pre-miRNA Information
pre-miRNA hsa-mir-8066   
Genomic Coordinates chr4: 101240795 - 101240872
Description Homo sapiens miR-8066 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-8066
Sequence 48| CAAUGUGAUCUUUUGGAUGUA |68
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs931560390 4 dbSNP
rs1189907448 6 dbSNP
rs1347410735 8 dbSNP
rs1422871438 10 dbSNP
rs1281396192 14 dbSNP
rs1236502030 19 dbSNP
rs929291819 20 dbSNP
rs756482594 21 dbSNP
Putative Targets

Gene Information
Gene Symbol MTMR4   
Synonyms FYVE-DSP2, ZFYVE11
Description myotubularin related protein 4
Transcript NM_004687   
Expression
Putative miRNA Targets on MTMR4
3'UTR of MTMR4
(miRNA target sites are highlighted)
>MTMR4|NM_004687|3'UTR
   1 ATGCCGGGGAGAAACCTGTCCAATTTTAGCAGGTTTGAAGGGAGGATCTTCTTCAGTTGTAGTTTGGAAGGTTCCTTGGT
  81 GTGGCTCATGAAATCACAGAGCTCAGAGATACCATCTTGAGAAATCCTCCTTGGTATCATGAAACTGGAGCAGAGGAATT
 161 GCAATTTAGCAGGAGGTCCTCTACTGGTGATACCCTCACCTTGGGGTAATGGTCCTAACCCAGACCCAGGGTCTGGAAGC
 241 TTAATGTTGAGTTGGTGACTCCAGCCTCTTTCTCCTGGAGGTCACAAGATGATGATTGCGTAGATGTTGCCTGGTGCAAA
 321 GTGCCCCAAACAGCAATAGAAAGGCATATGTATAACCAAACTCCAAGTGATAACCAGACCCATCTCTCCTCCACCTTGAC
 401 AAAAGCAGATTATAGTATACAAGGTAGGAATTCCTGTCCTATTTGAGATGAACTATATCCTGTACCTCTGTGCTCTGTGT
 481 CTGCATGAAGGCTCAGCCTTTAGAGGCACTCCTTCTAGTTGCATTAGTACTGTCTTTCTGTGGAGTTTGGTTTGAAGACT
 561 GGCTCAGCAAGTGGAGGTTTCAATGTATTTTTCAGTTGGCTCATCAGCCAGCATTGGTGAATATTCAGTTTAGGGGAACA
 641 GTTCTAGGGAGTGAGACATTTTTGGGAGCAGAGGAAAACTCTGCTGATGTTCGGTCCTGGCAAACATTGAGTTATTTTGA
 721 GCTGTGAAGGCAGTCGTCTCTGTTACACAGTGGCAGCTCTTGAGTTATGCACTGTGAAGAATGAGAAGGGAAAAGCAAAA
 801 ATTATCCTTGTGAAATATCTGCTGATTGTGCCCTACTCTTTGCACCTGACTTTTCCTAGTTGTCCTGGTGCTAACACAGG
 881 AGCTACACCTTGATCCTCTCCTGGCATGAAAATAAAACAAAGGTTTTCGTTGTTGTTGTTCCATTGCCCATTTCCCCCAT
 961 GTTGTCTTTCCCTTGGCTGATGCCTCCTCTGGGTCACATTGCTTCTTATCCTGAACACTTGACACCTTGAGGGTAGAATT
1041 TAGCGTTTGGTTTTTACCTCCTAGCATATGCTGTTTGGTATGTGAGGGTTTCAGTACAAATGCTGCTGTCTATTTCTGTG
1121 CACTTAACAATGGAACCCAAACAGAAGAGAATAAAGCCTTGATACCAAAATTGGGAAAGAACATGTGTCCATTTGGACCA
1201 AACGTTGTTGGTTTTTAAAAAATTTTATTTTGTTTTTTTGTTTTTGTTTTTGTTTTTTTTCATCTTAATATGTACCAGTG
1281 GCACTTAACCAAAAGATACAGTGATATAGCCATGTACTGTGGGTGGGACAGATACAGTCTCCTTGGCCTATAATGAAACC
1361 ACTAGGACTTTATACAGTTTTCCTTAATTTGTTGACATATAAATGGTAAATTATATTTAGGCTTATCCTGTTTTGAAATG
1441 ATGGTAGTCATCTTTCTTACTGCTACTTTCATGTTGCTTTCTAGAAAACAGCATTTCATTCCAAAATAACTAGGATCTGC
1521 ATTTAGAACAAGAATCATTATTTGTCCTGACCTTTTCAGTCCTACAGAGACGCATCTGTGGTTCTTTTGTACTTGCCATA
