Description myosin IC
Transcript NM_001080779   
Other Transcripts NM_001080950 , NM_033375   
Expression
Putative miRNA Targets on MYO1C
3'UTR of MYO1C
(miRNA target sites are highlighted)
>MYO1C|NM_001080779|3'UTR
   1 TAAAGGCGCCCACTGGACCCTCCCAACGCCCAATGCTTTGCTTTTCTCCTCCTCCCCTTCCCAGTTACCAAAGACTCGAA
  81 CTTCCAGACAGGGACCCAGGGACACCCCGAAGCCCACCTGCAATCTCCCACCTCCTGCCCATCCCTCTCTTGAGGGAGCA
 161 GCAGGGGCCAGGAGCTACCCCAGGAGTGGGCCAGGCCGGGCCACAGCAATAGGAAAGCCAGGGCCAGAGCGAGCCATGCC
 241 AGCCCTACTGCCGATGCCAAATATTTGAGAGAAGGGAACTTTTGCTGAGGTTTTCTCTGAGGTTTTTTTGATGCTTTATA
 321 GGAAACTATTTTTTAAAAAAAGCCATTTCCCACCCAAGGACACAGTGGATGTGTTTTCCCTGACTCCAGCAGGGCAAGGA
 401 ATGTAGCCGAGAGGTTGTGTGGGCTGGGCTCTGGTGCCCTCTTCCCTGGCCAGGACACCTCTCCTCCTGATTCCCTTGGC
 481 ACCTTGTCTTTCTGTCTGTTTACCTGTCTCCCTGCCTGCCCATCTGCATCTTTTGCAGCCCACTCTGACTTCCATCTGGG
 561 GGCTGAGACCACCCTTGCCTGCCCCCTTCTTTCTGCCTTAAGAATGTCCTTTTAGGCTGGGCATGGTGGCTCACGCCTGT
 641 AACCCCAGCACTTTGGGAGGCGGAGACGGGCAGATAACCTGAGGTCAGGATTTCGAGACCAACCTGACCTACATGGAGAA
 721 ACTCCGCCTCTAGTAAAAATACAAAATTAGCCGGGCATGGTGGTGCACGCCTCTAATCCCAGCTACTCGGGAGGCTGAGG
 801 CAGGAGAATCACTTGAACCCGGGAAGTGGAGGTTGCAGTGAGCCAAGAGTACACCACTGCACTCCAGCCTGGGCAACAGA
 881 GCGAGACTCCGTCTTAAAAAAAAAAAAAAAGAACGCCCTTTTACTGTCCTCATCATCCCAGTTTGAGGCAGTGCTGGAGT
 961 GGGGAAGGCCGTCTTAGACCATAGAGGTTGGAAGACGCTGAGAGATCATCCAGCCCAGCCCCTTGATGTTACAGAGCAGA
1041 AGACAGATGCCCAAACAGGAGAAGGCACTTGCCCACGGTCATACGGCAGGTTGCCACAAAACCAAGATGGCAGCCCTTCC
1121 TCAGCGTGCCTCACTGCCACTCCCAGAGCCAGGGAGCCCCATAAAACCCACATCATGTCTTAAGAGTATATCTGGCTCCT
1201 TGACCAGCAATCGGCCCTGGGAGCCACCAGGTGGGAAAAGCGCCTCTGCCAGAGTCCAGGCCTTGGGATGACAGACAGCT
1281 TGCCCGCACACTCGGGCCCCACTCAAGGATGTAGGGCCTTTTCTGGCCCCTGACCCCTCCCTGGCATGGGAGCGTGGGGA
1361 CGGGGCTGGCCTTGGGAGGAGCGGCAGGGGCATCACCTCCTTCTGCTGCTTCTCCCTGCTCCTACCCTCAAGGGCCTGGG
1441 GGCTGCCCAGCTGCCTCTATGCCCTTCTGGGGGTCTCAGCCCACTGCTGACACTTCTGCAATCCAGAGAAACACTAAATA
1521 AAGCAATACGTGTTTGCCAAAAAAAAAAAAAAAAAAAAAAA
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' ugcAAAUUUAAA------GUGGGGAAGa 5'
             |||:  |||      | ||||||| 
Target 5' tgcTTTGCTTTTCTCCTCCTCCCCTTCc 3'
34 - 61 149.00 -12.20
2
miRNA  3' ugcaaauuuaaaguGGGGAAGa 5'
                        ||||||| 
Target 5' ccacccttgcctgcCCCCTTCt 3'
569 - 590 140.00 -13.40
3
miRNA  3' ugcaaauuuaaAGU-GGGGAAGa 5'
                     ||| |:||||| 
Target 5' cggcaggggcaTCACCTCCTTCt 3'
1382 - 1404 131.00 -15.60
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
1183863 197 ClinVar
COSN28882938 10 COSMIC
COSN30163224 22 COSMIC
COSN20060348 27 COSMIC
COSN31602132 125 COSMIC
COSN30481334 127 COSMIC
COSN30580662 158 COSMIC
COSN30136542 167 COSMIC
COSN26601933 201 COSMIC
COSN31579867 250 COSMIC
COSN31601383 252 COSMIC
COSN21767487 334 COSMIC
COSN22158181 335 COSMIC
COSN26664238 616 COSMIC
