miRTarBase - #MIRT469973


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pre-miRNA Information
pre-miRNA hsa-mir-6768   
Genomic Coordinates chr16: 2463967 - 2464038
Description Homo sapiens miR-6768 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-6768-3p
Sequence 45| CAAAGGCCACAUUCUCCUGUGCAC |68
Evidence Experimental
Experiments Meta-analysis
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN28846463 17 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs372529217 1 dbSNP
rs375499936 3 dbSNP
rs754371523 6 dbSNP
rs757893316 7 dbSNP
rs1234310587 11 dbSNP
rs369572179 12 dbSNP
rs746522005 14 dbSNP
rs768134371 15 dbSNP
rs372852875 16 dbSNP
rs572852254 17 dbSNP
rs769601549 18 dbSNP
rs773041368 20 dbSNP
rs762865317 23 dbSNP
rs770921850 24 dbSNP
Putative Targets

Gene Information
Gene Symbol PTPRF   
Synonyms BNAH2, LAR
Description protein tyrosine phosphatase, receptor type F
Transcript NM_002840   
Other Transcripts NM_130440   
Expression
Putative miRNA Targets on PTPRF
3'UTR of PTPRF
(miRNA target sites are highlighted)		 
>PTPRF|NM_002840|3'UTR
   1 CTACCGCTCCCCTCTCCTCCGCCACCCCCGCCGTGGGGCTCCGGAGGGGACCCAGCTCCTCTGAGCCATACCGACCATCG
  81 TCCAGCCCTCCTACGCAGATGCTGTCACTGGCAGAGCACAGCCCACGGGGATCACAGCGTTTCAGGAACGTTGCCACACC
 161 AATCAGAGAGCCTAGAACATCCCTGGGCAAGTGGATGGCCCAGCAGGCAGGCACTGTGGCCCTTCTGTCCACCAGACCCA
 241 CCTGGAGCCCGCTTCAAGCTCTCTGTTGCGCTCCCGCATTTCTCATGCTTCTTCTCATGGGGTGGGGTTGGGGCAAAGCC
 321 TCCTTTTTAATACATTAAGTGGGGTAGACTGAGGGATTTTAGCCTCTTCCCTCTGATTTTTCCTTTCGCGAATCCGTATC
 401 TGCAGAATGGGCCACTGTAGGGGTTGGGGTTTATTTTGTTTTGTTTTTTTTTTTCTTGAGTTCACTTTGGATCCTTATTT
 481 TGTATGACTTCTGCTGAAGGACAGAACATTGCCTTCCTCGTGCAGAGCTGGGGCTGCCAGCCTGAGCGGAGGCTCGGCCG
 561 TGGGCCGGGAGGCAGTGCTGATCCGGCTGCTCCTCCAGCCCTTCAGACGAGATCCTGTTTCAGCTAAATGCAGGGAAACT
 641 CAATGTTTTTTTAAGTTTTGTTTTCCCTTTAAAGCCTTTTTTTAGGCCACATTGACAGTGGTGGGCGGGGAGAAGATAGG
 721 GAACACTCATCCCTGGTCGTCTATCCCAGTGTGTGTTTAACATTCACAGCCCAGAACCACAGATGTGTCTGGGAGAGCCT
 801 GGCAAGGCATTCCTCATCACCATCGTGTTTGCAAAGGTTAAAACAAAAACAAAAAACCACAAAAATAAAAAACAAAAAAA
 881 ACAAAAAACCCAAGAAAAAAAAAAAGAGTCAGCCCTTGGCTTCTGCTTCAAACCCTCAAGAGGGGAAGCAACTCCGTGTG
 961 CCTGGGGTTCCCGAGGGAGCTGCTGGCTGACCTGGGCCCACAGAGCCTGGCTTTGGTCCCCAGCATTGCAGTATGGTGTG
1041 GTGTTTGTAGGCTGTGGGGTCTGGCTGTGTGGCCAAGGTGAATAGCACAGGTTAGGGTGTGTGCCACACCCCATGCACCT
1121 CAGGGCCAAGCGGGGGCGTGGCTGGCCTTTCAGGTCCAGGCCAGTGGGCCTGGTAGCACATGTCTGTCCTCAGAGCAGGG
1201 GCCAGATGATTTTCCTCCCTGGTTTGCAGCTGTTTTCAAAGCCCCCGATAATCGCTCTTTTCCACTCCAAGATGCCCTCA