1601 GATGTAACCTAAAAAGTTTTGGCATATTTAGGTCAGCCTAGCGGAACTTTTTTTTTCATTTAAATGGAGCTGAATAATGG
1681 AGATTTTGTGTCTGCAAAATTCCTGAGATCATTGAAAAAGTAACAAGCTGTTCCTTGTTTCTGATACATAAAATTATTTT
1761 AAGCATTTTATCAATCATTAAAATTTACTGCCAGTTGTGAGTGGCTTTTTAATTAACTTGTCTTTCATTGCACTTCACTC
1841 TGCCTGTTTTCAAGGGGAGTAAGATTGGTAACATTTGGGGAGACTGTATCTGTCTACTTAGCGTGGCTGTTTTGAGGGAC
1921 TGTCCCATCAGTGAACAAACTGCATGGCCTTGGAGAGAGACTCTGGGCTCTTGGCTCAGATGTGTTCATCAAATACTCCT
2001 TTCAGAGCTGTTGTGGGTGTAAGTGACATGATGTGGCCAAAAATCCAAACTGTGCAGTTGCGTTGTGACAAACATGCAAT
2081 GTGCTGTAAAAATTCAATACAGTTTAAATAAAATCTCTATATTAGTGCTGCAAAAAAAAAAAAAAAAAA
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' auGUAGGUUUUCUAGUGUAAc 5'
            | |||   :|:||||||| 
Target 5' tgCCTCCTCTGGGTCACATTg 3'
981 - 1001 155.00 -18.60
2
miRNA  3' auguAGGUUUUCUAGUGUaac 5'
              ||| ::||:|||||   
Target 5' tttcTCCTGGAGGTCACAaga 3'
269 - 289 125.00 -13.02
3
miRNA  3' auGU-AGGUUUU-------CUAG-UGUAAc 5'
            || |||||||       |||| :|||| 
Target 5' ttCATTCCAAAATAACTAGGATCTGCATTt 3'
1495 - 1524 119.00 -10.41
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN31535562 2 COSMIC
COSN31488604 56 COSMIC
COSN1724242 136 COSMIC
COSN31578827 226 COSMIC
COSN26537470 400 COSMIC
COSN31544931 438 COSMIC
COSN9671573 688 COSMIC
COSN1199143 722 COSMIC
COSN21764835 753 COSMIC
COSN29450067 823 COSMIC
COSN26482352 900 COSMIC
COSN31552598 938 COSMIC
COSN19437116 1021 COSMIC
COSN31479623 1161 COSMIC
COSN31532228 1232 COSMIC
COSN29963399 1252 COSMIC
COSN24294764 1355 COSMIC
COSN28646891 1412 COSMIC
COSN6108008 1591 COSMIC
COSN31576033 1647 COSMIC
COSN31610910 1647 COSMIC
COSN30539230 1808 COSMIC
COSN26549035 1838 COSMIC
COSN31544208 1840 COSMIC
COSN31591559 1890 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1056396519 4 dbSNP
rs180972693 5 dbSNP
rs749793644 6 dbSNP
rs1297485509 14 dbSNP
rs778355584 15 dbSNP
rs1398179845 16 dbSNP
rs756700071 24 dbSNP
rs1466334582 29 dbSNP
rs1205877604 32 dbSNP
rs375200949 40 dbSNP
rs773627337 43 dbSNP
rs1425875658 44 dbSNP
rs1415193637 45 dbSNP
rs1270302147 59 dbSNP
rs981744616 62 dbSNP
rs1427224456 63 dbSNP
rs1362696800 64 dbSNP
rs140635960 71 dbSNP
rs1159872117 72 dbSNP
rs1173860012 79 dbSNP
rs1016886283 80 dbSNP
rs1303500115 81 dbSNP
rs760017812 88 dbSNP
rs950917953 91 dbSNP
rs1375658643 102 dbSNP
rs1326946963 111 dbSNP
rs1183765953 114 dbSNP
rs1419555125 115 dbSNP
rs576496584 121 dbSNP
rs865871584 127 dbSNP
rs529007495 131 dbSNP
rs774741419 140 dbSNP