COSN26567342 619 COSMIC
COSN30544845 635 COSMIC
COSN8831701 668 COSMIC
COSN28162908 890 COSMIC
COSN21503955 917 COSMIC
COSN30175929 997 COSMIC
COSN8240340 1018 COSMIC
COSN31514872 1126 COSMIC
COSN26509527 1206 COSMIC
COSN28726267 1221 COSMIC
COSN30165157 1307 COSMIC
COSN31595002 1469 COSMIC
COSN31555585 1486 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs772871115 1 dbSNP
rs769839215 3 dbSNP
rs769837724 5 dbSNP
rs761710266 6 dbSNP
rs779020986 6 dbSNP
rs548792139 7 dbSNP
rs373989989 8 dbSNP
rs746482131 10 dbSNP
rs1036506968 13 dbSNP
rs1161187830 18 dbSNP
rs779681383 19 dbSNP
rs771562248 27 dbSNP
rs372318243 28 dbSNP
rs777992599 31 dbSNP
rs958609717 32 dbSNP
rs371622828 33 dbSNP
rs1449829152 34 dbSNP
rs753281962 41 dbSNP
rs556221831 42 dbSNP
rs755114267 46 dbSNP
rs1445144322 48 dbSNP
rs751636919 49 dbSNP
rs766685895 51 dbSNP
rs989444316 52 dbSNP
rs1239827425 56 dbSNP
rs967123854 56 dbSNP
rs370234417 60 dbSNP
rs1030896809 63 dbSNP
rs563141164 75 dbSNP
rs965613046 77 dbSNP
rs377690275 78 dbSNP
rs1402712020 86 dbSNP
rs1050657404 89 dbSNP
rs1316220801 90 dbSNP
rs1291929907 93 dbSNP
rs1324749445 95 dbSNP
rs1437384277 100 dbSNP
rs1208720633 108 dbSNP
rs74477362 109 dbSNP
rs1369564227 117 dbSNP
rs1370569550 118 dbSNP
rs888168985 134 dbSNP
rs565548397 136 dbSNP
rs545652606 139 dbSNP
rs901821706 143 dbSNP
rs1346196831 144 dbSNP
rs1205053482 150 dbSNP
rs1282833452 151 dbSNP
rs1471832855 152 dbSNP
rs1465812004 154 dbSNP
rs764277066 155 dbSNP
rs1251941615 160 dbSNP
rs940700657 168 dbSNP
rs557172939 170 dbSNP
rs573466740 172 dbSNP
rs559846706 179 dbSNP
rs760701365 181 dbSNP
rs919796678 189 dbSNP
rs11538162 197 dbSNP
rs1207552644 198 dbSNP
rs574042046 204 dbSNP
rs1321325110 207 dbSNP
rs1393894457 208 dbSNP
rs958674545 213 dbSNP
rs906732254 214 dbSNP
rs1332025114 221 dbSNP
rs1045226167 231 dbSNP
rs928554119 233 dbSNP
rs1331873823 234 dbSNP
rs1229604545 236 dbSNP
rs948141398 243 dbSNP
rs1002416367 246 dbSNP
rs967448712 252 dbSNP
rs11538164 253 dbSNP
rs989497088 262 dbSNP
rs935350678 267 dbSNP
rs781083014 271 dbSNP
rs557096082 292 dbSNP
rs923921257 301 dbSNP
rs1029188342 302 dbSNP
rs757389559 304 dbSNP
rs1414031705 309 dbSNP
rs1472863658 310 dbSNP
rs537425881 312 dbSNP
rs1164175301 313 dbSNP
rs1417241050 319 dbSNP
rs866219951 332 dbSNP
rs577542349 334 dbSNP
rs878944818 335 dbSNP
rs1004846430 342 dbSNP
rs985272710 344 dbSNP
rs886449820 347 dbSNP
rs1352761705 356 dbSNP
rs1299392949 363 dbSNP
rs1293279421 377 dbSNP
rs1331959723 380 dbSNP
rs1246357474 382 dbSNP
rs188847316 384 dbSNP
rs1338368694 385 dbSNP
rs1026662168 386 dbSNP
rs1193766053 400 dbSNP
rs993864597 402 dbSNP
rs534545283 403 dbSNP
rs896849054 408 dbSNP
rs1255333210 409 dbSNP
rs1422059388 415 dbSNP
rs1035315074 419 dbSNP