1281 TAAACCAATGTGGCAAGACTACTGGACTTCTATCAATGGTACTCTAATCAGTCCTTATTATCCCAGCTTGCTGAGGGGCA
1361 GGGAGAGCGCCTCTTCCTCTGGGCAGCGCTATCTAGATAGGTAAGTGGGGGCGGGGAAGGGTGCATAGCTGTTTTAGCTG
1441 AGGGACGTGGTGCCGACGTCCCCAAACCTAGCTAGGCTAAGTCAAGATCAACATTCCAGGGTTGGTAATGTTGGATGATG
1521 AAACATTCATTTTTACCTTGTGGATGCTAGTGCTGTAGAGTTCACTGTTGTACACAGTCTGTTTTCTATTTGTTAAGAAA
1601 AACTACAGCATCATTGCATAATTCTTGATGGTAATAAATTTGAATAATCAGATTTCTTACAAACCAGGAAAAAAAAAAAA
1681 AAAAAA
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' cacgUGUCCUCUUAC--ACCGGAAAc 5'
              :|:||:| :||  |||||||| 
Target 5' ccaaGCGGGGGCGTGGCTGGCCTTTc 3'
 1126 - 1151 166.00 -20.80
2 
miRNA  3' caCGU--GUCCUCUUACACCGGAAAc 5'
            |||  ||||  | ||||||| || 
Target 5' caGCAGGCAGG-CACTGTGGCCCTTc 3'
 201 - 225 139.00 -18.56
3 
miRNA  3' caCGU---GUCCUCUUACACCGGAAAc 5'
            |||   ||| | ::|||||: ||| 
Target 5' caGCATTGCAGTATGGTGTGGTGTTTg 3'
 1021 - 1047 126.00 -17.20
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30191026 4 COSMIC
COSN31493735 6 COSMIC
COSN31540972 6 COSMIC
COSN13546301 7 COSMIC
COSN30475936 17 COSMIC
COSN30104293 19 COSMIC
COSN30522118 20 COSMIC
COSN30100843 21 COSMIC
COSN30482587 28 COSMIC
COSN26991033 30 COSMIC
COSN31503622 33 COSMIC
COSN24297451 34 COSMIC
COSN31502564 37 COSMIC
COSN30193374 44 COSMIC
COSN16130872 45 COSMIC
COSN30150132 45 COSMIC
COSN13546303 59 COSMIC
COSN30502193 70 COSMIC
COSN30187324 73 COSMIC
COSN26635738 74 COSMIC
COSN30131488 80 COSMIC
COSN30495403 80 COSMIC
COSN31601381 95 COSMIC
COSN30161023 96 COSMIC
COSN26440585 162 COSMIC
COSN25575671 179 COSMIC
COSN4603780 307 COSMIC
COSN18777721 455 COSMIC
COSN25304224 498 COSMIC
COSN8470448 576 COSMIC
COSN26649852 687 COSMIC
COSN28808451 824 COSMIC
COSN19655896 851 COSMIC
COSN25554550 857 COSMIC
COSN8470449 871 COSMIC
COSN31487994 906 COSMIC
COSN16128175 1116 COSMIC
COSN16131707 1152 COSMIC
COSN31542479 1340 COSMIC
COSN31564540 1413 COSMIC
COSN31545846 1441 COSMIC
COSN26505494 1447 COSMIC
COSN16626360 1579 COSMIC
COSN31515421 1645 COSMIC
COSN16129668 1650 COSMIC
rs72673097 252 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1256293636 3 dbSNP
rs755004036 4 dbSNP
rs1380633934 5 dbSNP
rs369551279 6 dbSNP
rs769423424 7 dbSNP
rs777303787 11 dbSNP
rs1237972970 12 dbSNP
rs748783332 13 dbSNP
rs775283573 14 dbSNP
rs373276106 15 dbSNP
rs1203940214 16 dbSNP
rs770382639 19 dbSNP
rs773894461 20 dbSNP