rs1245757656 153 dbSNP
rs1482112751 154 dbSNP
rs896275958 156 dbSNP
rs1332698535 162 dbSNP
rs114469132 164 dbSNP
rs1249217542 165 dbSNP
rs1211797466 169 dbSNP
rs1347466116 175 dbSNP
rs189108812 178 dbSNP
rs1240932168 179 dbSNP
rs377474019 183 dbSNP
rs903524624 194 dbSNP
rs564803072 197 dbSNP
rs763328703 199 dbSNP
rs1306906194 201 dbSNP
rs1408596750 204 dbSNP
rs1460405036 207 dbSNP
rs1356748977 214 dbSNP
rs1312965971 223 dbSNP
rs1395885572 227 dbSNP
rs1392088885 230 dbSNP
rs975232487 252 dbSNP
rs1399645603 253 dbSNP
rs964066672 265 dbSNP
rs1316188960 266 dbSNP
rs772754480 269 dbSNP
rs769423318 282 dbSNP
rs540353028 299 dbSNP
rs1008143089 300 dbSNP
rs951380302 303 dbSNP
rs184937106 305 dbSNP
rs1363081714 317 dbSNP
rs554591070 322 dbSNP
rs1476155778 326 dbSNP
rs1200054837 329 dbSNP
rs3087762 344 dbSNP
rs995758966 346 dbSNP
rs1183746605 349 dbSNP
rs1441964764 357 dbSNP
rs780738085 358 dbSNP
rs1055944924 360 dbSNP
rs1322275985 364 dbSNP
rs575149521 374 dbSNP
rs1192170249 375 dbSNP
rs539852101 382 dbSNP
rs1463461893 391 dbSNP
rs1172989262 394 dbSNP
rs879116965 396 dbSNP
rs1403930570 408 dbSNP
rs1469488701 413 dbSNP
rs746910560 415 dbSNP
rs780099299 420 dbSNP
rs181166910 427 dbSNP
rs974808372 430 dbSNP
rs1327588226 438 dbSNP
rs758285874 450 dbSNP
rs909226503 462 dbSNP
rs796241886 466 dbSNP
rs781104937 468 dbSNP
rs762423453 470 dbSNP
rs951018777 485 dbSNP
rs1486388222 486 dbSNP
rs1262155506 493 dbSNP
rs949156902 508 dbSNP
rs913562151 511 dbSNP
rs538410556 514 dbSNP
rs767493652 517 dbSNP
rs1052560853 521 dbSNP
rs190246758 522 dbSNP
rs1177217507 538 dbSNP
rs1361185986 544 dbSNP
rs960872426 561 dbSNP
rs1033390450 565 dbSNP
rs1386043699 566 dbSNP
rs1402428577 571 dbSNP
rs1001973776 573 dbSNP
rs1345405737 577 dbSNP
rs866819796 582 dbSNP
rs1293318196 583 dbSNP
rs925202405 592 dbSNP
rs1314827646 595 dbSNP
rs975180100 598 dbSNP
rs1237811138 601 dbSNP
rs1021990898 605 dbSNP
rs184192578 614 dbSNP
rs1220194558 615 dbSNP
rs1009881486 617 dbSNP
rs912434887 633 dbSNP
rs1229655700 634 dbSNP
rs891374942 635 dbSNP
rs1158602559 650 dbSNP
rs986838883 663 dbSNP
rs1421953244 670 dbSNP
rs1301640259 673 dbSNP
rs1382493486 685 dbSNP
rs1365582496 692 dbSNP
rs144883664 693 dbSNP
rs567540207 694 dbSNP
rs995932472 699 dbSNP
rs1294789489 706 dbSNP
rs1318303368 711 dbSNP
rs1370458678 712 dbSNP
rs1462902738 719 dbSNP
rs1307206300 725 dbSNP
rs962964774 735 dbSNP
rs1034609310 736 dbSNP
rs756352974 740 dbSNP
rs1360088553 750 dbSNP