rs1004234826 425 dbSNP
rs1369180936 427 dbSNP
rs898317638 428 dbSNP
rs906748875 429 dbSNP
rs1167023274 434 dbSNP
rs1372787306 441 dbSNP
rs1327971394 444 dbSNP
rs1045640627 445 dbSNP
rs774926934 448 dbSNP
rs1377663776 451 dbSNP
rs1397219642 453 dbSNP
rs1055522335 456 dbSNP
rs1325386417 466 dbSNP
rs1224783395 469 dbSNP
rs1276403159 473 dbSNP
rs937187688 474 dbSNP
rs928528685 479 dbSNP
rs553012656 482 dbSNP
rs565533302 486 dbSNP
rs1278046429 491 dbSNP
rs146109048 495 dbSNP
rs537979117 496 dbSNP
rs945724233 502 dbSNP
rs912941106 503 dbSNP
rs893968339 510 dbSNP
rs1053898060 516 dbSNP
rs957136448 521 dbSNP
rs1365193459 532 dbSNP
rs1028760934 535 dbSNP
rs935401504 538 dbSNP
rs974916417 555 dbSNP
rs966613886 558 dbSNP
rs1432206770 583 dbSNP
rs1383600157 586 dbSNP
rs1019159955 595 dbSNP
rs1299271038 603 dbSNP
rs142945535 606 dbSNP
rs976746221 608 dbSNP
rs1463541688 609 dbSNP
rs1267355259 610 dbSNP
rs1313812392 613 dbSNP
rs569698386 618 dbSNP
rs1260090924 622 dbSNP
rs1352514748 623 dbSNP
rs1027638161 634 dbSNP
rs943956331 635 dbSNP
rs138624977 646 dbSNP
rs911117231 651 dbSNP
rs184606761 661 dbSNP
rs1055137327 662 dbSNP
rs937154774 666 dbSNP
rs759924946 667 dbSNP
rs907062574 668 dbSNP
rs1177350126 670 dbSNP
rs1363729543 674 dbSNP
rs778109356 687 dbSNP
rs1321995030 688 dbSNP
rs1331875847 694 dbSNP
rs1439706344 695 dbSNP
rs945976737 699 dbSNP
rs1138599 702 dbSNP
rs1369394944 706 dbSNP
rs1219589737 707 dbSNP
rs192120099 709 dbSNP
rs1327028574 710 dbSNP
rs989787354 712 dbSNP
rs1365102036 713 dbSNP
rs747678054 714 dbSNP
rs867703940 718 dbSNP
rs1321738900 722 dbSNP
rs144651285 725 dbSNP
rs528749137 726 dbSNP
rs1035770733 727 dbSNP
rs1138603 732 dbSNP
rs1138604 736 dbSNP
rs1138605 737 dbSNP
rs1138606 738 dbSNP
rs1002501367 740 dbSNP
rs1138607 741 dbSNP
rs1250367656 742 dbSNP
rs1172339833 745 dbSNP
rs974906340 748 dbSNP
rs1465288612 750 dbSNP
rs971402621 752 dbSNP
rs1023921329 753 dbSNP
rs1012896784 755 dbSNP
rs1460482062 763 dbSNP
rs1162185298 766 dbSNP
rs894020307 768 dbSNP
rs1053952765 769 dbSNP
rs780621861 773 dbSNP
rs966231585 782 dbSNP
rs999619456 785 dbSNP
rs187495378 788 dbSNP
rs1193759331 789 dbSNP
rs754629969 797 dbSNP
rs1138626 802 dbSNP
rs1199649133 803 dbSNP
rs1138627 808 dbSNP
rs994755962 817 dbSNP
rs751207950 818 dbSNP
rs543174713 820 dbSNP
rs1004074966 821 dbSNP
rs1138638 825 dbSNP
rs1253175859 826 dbSNP
rs1474572517 830 dbSNP
rs944024311 837 dbSNP
rs911200111 838 dbSNP
rs1415396169 842 dbSNP
rs1405562637 848 dbSNP
rs1169388780 850 dbSNP
rs549335507 852 dbSNP
rs931226157 853 dbSNP
rs919792117 858 dbSNP
rs140741038 862 dbSNP
rs1341482926 863 dbSNP
rs1447320088 867 dbSNP
rs1282477071 874 dbSNP
rs1381479473 874 dbSNP
rs961111964 875 dbSNP
rs928378815 883 dbSNP
rs1299027757 888 dbSNP