rs375151591 21 dbSNP
rs369952718 22 dbSNP
rs762085668 23 dbSNP
rs1467751161 25 dbSNP
rs765438541 25 dbSNP
rs373367448 30 dbSNP
rs377036580 31 dbSNP
rs751737122 33 dbSNP
rs754963221 34 dbSNP
rs973446485 40 dbSNP
rs368899845 43 dbSNP
rs929393703 44 dbSNP
rs752479708 46 dbSNP
rs1016479224 48 dbSNP
rs570547207 69 dbSNP
rs539468719 72 dbSNP
rs570743034 74 dbSNP
rs890961261 80 dbSNP
rs993667231 81 dbSNP
rs1210637730 82 dbSNP
rs772512205 84 dbSNP
rs1312177140 86 dbSNP
rs573467565 95 dbSNP
rs1335296174 96 dbSNP
rs749660576 98 dbSNP
rs899751880 117 dbSNP
rs536099288 118 dbSNP
rs954871692 125 dbSNP
rs1011636694 127 dbSNP
rs377470816 128 dbSNP
rs1021305345 131 dbSNP
rs773672788 139 dbSNP
rs757603415 140 dbSNP
rs1245977908 144 dbSNP
rs539467425 150 dbSNP
rs555727386 151 dbSNP
rs575781647 160 dbSNP
rs765005753 161 dbSNP
rs1256443433 162 dbSNP
rs544355533 163 dbSNP
rs1488842439 165 dbSNP
rs1286759350 166 dbSNP
rs564146178 167 dbSNP
rs1350630765 169 dbSNP
rs1266482496 170 dbSNP
rs991618545 175 dbSNP
rs1247104935 182 dbSNP
rs989487407 183 dbSNP
rs1023148068 184 dbSNP
rs913858411 188 dbSNP
rs1342553172 192 dbSNP
rs1315996282 211 dbSNP
rs1399827831 215 dbSNP
rs115324559 216 dbSNP
rs1164912012 219 dbSNP
rs974091953 228 dbSNP
rs919246218 231 dbSNP
rs950815987 233 dbSNP
rs1478613119 234 dbSNP
rs1239967247 242 dbSNP
rs1191496047 243 dbSNP
rs981971925 244 dbSNP
rs1249418061 248 dbSNP
rs1216093340 250 dbSNP
rs72673097 252 dbSNP
rs1182924276 253 dbSNP
rs371811751 256 dbSNP
rs1272649990 260 dbSNP
rs1383102237 262 dbSNP
rs1406910077 264 dbSNP
rs1165269674 266 dbSNP
rs1268577519 269 dbSNP
rs1344807978 270 dbSNP
rs911988594 271 dbSNP
rs560151700 276 dbSNP
rs943813889 277 dbSNP
rs1393582579 279 dbSNP
rs1039577702 285 dbSNP
rs1331480689 288 dbSNP
rs1055286072 290 dbSNP
rs1452478322 291 dbSNP
rs1166949604 297 dbSNP
rs921153062 302 dbSNP
rs55647429 303 dbSNP
rs941058331 317 dbSNP
rs150847540 322 dbSNP
rs1252844297 328 dbSNP
rs898110070 334 dbSNP
rs902848024 339 dbSNP
rs1229222107 340 dbSNP
rs562583701 341 dbSNP
rs1051941337 342 dbSNP
rs1056766164 343 dbSNP
rs895586096 347 dbSNP
rs1305388993 350 dbSNP
rs1315960926 352 dbSNP
rs369506012 353 dbSNP
rs114773270 354 dbSNP
rs1023119714 364 dbSNP
rs1352256477 367 dbSNP
rs1380540984 374 dbSNP
rs963903484 375 dbSNP
rs1414705472 387 dbSNP
rs995097672 388 dbSNP
rs1027017015 389 dbSNP
rs368342124 390 dbSNP
rs1010933949 391 dbSNP
rs1471220861 394 dbSNP
rs987473205 396 dbSNP