rs79308060 756 dbSNP
rs1248559354 759 dbSNP
rs909185432 768 dbSNP
rs530929835 770 dbSNP
rs1176666992 773 dbSNP
rs1239055659 778 dbSNP
rs1366849741 781 dbSNP
rs1195521053 783 dbSNP
rs1162132052 789 dbSNP
rs1447802017 797 dbSNP
rs1247756995 802 dbSNP
rs1013330216 807 dbSNP
rs1167483710 815 dbSNP
rs767557575 819 dbSNP
rs1440903509 831 dbSNP
rs1052077169 841 dbSNP
rs1274326106 843 dbSNP
rs1209836959 845 dbSNP
rs1449938199 856 dbSNP
rs1353631452 859 dbSNP
rs929539566 866 dbSNP
rs546457059 867 dbSNP
rs1229979650 868 dbSNP
rs1270852962 869 dbSNP
rs1306813029 869 dbSNP
rs1203992993 873 dbSNP
rs1258783743 876 dbSNP
rs1271445230 882 dbSNP
rs936339814 883 dbSNP
rs1242955113 886 dbSNP
rs925182597 889 dbSNP
rs1039594134 896 dbSNP
rs1473303171 899 dbSNP
rs1364034715 901 dbSNP
rs1183943184 903 dbSNP
rs942654501 929 dbSNP
rs1409892550 938 dbSNP
rs1170787144 941 dbSNP
rs1401758959 949 dbSNP
rs1295008975 964 dbSNP
rs1335611996 965 dbSNP
rs1359354876 971 dbSNP
rs563939524 977 dbSNP
rs912381071 986 dbSNP
rs573905249 993 dbSNP
rs1215033607 998 dbSNP
rs1278928046 1007 dbSNP
rs986619506 1014 dbSNP
rs951474010 1016 dbSNP
rs918681052 1025 dbSNP
rs974068204 1032 dbSNP
rs960841754 1045 dbSNP
rs1212767027 1051 dbSNP
rs552127621 1058 dbSNP
rs1475375773 1065 dbSNP
rs1194978465 1066 dbSNP
rs1425177871 1077 dbSNP
rs1388583227 1078 dbSNP
rs1175042916 1083 dbSNP
rs1033861580 1085 dbSNP
rs1415804672 1087 dbSNP
rs533547112 1088 dbSNP
rs1315980769 1097 dbSNP
rs1344318208 1103 dbSNP
rs980504706 1111 dbSNP
rs1400574861 1112 dbSNP
rs759576425 1112 dbSNP
rs980344513 1120 dbSNP
rs1343542001 1137 dbSNP
rs1221806612 1144 dbSNP
rs752087750 1161 dbSNP
rs192090807 1181 dbSNP
rs1274334139 1185 dbSNP
rs1346053214 1186 dbSNP
rs971669645 1203 dbSNP
rs1282631434 1204 dbSNP
rs967849019 1205 dbSNP
rs1022377405 1208 dbSNP
rs1024462731 1217 dbSNP
rs1490000531 1222 dbSNP
rs1389761572 1232 dbSNP
rs892135575 1232 dbSNP
rs1478810627 1238 dbSNP
rs1186957904 1240 dbSNP
rs539943409 1241 dbSNP
rs998068943 1244 dbSNP
rs1160203325 1249 dbSNP
rs1254085738 1250 dbSNP
rs1198708065 1252 dbSNP
rs1450400450 1257 dbSNP
rs539051675 1258 dbSNP
rs115198502 1260 dbSNP
rs1039542695 1261 dbSNP
rs943450779 1261 dbSNP
rs1241408565 1262 dbSNP
rs1353219270 1262 dbSNP
rs1288580013 1271 dbSNP
rs892178912 1275 dbSNP
rs887908389 1281 dbSNP
rs1267482338 1289 dbSNP
rs1272036755 1295 dbSNP
rs1031168446 1307 dbSNP
rs1179023261 1313 dbSNP
rs1231994111 1324 dbSNP
rs1000657806 1326 dbSNP