rs1274211467 889 dbSNP
rs1340403200 890 dbSNP
rs1207783867 891 dbSNP
rs1275914534 892 dbSNP
rs74487886 893 dbSNP
rs74409989 894 dbSNP
rs1427368031 895 dbSNP
rs74354330 896 dbSNP
rs1238698638 906 dbSNP
rs1472873063 906 dbSNP
rs1185514845 907 dbSNP
rs10655321 910 dbSNP
rs1451054824 910 dbSNP
rs1169007114 911 dbSNP
rs1336159629 911 dbSNP
rs1374674686 911 dbSNP
rs1412653194 911 dbSNP
rs201219288 911 dbSNP
rs557106289 911 dbSNP
rs1054377856 913 dbSNP
rs1344834372 914 dbSNP
rs1442424797 914 dbSNP
rs981588392 914 dbSNP
rs1245763270 915 dbSNP
rs1465954431 918 dbSNP
rs1339217313 926 dbSNP
rs372875944 929 dbSNP
rs1023052244 931 dbSNP
rs1476928413 934 dbSNP
rs1012539970 935 dbSNP
rs1425830647 941 dbSNP
rs1375694384 943 dbSNP
rs1175076677 944 dbSNP
rs1386597356 954 dbSNP
rs958243499 956 dbSNP
rs1437545079 957 dbSNP
rs1321538376 959 dbSNP
rs1389056855 960 dbSNP
rs1330823800 968 dbSNP
rs1231533460 970 dbSNP
rs766246646 971 dbSNP
rs115607969 982 dbSNP
rs758098121 984 dbSNP
rs902610625 987 dbSNP
rs754880297 996 dbSNP
rs1208904791 999 dbSNP
rs1041164223 1007 dbSNP
rs950885845 1025 dbSNP
rs1008710599 1027 dbSNP
rs536186509 1034 dbSNP
rs182867532 1037 dbSNP
rs1050182933 1047 dbSNP
rs14269 1052 dbSNP
rs534604960 1055 dbSNP
rs1390328572 1059 dbSNP
rs1385404397 1061 dbSNP
rs569514314 1062 dbSNP
rs1332077856 1066 dbSNP
rs1234311154 1068 dbSNP
rs919802880 1072 dbSNP
rs1287067216 1076 dbSNP
rs1036841919 1077 dbSNP
rs939825780 1081 dbSNP
rs928442164 1084 dbSNP
rs766060179 1085 dbSNP
rs1290324257 1093 dbSNP
rs981255418 1113 dbSNP
rs1253890774 1114 dbSNP
rs555288657 1116 dbSNP
rs1182648147 1121 dbSNP
rs970205088 1122 dbSNP
rs1456551342 1123 dbSNP
rs1369544147 1125 dbSNP
rs535608410 1126 dbSNP
rs879094841 1129 dbSNP
rs1411088863 1134 dbSNP
rs569677692 1136 dbSNP
rs971190248 1144 dbSNP
rs958294601 1156 dbSNP
rs1032567246 1161 dbSNP
rs1352892532 1162 dbSNP
rs1162531296 1169 dbSNP
rs978326246 1170 dbSNP
rs1475428441 1174 dbSNP
rs1425626512 1179 dbSNP
rs1246519649 1185 dbSNP
rs1284440438 1186 dbSNP
rs1010035333 1208 dbSNP
rs941456806 1210 dbSNP
rs569121463 1212 dbSNP
rs1008344886 1213 dbSNP
rs889832709 1215 dbSNP
rs556214496 1216 dbSNP
rs1054366476 1217 dbSNP
rs1028282386 1221 dbSNP
rs1422192753 1223 dbSNP
rs1189805806 1230 dbSNP
rs995441795 1241 dbSNP
rs550839340 1244 dbSNP
rs900149853 1252 dbSNP
rs898429167 1253 dbSNP
rs1036935027 1254 dbSNP
rs1039139981 1256 dbSNP
rs1233602531 1263 dbSNP
rs939933022 1270 dbSNP
rs1302835018 1273 dbSNP
rs1206736275 1276 dbSNP
rs1449889476 1279 dbSNP
rs1397277135 1285 dbSNP
rs111518969 1286 dbSNP
rs911590692 1290 dbSNP
rs1337558444 1291 dbSNP
rs765111540 1293 dbSNP
rs948501411 1294 dbSNP
rs1342688635 1296 dbSNP
rs1232421145 1299 dbSNP
rs1254187225 1309 dbSNP
rs1228159551 1315 dbSNP