rs1182223779 397 dbSNP
rs6696481 401 dbSNP
rs539505691 406 dbSNP
rs139903281 409 dbSNP
rs566855750 413 dbSNP
rs535810053 417 dbSNP
rs1389416053 425 dbSNP
rs959475561 427 dbSNP
rs1334847442 430 dbSNP
rs990661793 442 dbSNP
rs1274529553 444 dbSNP
rs867714450 444 dbSNP
rs909664647 444 dbSNP
rs1310681702 445 dbSNP
rs868206752 447 dbSNP
rs376571493 449 dbSNP
rs1159832202 455 dbSNP
rs1449490195 458 dbSNP
rs575774447 459 dbSNP
rs538461167 471 dbSNP
rs558351526 489 dbSNP
rs1473135376 491 dbSNP
rs1259947873 493 dbSNP
rs921091187 501 dbSNP
rs750301676 520 dbSNP
rs756279907 521 dbSNP
rs1042942752 531 dbSNP
rs924523393 538 dbSNP
rs1283399650 543 dbSNP
rs1051972866 548 dbSNP
rs577824810 549 dbSNP
rs1008180077 556 dbSNP
rs1039183611 561 dbSNP
rs1340690769 563 dbSNP
rs1444064891 567 dbSNP
rs367863653 568 dbSNP
rs1056737655 579 dbSNP
rs1159005392 581 dbSNP
rs1406093385 585 dbSNP
rs780268019 586 dbSNP
rs1481964541 589 dbSNP
rs1163112648 593 dbSNP
rs1184123749 598 dbSNP
rs1475016251 607 dbSNP
rs754015175 609 dbSNP
rs1480263813 610 dbSNP
rs1044577370 616 dbSNP
rs1174358210 633 dbSNP
rs1427359827 636 dbSNP
rs1222174072 637 dbSNP
rs1336366121 641 dbSNP
rs1415485908 643 dbSNP
rs899323522 644 dbSNP
rs1353077744 650 dbSNP
rs995422537 655 dbSNP
rs1412033333 668 dbSNP
rs1026528622 677 dbSNP
rs1232112373 683 dbSNP
rs1350718047 688 dbSNP
rs755073476 690 dbSNP
rs1222596396 691 dbSNP
rs1318169310 692 dbSNP
rs1297206359 693 dbSNP
rs555395725 702 dbSNP
rs1003514222 706 dbSNP
rs190180934 707 dbSNP
rs748639663 708 dbSNP
rs1340026101 710 dbSNP
rs1460932811 715 dbSNP
rs1207014090 717 dbSNP
rs1373911207 718 dbSNP
rs959318449 721 dbSNP
rs1426558671 734 dbSNP
rs1418498407 736 dbSNP
rs1191499841 737 dbSNP
rs1252348915 738 dbSNP
rs1469788881 739 dbSNP
rs1250992405 740 dbSNP
rs974823813 744 dbSNP
rs1022837964 748 dbSNP
rs181616057 752 dbSNP
rs573572526 754 dbSNP
rs1306174417 767 dbSNP
rs747017196 770 dbSNP
rs968539485 772 dbSNP
rs979019140 773 dbSNP
rs1167450468 782 dbSNP
rs924521913 802 dbSNP
rs1235430791 821 dbSNP
rs1373844184 823 dbSNP
rs1301861648 825 dbSNP
rs934564551 826 dbSNP
rs1397261085 828 dbSNP
rs1300163680 838 dbSNP
rs1174039924 840 dbSNP
rs1388834214 840 dbSNP
rs1460675433 840 dbSNP
rs1192931591 845 dbSNP
rs1455378479 845 dbSNP
rs909729201 845 dbSNP
rs1432234372 846 dbSNP
rs1439816265 851 dbSNP
rs1252023288 858 dbSNP
rs962493628 861 dbSNP
rs1256163184 863 dbSNP
rs1130522 867 dbSNP
rs972457269 867 dbSNP