rs1482296292 1320 dbSNP
rs1372161411 1322 dbSNP
rs1243880177 1331 dbSNP
rs1279710499 1336 dbSNP
rs1186982842 1341 dbSNP
rs1392402110 1342 dbSNP
rs1443764867 1350 dbSNP
rs1429497173 1353 dbSNP
rs377283936 1354 dbSNP
rs915623764 1358 dbSNP
rs929466738 1361 dbSNP
rs920800356 1362 dbSNP
rs1461953879 1363 dbSNP
rs1432434582 1366 dbSNP
rs775718708 1369 dbSNP
rs570465173 1376 dbSNP
rs1156694322 1382 dbSNP
rs1472110922 1383 dbSNP
rs78635371 1384 dbSNP
rs1179131054 1385 dbSNP
rs1477145349 1387 dbSNP
rs978378781 1390 dbSNP
rs1328648817 1391 dbSNP
rs1246252565 1394 dbSNP
rs967355500 1398 dbSNP
rs926906699 1399 dbSNP
rs190206678 1402 dbSNP
rs1208509697 1405 dbSNP
rs1317844310 1416 dbSNP
rs970756599 1418 dbSNP
rs57305444 1419 dbSNP
rs879461107 1420 dbSNP
rs955855919 1423 dbSNP
rs1457138872 1426 dbSNP
rs1032871474 1428 dbSNP
rs1369548176 1434 dbSNP
rs759900227 1438 dbSNP
rs1225152922 1440 dbSNP
rs549341388 1442 dbSNP
rs1028333243 1445 dbSNP
rs995534621 1448 dbSNP
rs900390871 1459 dbSNP
rs1302146640 1461 dbSNP
rs1317717885 1461 dbSNP
rs1440924545 1462 dbSNP
rs898543514 1463 dbSNP
rs1489705004 1464 dbSNP
rs564981961 1467 dbSNP
rs1251733730 1473 dbSNP
rs1452831764 1474 dbSNP
rs1471300720 1474 dbSNP
rs1015542677 1483 dbSNP
rs1183689430 1493 dbSNP
rs1408130420 1496 dbSNP
rs1004142860 1497 dbSNP
rs907077304 1517 dbSNP
rs1351349772 1523 dbSNP
rs774689703 1529 dbSNP
rs1307298759 1530 dbSNP
rs1368656385 1532 dbSNP
rs1047464311 1535 dbSNP
rs529472964 1540 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
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 GSM545215. RNA binding protein: AGO4. Condition:Control ...

- Hafner M; Landthaler M; Burger L; Khorshid et al., 2010, Cell.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' ugcaaauuuaAAGUGGGGAAGa 5'
                    | | ||||||| 
Target 5' -----ucuccUCCUCCCCUUCc 3'
1 - 17
Article - Hafner M; Landthaler M; Burger L; Khorshid et al.
- Cell, 2010
RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.
LinkOut: [PMID: 20371350]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions C8166 , 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 GSM1462572. RNA binding protein: AGO2. Condition:C8166 NL4-3 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.

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]
Experimental Support 3 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HCT116
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 ERX177622. RNA binding protein: AGO2. Condition:KO_V_AGO_CLIP_3_12 PAR-CLIP data was present in ERX177634. RNA binding protein: AGO2. Condition:KO_V_AGO_CLIP_4_12 ...

- Krell J; Stebbing J; Carissimi C; Dabrowska et al., 2016, Genome research.

Article - Krell J; Stebbing J; Carissimi C; Dabrowska et al.
- Genome research, 2016
DNA damage activates TP53-regulated surveillance mechanisms that are crucial in suppressing tumorigenesis. TP53 orchestrates these responses directly by transcriptionally modulating genes, including microRNAs (miRNAs), and by regulating miRNA biogenesis through interacting with the DROSHA complex. However, whether the association between miRNAs and AGO2 is regulated following DNA damage is not yet known. Here, we show that, following DNA damage, TP53 interacts with AGO2 to induce or reduce AGO2's association of a subset of miRNAs, including multiple let-7 family members. Furthermore, we show that specific mutations in TP53 decrease rather than increase the association of let-7 family miRNAs, reducing their activity without preventing TP53 from interacting with AGO2. This is consistent with the oncogenic properties of these mutants. Using AGO2 RIP-seq and PAR-CLIP-seq, we show that the DNA damage-induced increase in binding of let-7 family members to the RISC complex is functional. We unambiguously determine the global miRNA-mRNA interaction networks involved in the DNA damage response, validating them through the identification of miRNA-target chimeras formed by endogenous ligation reactions. We find that the target complementary region of the let-7 seed tends to have highly fixed positions and more variable ones. Additionally, we observe that miRNAs, whose cellular abundance or differential association with AGO2 is regulated by TP53, are involved in an intricate network of regulatory feedback and feedforward circuits. TP53-mediated regulation of AGO2-miRNA interaction represents a new mechanism of miRNA regulation in carcinogenesis.
LinkOut: [PMID: 26701625]
CLIP-seq Support 1 for dataset GSM4903829
Method / RBP HITS-CLIP / AGO
Cell line / Condition Human neurons / CTLTD_shCTL_a
Location of target site NM_001080950 | 3UTR | CCCCUUCCCAGUUACCA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161238
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM4903830
Method / RBP HITS-CLIP / AGO
Cell line / Condition Human neurons / CTLTD_shCTL_b
Location of target site NM_001080950 | 3UTR | CCCCUUCCCAGUUACCA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161238
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM545215
Method / RBP PAR-CLIP / AGO4
Cell line / Condition HEK293 / Control
Location of target site ENST00000359786.5 | 3UTR | UCUCCUCCUCCCCUUCC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM1462572
Method / RBP PAR-CLIP / AGO2
Cell line / Condition C8166 / C8166 NL4-3
Location of target site ENST00000359786.5 | 3UTR | CUCCUCCUCCCCUUCC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23592263 / GSE59944
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM1462573
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl BaL
Location of target site ENST00000359786.5 | 3UTR | UUCUCCUCCUCCCCUUCCC
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
Click to see details
Click to see details
133 hsa-miR-3179 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT102087 GIGYF1 GRB10 interacting GYF protein 1 2 4
MIRT110061 OGT O-linked N-acetylglucosamine (GlcNAc) transferase 2 6
MIRT112198 BTG2 BTG anti-proliferation factor 2 2 2
MIRT117668 SCAMP4 secretory carrier membrane protein 4 2 2
MIRT146657 MINK1 misshapen like kinase 1 2 2
MIRT175505 ZBTB33 zinc finger and BTB domain containing 33 2 4
MIRT180535 TXNIP thioredoxin interacting protein 2 2
MIRT190624 BCL2L2-PABPN1 BCL2L2-PABPN1 readthrough 2 2
MIRT190650 PABPN1 poly(A) binding protein nuclear 1 2 2
MIRT366902 NONO non-POU domain containing octamer binding 2 2
MIRT443554 ZFP3 ZFP3 zinc finger protein 2 2