rs918299520 869 dbSNP
rs1234169272 870 dbSNP
rs1365350132 870 dbSNP
rs1336818223 871 dbSNP
rs1403895166 873 dbSNP
rs1313705349 874 dbSNP
rs1389675341 874 dbSNP
rs1436429730 874 dbSNP
rs933691590 874 dbSNP
rs1172989176 883 dbSNP
rs1373364410 883 dbSNP
rs1454269068 883 dbSNP
rs1365427413 887 dbSNP
rs1179053923 889 dbSNP
rs772742914 889 dbSNP
rs916911584 890 dbSNP
rs1486885342 894 dbSNP
rs201298308 894 dbSNP
rs1130523 895 dbSNP
rs879143289 895 dbSNP
rs879224963 895 dbSNP
rs912154098 895 dbSNP
rs145370622 896 dbSNP
rs1269134832 897 dbSNP
rs552049495 900 dbSNP
rs574957781 901 dbSNP
rs1294181157 903 dbSNP
rs1339963179 904 dbSNP
rs1039666862 905 dbSNP
rs1491332008 906 dbSNP
rs1230521070 907 dbSNP
rs756801665 907 dbSNP
rs1275011619 909 dbSNP
rs1358492931 910 dbSNP
rs946828468 921 dbSNP
rs1292251878 922 dbSNP
rs1042503740 924 dbSNP
rs1166402876 926 dbSNP
rs902595446 928 dbSNP
rs1256282727 932 dbSNP
rs1187296379 945 dbSNP
rs147659161 953 dbSNP
rs1452460366 956 dbSNP
rs1044118385 957 dbSNP
rs531475270 965 dbSNP
rs1235171432 971 dbSNP
rs1332969411 973 dbSNP
rs1035011584 974 dbSNP
rs1227969954 982 dbSNP
rs184834399 987 dbSNP
rs1048375566 989 dbSNP
rs1316193230 999 dbSNP
rs886637517 1008 dbSNP
rs570439684 1011 dbSNP
rs1384951802 1014 dbSNP
rs1416795452 1016 dbSNP
rs1168134296 1023 dbSNP
rs1475971446 1024 dbSNP
rs1019248904 1025 dbSNP
rs533296997 1026 dbSNP
rs1449426354 1034 dbSNP
rs1254104492 1037 dbSNP
rs996580855 1047 dbSNP
rs1022352595 1048 dbSNP
rs955106357 1060 dbSNP
rs1196580972 1064 dbSNP
rs1341676734 1066 dbSNP
rs986900163 1078 dbSNP
rs968549500 1088 dbSNP
rs978228889 1096 dbSNP
rs1371655689 1105 dbSNP
rs1305518758 1106 dbSNP
rs910901437 1107 dbSNP
rs942339134 1112 dbSNP
rs1329190750 1114 dbSNP
rs1411327865 1122 dbSNP
rs1319219646 1130 dbSNP
rs1166522124 1132 dbSNP
rs747462734 1132 dbSNP
rs540396539 1133 dbSNP
rs1031446213 1138 dbSNP
rs975026107 1139 dbSNP
rs915462374 1141 dbSNP
rs1182569447 1148 dbSNP
rs1437127404 1150 dbSNP
rs946903908 1156 dbSNP
rs1204246700 1158 dbSNP
rs1348322147 1164 dbSNP
rs1042578276 1165 dbSNP
rs1231969124 1168 dbSNP
rs1242312596 1169 dbSNP
rs1366764248 1174 dbSNP
rs1241264465 1179 dbSNP
rs955911907 1184 dbSNP
rs768586733 1206 dbSNP
rs1443657997 1213 dbSNP
rs1285797824 1214 dbSNP
rs902624796 1237 dbSNP
rs939405213 1242 dbSNP
rs1429556379 1243 dbSNP
rs1376418788 1247 dbSNP
rs537432031 1248 dbSNP
rs560451224 1251 dbSNP
rs1424997038 1252 dbSNP
rs1159228937 1254 dbSNP
rs775140763 1255 dbSNP
rs189730110 1257 dbSNP
rs1243041034 1269 dbSNP
rs566784404 1273 dbSNP
rs1422640136 1280 dbSNP
rs980195011 1281 dbSNP
rs1190042531 1287 dbSNP
rs535816870 1289 dbSNP
rs1284796799 1296 dbSNP
rs920329185 1302 dbSNP
rs549077723 1307 dbSNP
rs898415843 1309 dbSNP
rs993984319 1311 dbSNP
rs1415040960 1313 dbSNP
rs930376870 1317 dbSNP
rs1025418488 1319 dbSNP
rs1047499592 1326 dbSNP
rs1472887427 1329 dbSNP
rs955178920 1332 dbSNP
rs762617225 1334 dbSNP
rs944892808 1344 dbSNP
rs1473096018 1355 dbSNP
rs1405860425 1357 dbSNP
rs139767865 1358 dbSNP
rs986587237 1363 dbSNP
rs1320700084 1369 dbSNP
rs556138842 1370 dbSNP
rs900771133 1380 dbSNP
rs1394288697 1383 dbSNP
rs996161637 1386 dbSNP
rs1022703553 1388 dbSNP
rs903875751 1389 dbSNP
rs1266974682 1391 dbSNP
rs1238544108 1400 dbSNP
rs1291038850 1401 dbSNP
rs1227027159 1407 dbSNP
rs1000014440 1408 dbSNP
rs1378857763 1413 dbSNP
rs990214964 1413 dbSNP
rs1031079112 1414 dbSNP
rs1331544199 1420 dbSNP
rs538501568 1422 dbSNP
rs1461978532 1426 dbSNP
rs1229065870 1429 dbSNP
rs1163049890 1443 dbSNP
rs1423070787 1445 dbSNP
rs1262658604 1446 dbSNP
rs768132802 1447 dbSNP
rs773892267 1448 dbSNP
rs946936308 1455 dbSNP
rs558388767 1456 dbSNP
rs376077434 1458 dbSNP
rs1296785569 1459 dbSNP
rs571869696 1461 dbSNP
rs181200218 1462 dbSNP
rs1363660842 1468 dbSNP
rs1056558035 1472 dbSNP
rs1373250888 1476 dbSNP
rs553815311 1492 dbSNP
rs779452917 1498 dbSNP
rs1038314962 1499 dbSNP
rs1355266125 1520 dbSNP
rs573584395 1522 dbSNP
rs951786139 1526 dbSNP
rs1389548617 1527 dbSNP
rs983193555 1529 dbSNP
rs1455230320 1538 dbSNP
rs1250627130 1540 dbSNP
rs767502837 1541 dbSNP
rs1480759293 1551 dbSNP
rs994057787 1561 dbSNP
rs3189536 1565 dbSNP
rs1207134950 1581 dbSNP
rs1159256011 1590 dbSNP
rs1340478007 1595 dbSNP
rs542631623 1598 dbSNP
rs1235639855 1604 dbSNP
rs944829843 1607 dbSNP
rs145294623 1614 dbSNP
rs74511822 1616 dbSNP
rs1299287705 1619 dbSNP
rs922120744 1620 dbSNP
rs185205908 1625 dbSNP
rs1374406668 1630 dbSNP
rs1407804234 1632 dbSNP
rs1369689331 1633 dbSNP
rs1173976360 1639 dbSNP
rs932213811 1640 dbSNP
rs1375798842 1642 dbSNP
rs1304540801 1650 dbSNP
rs1419140651 1654 dbSNP
rs1252313381 1659 dbSNP
rs754039090 1661 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions TZM-bl
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... PAR-CLIP data was present in GSM1462574. RNA binding protein: AGO2. Condition:TZM-bl ami BaL ...