MIRT445953 MLLT11 MLLT11, transcription factor 7 cofactor 2 2
MIRT446042 HMCN1 hemicentin 1 2 2
MIRT447968 MSH6 mutS homolog 6 2 2
MIRT448634 ONECUT1 one cut homeobox 1 2 2
MIRT449316 MRO maestro 2 2
MIRT451380 C19orf43 telomerase RNA component interacting RNase 2 2
MIRT451547 CIAPIN1 cytokine induced apoptosis inhibitor 1 2 2
MIRT451807 CDCA3 cell division cycle associated 3 2 4
MIRT451916 ILK integrin linked kinase 2 2
MIRT451938 TMPRSS5 transmembrane protease, serine 5 2 2
MIRT452189 KIAA1456 KIAA1456 2 2
MIRT452498 HMGXB3 HMG-box containing 3 2 2
MIRT452548 ZNF467 zinc finger protein 467 2 2
MIRT453844 SDK1 sidekick cell adhesion molecule 1 2 2
MIRT454515 ZFYVE27 zinc finger FYVE-type containing 27 2 2
MIRT455363 KDM5C lysine demethylase 5C 2 2
MIRT455455 EPB41L4B erythrocyte membrane protein band 4.1 like 4B 2 2
MIRT455628 PABPC1L2B poly(A) binding protein cytoplasmic 1 like 2B 2 10
MIRT455639 PABPC1L2A poly(A) binding protein cytoplasmic 1 like 2A 2 10
MIRT455690 GLO1 glyoxalase I 2 2
MIRT456300 ASH1L ASH1 like histone lysine methyltransferase 2 2
MIRT456784 MTHFSD methenyltetrahydrofolate synthetase domain containing 2 2
MIRT456819 PIGP phosphatidylinositol glycan anchor biosynthesis class P 2 2
MIRT457566 ZNF34 zinc finger protein 34 2 2
MIRT457604 IDS iduronate 2-sulfatase 2 2
MIRT458236 NXPH3 neurexophilin 3 2 2
MIRT458313 TNFAIP8L3 TNF alpha induced protein 8 like 3 2 2
MIRT458350 NOC2L NOC2 like nucleolar associated transcriptional repressor 2 2
MIRT458670 GPR35 G protein-coupled receptor 35 2 2
MIRT459675 VPS37C VPS37C, ESCRT-I subunit 2 2
MIRT461126 RAB36 RAB36, member RAS oncogene family 2 2
MIRT461918 NECAB3 N-terminal EF-hand calcium binding protein 3 2 2
MIRT462301 PPM1H protein phosphatase, Mg2+/Mn2+ dependent 1H 2 2
MIRT463520 ZBTB7B zinc finger and BTB domain containing 7B 2 2
MIRT464378 URM1 ubiquitin related modifier 1 2 2
MIRT464614 UBE4B ubiquitination factor E4B 2 2
MIRT464711 UBE2V1 ubiquitin conjugating enzyme E2 V1 2 2
MIRT465520 PRICKLE4 prickle planar cell polarity protein 4 2 2
MIRT465974 TMEM189-UBE2V1 TMEM189-UBE2V1 readthrough 2 2
MIRT466058 TMEM189 transmembrane protein 189 2 2
MIRT466548 TBL1XR1 transducin beta like 1 X-linked receptor 1 2 2
MIRT466647 TAGLN2 transgelin 2 2 2
MIRT467357 SP2 Sp2 transcription factor 2 2
MIRT468744 SDC2 syndecan 2 2 2
MIRT470244 PRRC2A proline rich coiled-coil 2A 2 2
MIRT471426 PDIA6 protein disulfide isomerase family A member 6 2 2
MIRT471732 OTUB1 OTU deubiquitinase, ubiquitin aldehyde binding 1 2 2
MIRT472190 NHP2L1 small nuclear ribonucleoprotein 13 2 2
MIRT472450 NAV2 neuron navigator 2 2 6
MIRT474563 KLHDC3 kelch domain containing 3 2 2
MIRT474936 KCTD15 potassium channel tetramerization domain containing 15 2 2
MIRT475165 IP6K1 inositol hexakisphosphate kinase 1 2 2
MIRT475399 ICMT isoprenylcysteine carboxyl methyltransferase 2 4
MIRT475426 ICK intestinal cell kinase 2 2
MIRT477090 FAM168A family with sequence similarity 168 member A 2 2
MIRT478458 DAB2 DAB2, clathrin adaptor protein 2 2
MIRT478953 COX15 COX15, cytochrome c oxidase assembly homolog 2 2
MIRT480096 CALR calreticulin 2 2
MIRT481924 ANKRD33B ankyrin repeat domain 33B 2 2
MIRT483217 APOA1 apolipoprotein A1 2 6
MIRT483882 TGIF1 TGFB induced factor homeobox 1 2 2
MIRT483923 SPSB1 splA/ryanodine receptor domain and SOCS box containing 1 2 2
MIRT483942 LENG8 leukocyte receptor cluster member 8 2 4
MIRT484209 SUMO1 small ubiquitin-like modifier 1 2 2
MIRT484512 SYT7 synaptotagmin 7 2 2
MIRT484709 RNF11 ring finger protein 11 2 2
MIRT485356 MYO1C myosin IC 2 4
MIRT485615 FOSL1 FOS like 1, AP-1 transcription factor subunit 2 4