- Whisnant AW; Bogerd HP; Flores O; Ho P; et al., 2013, mBio.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' cacguguccucuuacaccGGAAAc 5'
                            ||| | 
Target 5' --------cucacugcaaCCUCUg 3'
 		1 - 16
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 GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000372414.3 | 3UTR | CUCACUGCAACCUCUGCCCCCCGGGUUCAAGCAAUUCUUCUG
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
95 hsa-miR-6768-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT060980 LAMC1 laminin subunit gamma 1 2 2
MIRT145633 LASP1 LIM and SH3 protein 1 2 2
MIRT161065 CDV3 CDV3 homolog 2 2
MIRT161171 SLC25A36 solute carrier family 25 member 36 2 2
MIRT177407 ZMYND11 zinc finger MYND-type containing 11 2 2
MIRT262237 WAC WW domain containing adaptor with coiled-coil 2 2
MIRT300236 INO80D INO80 complex subunit D 2 2
MIRT373993 PEBP1 phosphatidylethanolamine binding protein 1 2 4
MIRT379949 CRY2 cryptochrome circadian clock 2 2 2
MIRT405244 ADIPOR2 adiponectin receptor 2 2 2
MIRT441622 ROCK1 Rho associated coiled-coil containing protein kinase 1 2 6
MIRT441807 NOC3L NOC3 like DNA replication regulator 2 2
MIRT442007 NDUFV3 NADH:ubiquinone oxidoreductase subunit V3 2 2
MIRT442254 DCTN5 dynactin subunit 5 2 2
MIRT442413 LIMD1 LIM domains containing 1 2 2
MIRT442741 SERINC5 serine incorporator 5 2 2
MIRT442796 CEP170 centrosomal protein 170 2 2
MIRT443332 OCRL OCRL, inositol polyphosphate-5-phosphatase 2 2
MIRT443602 ZNF91 zinc finger protein 91 2 2
MIRT443695 KCNN3 potassium calcium-activated channel subfamily N member 3 2 2
MIRT443749 ELL2 elongation factor for RNA polymerase II 2 2 2
MIRT446376 THSD4 thrombospondin type 1 domain containing 4 2 2
MIRT452491 BANK1 B-cell scaffold protein with ankyrin repeats 1 2 16
MIRT456028 PSMA7 proteasome subunit alpha 7 2 2
MIRT461191 TRIP4 thyroid hormone receptor interactor 4 2 16
MIRT464498 UCK2 uridine-cytidine kinase 2 2 2
MIRT466640 TAOK1 TAO kinase 1 2 16
MIRT466703 TAF13 TATA-box binding protein associated factor 13 2 4
MIRT467765 SLC30A7 solute carrier family 30 member 7 2 2
MIRT469973 PTPRF protein tyrosine phosphatase, receptor type F 2 2
MIRT470539 COASY Coenzyme A synthase 2 2
MIRT474827 KIAA0226 RUN and cysteine rich domain containing beclin 1 interacting protein 2 2
MIRT475961 GXYLT1 glucoside xylosyltransferase 1 2 4
MIRT476459 GBA2 glucosylceramidase beta 2 2 2
MIRT477658 EFNA1 ephrin A1 2 2
MIRT485320 MZT1 mitotic spindle organizing protein 1 2 4
MIRT485656 CYP1B1 cytochrome P450 family 1 subfamily B member 1 2 2
MIRT494145 CTC1 CST telomere replication complex component 1 2 10
MIRT495127 CXorf67 chromosome X open reading frame 67 2 2
MIRT498279 POFUT1 protein O-fucosyltransferase 1 2 2
MIRT498432 DDX39A DExD-box helicase 39A 2 2
MIRT498853 LITAF lipopolysaccharide induced TNF factor 2 4
MIRT499661 SDR42E1 short chain dehydrogenase/reductase family 42E, member 1 2 2
MIRT502927 CDC42SE1 CDC42 small effector 1 2 4
MIRT503758 CEP19 centrosomal protein 19 2 6
MIRT507753 CERS2 ceramide synthase 2 2 4
MIRT507893 CAMSAP2 calmodulin regulated spectrin associated protein family member 2 2 4
MIRT510091 PPWD1 peptidylprolyl isomerase domain and WD repeat containing 1 2 8
MIRT527065 PPP6R1 protein phosphatase 6 regulatory subunit 1 2 2
MIRT530314 TNFRSF10D TNF receptor superfamily member 10d 2 2
MIRT530702 P2RY1 purinergic receptor P2Y1 2 2
MIRT532378 LINC00598 long intergenic non-protein coding RNA 598 2 2
MIRT532969 ZNF148 zinc finger protein 148 2 2
MIRT533958 TAF1D TATA-box binding protein associated factor, RNA polymerase I subunit D 2 2
MIRT535186 PLEKHA8 pleckstrin homology domain containing A8 2 2
MIRT538751 CADM1 cell adhesion molecule 1 2 2
MIRT539473 ADARB2 adenosine deaminase, RNA specific B2 (inactive) 2 2
MIRT543858 APIP APAF1 interacting protein 2 2
MIRT558802 CDON cell adhesion associated, oncogene regulated 2 2
MIRT560208 AK4 adenylate kinase 4 2 2
MIRT560318 EFHD2 EF-hand domain family member D2 2 2
MIRT560439 GOLGA7B golgin A7 family member B 2 2
MIRT560846 SUV39H2 suppressor of variegation 3-9 homolog 2 2 2
MIRT562787 LIMA1 LIM domain and actin binding 1 2 2
MIRT563476 POLE3 DNA polymerase epsilon 3, accessory subunit 2 2
MIRT563829 RIPK4 receptor interacting serine/threonine kinase 4 2 2
MIRT563996 SLFN11 schlafen family member 11 2 2
MIRT564596 ZNF791 zinc finger protein 791 2 2
MIRT565442 SURF4 surfeit 4 2 2
MIRT566020 RHOA ras homolog family member A 2 2
MIRT566185 PTPN14 protein tyrosine phosphatase, non-receptor type 14 2 2
MIRT567643 FAM160A1 family with sequence similarity 160 member A1 2 2
MIRT568484 ARL5B ADP ribosylation factor like GTPase 5B 2 2
MIRT568553 AKT2 AKT serine/threonine kinase 2 2 2
MIRT613420 XRCC3 X-ray repair cross complementing 3 2 2
MIRT613638 ARHGAP35 Rho GTPase activating protein 35 2 2
MIRT614841 POU2F2 POU class 2 homeobox 2 2 2
MIRT630143 ZFYVE9 zinc finger FYVE-type containing 9 2 2
MIRT634123 ZMYM1 zinc finger MYM-type containing 1 2 4
MIRT641841 TCF7L2 transcription factor 7 like 2 2 2
MIRT647123 ZNF446 zinc finger protein 446 2 2
MIRT647968 FBXO31 F-box protein 31 2 2
MIRT658186 FBXO9 F-box protein 9 2 2
MIRT659097 DENR density regulated re-initiation and release factor 2 2
MIRT668980 CLCN3 chloride voltage-gated channel 3 2 2
MIRT670351 C1orf106 chromosome 1 open reading frame 106 2 4
MIRT671826 TRPM6 transient receptor potential cation channel subfamily M member 6 2 2
MIRT695610 GATAD1 GATA zinc finger domain containing 1 2 2
MIRT697722 USP8 ubiquitin specific peptidase 8 2 2
MIRT700069 RPL14 ribosomal protein L14 2 2
MIRT708474 MAPKAPK5 mitogen-activated protein kinase-activated protein kinase 5 2 2
MIRT717001 ARL6IP4 ADP ribosylation factor like GTPase 6 interacting protein 4 2 2
MIRT719591 TFCP2L1 transcription factor CP2 like 1 2 2
MIRT722026 CBY3 chibby family member 3 2 2
MIRT722901 LRRC20 leucine rich repeat containing 20 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-6768 Ceritinib 57379345 NSC776422 approved sensitive High Non-Small Cell Lung Cancer cell line (H3122, H2228)
hsa-mir-6768 Paclitaxel 36314 NSC125973 approved resistant cell line (A2780)
hsa-mir-6768 Cisplatin 5460033 NSC119875 approved resistant cell line (A2780)
hsa-mir-6768 Ceritinib 57379345 NSC776422 approved sensitive cell line (H3122)
hsa-miR-6768-3p Osimertinib 71496458 NSC779217 approved sensitive cell line (PC9)
hsa-miR-6768-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)

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