MIRT486584 ZNF619 zinc finger protein 619 2 2
MIRT487013 C2orf82 chromosome 2 open reading frame 82 2 2
MIRT487621 C20orf96 chromosome 20 open reading frame 96 2 2
MIRT487801 GPR20 G protein-coupled receptor 20 2 4
MIRT488134 GPR107 G protein-coupled receptor 107 2 2
MIRT488773 FXYD1 FXYD domain containing ion transport regulator 1 2 2
MIRT488854 UBTF upstream binding transcription factor, RNA polymerase I 2 2
MIRT489783 GRINA glutamate ionotropic receptor NMDA type subunit associated protein 1 2 2
MIRT490102 FN3K fructosamine 3 kinase 2 2
MIRT490389 LHFPL3 LHFPL tetraspan subfamily member 3 2 2
MIRT490434 MYL9 myosin light chain 9 2 2
MIRT490451 GLUD1 glutamate dehydrogenase 1 2 2
MIRT490880 OSBP oxysterol binding protein 2 2
MIRT491037 ALPK3 alpha kinase 3 2 2
MIRT491250 HCN2 hyperpolarization activated cyclic nucleotide gated potassium and sodium channel 2 2 2
MIRT491748 SEMA3F semaphorin 3F 2 2
MIRT492235 SLC48A1 solute carrier family 48 member 1 2 2
MIRT492490 RAPGEF1 Rap guanine nucleotide exchange factor 1 2 2
MIRT492505 RANBP10 RAN binding protein 10 2 4
MIRT492773 PDGFB platelet derived growth factor subunit B 2 2
MIRT492922 NFAT5 nuclear factor of activated T-cells 5 2 2
MIRT493459 ITFG3 family with sequence similarity 234 member A 2 2
MIRT493654 HDLBP high density lipoprotein binding protein 2 2
MIRT494011 DUSP9 dual specificity phosphatase 9 2 2
MIRT499412 PLCG2 phospholipase C gamma 2 2 4
MIRT499552 C15orf43 telomere repeat binding bouquet formation protein 2 2 2
MIRT501836 NCOA2 nuclear receptor coactivator 2 2 2
MIRT501950 MAT2A methionine adenosyltransferase 2A 2 10
MIRT504066 KCTD12 potassium channel tetramerization domain containing 12 2 4
MIRT504509 PPP1R9B protein phosphatase 1 regulatory subunit 9B 2 2
MIRT508466 HOXB6 homeobox B6 2 4
MIRT512373 CPM carboxypeptidase M 2 2
MIRT513578 EVX1 even-skipped homeobox 1 2 2
MIRT517763 ZNF366 zinc finger protein 366 2 4
MIRT519773 ZNF354B zinc finger protein 354B 2 8
MIRT523568 GGCX gamma-glutamyl carboxylase 2 4
MIRT532802 CLDN11 claudin 11 2 2
MIRT544299 TSPYL1 TSPY like 1 2 2
MIRT544862 MYH2 myosin heavy chain 2 2 4
MIRT556731 KLHL15 kelch like family member 15 2 4
MIRT564347 AKR1B10 aldo-keto reductase family 1 member B10 2 2
MIRT568924 SMCR8 Smith-Magenis syndrome chromosome region, candidate 8 2 2
MIRT569012 CXorf36 chromosome X open reading frame 36 2 2
MIRT569256 FAM129B family with sequence similarity 129 member B 2 2
MIRT569591 PRELP proline and arginine rich end leucine rich repeat protein 2 2
MIRT569779 SAMD14 sterile alpha motif domain containing 14 2 2
MIRT570034 FAM228A family with sequence similarity 228 member A 2 2
MIRT573803 FRMPD4 FERM and PDZ domain containing 4 2 2
MIRT574190 ZNF264 zinc finger protein 264 2 2
MIRT576153 Hmox1 heme oxygenase 1 2 2
MIRT611311 CA8 carbonic anhydrase 8 2 4
MIRT673429 APAF1 apoptotic peptidase activating factor 1 2 2
MIRT674976 SH3BP2 SH3 domain binding protein 2 2 2
MIRT692712 MEAF6 MYST/Esa1 associated factor 6 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-3179 Gemcitabine 60750 NSC613327 approved resistant High Pancreatic Cancer cell line (AsPC-1)
hsa-miR-3179 Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-3179 Gefitinib 123631 NSC715055 approved sensitive cell line (PC9)
hsa-miR-3179 Osimertinib 71496458 NSC779217 approved sensitive cell line (HCC827)
hsa-miR-3179 Osimertinib 71496458 NSC779217 approved sensitive cell line (PC9)
hsa-miR-3179 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-3179 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (100 ng/ml)
hsa-miR-3179 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)

Error report submission