rs1180340800 1346 dbSNP
rs903521033 1350 dbSNP
rs1423966143 1351 dbSNP
rs1163719675 1356 dbSNP
rs1236115396 1361 dbSNP
rs1039373680 1362 dbSNP
rs1407192828 1371 dbSNP
rs1274030441 1375 dbSNP
rs1376509334 1380 dbSNP
rs1434156629 1394 dbSNP
rs929289120 1400 dbSNP
rs942602163 1402 dbSNP
rs560823718 1407 dbSNP
rs1329520177 1409 dbSNP
rs919264732 1410 dbSNP
rs189441787 1412 dbSNP
rs763232293 1419 dbSNP
rs200739874 1421 dbSNP
rs574907365 1429 dbSNP
rs1056706884 1438 dbSNP
rs1266600905 1445 dbSNP
rs1359045888 1456 dbSNP
rs1193642856 1458 dbSNP
rs891059077 1460 dbSNP
rs773623812 1461 dbSNP
rs1180053750 1471 dbSNP
rs1410577145 1488 dbSNP
rs939606410 1504 dbSNP
rs1166933311 1511 dbSNP
rs1370189505 1514 dbSNP
rs1436831933 1531 dbSNP
rs556808969 1534 dbSNP
rs1166240041 1537 dbSNP
rs778984551 1552 dbSNP
rs1396000824 1559 dbSNP
rs55695958 1565 dbSNP
rs1477271478 1566 dbSNP
rs918640276 1569 dbSNP
rs914954831 1571 dbSNP
rs577746907 1572 dbSNP
rs941491445 1585 dbSNP
rs1260910261 1590 dbSNP
rs1482721265 1593 dbSNP
rs1200878817 1596 dbSNP
rs956377587 1597 dbSNP
rs1445212332 1611 dbSNP
rs1192796970 1621 dbSNP
rs139042641 1630 dbSNP
rs1478219120 1642 dbSNP
rs980124097 1643 dbSNP
rs1172873387 1657 dbSNP
rs998047473 1657 dbSNP
rs971609035 1664 dbSNP
rs963965961 1665 dbSNP
rs1404718817 1668 dbSNP
rs1212488660 1671 dbSNP
rs1341645607 1677 dbSNP
rs1220009216 1704 dbSNP
rs1018061704 1708 dbSNP
rs1348187515 1712 dbSNP
rs1277590874 1720 dbSNP
rs1257571268 1727 dbSNP
rs1005345918 1730 dbSNP
rs35521907 1735 dbSNP
rs1024569177 1745 dbSNP
rs1217245328 1746 dbSNP
rs988953095 1753 dbSNP
rs1050751617 1755 dbSNP
rs1215602919 1764 dbSNP
rs956399443 1780 dbSNP
rs1263870503 1781 dbSNP
rs888285888 1782 dbSNP
rs1196011001 1785 dbSNP
rs1033215135 1788 dbSNP
rs1265287605 1814 dbSNP
rs1432826749 1817 dbSNP
rs1177010859 1819 dbSNP
rs1379565678 1826 dbSNP
rs534803645 1836 dbSNP
rs1452134995 1842 dbSNP
rs1352627170 1843 dbSNP
rs1280065410 1851 dbSNP
rs1001010288 1854 dbSNP
rs1409201323 1857 dbSNP
rs903635528 1874 dbSNP
rs1349886371 1887 dbSNP
rs1300748114 1888 dbSNP
rs114195341 1891 dbSNP
rs184658698 1896 dbSNP
rs1303022398 1903 dbSNP
rs200467804 1914 dbSNP
rs1314735171 1919 dbSNP
rs891009765 1920 dbSNP
rs1359991906 1931 dbSNP
rs537416872 1932 dbSNP
rs1051455379 1937 dbSNP
rs1220075512 1957 dbSNP
rs1263791397 1969 dbSNP
rs9893202 1979 dbSNP
rs1488171407 1983 dbSNP
rs9984 1984 dbSNP
rs14823 1987 dbSNP
rs929948824 2016 dbSNP
rs1191810324 2019 dbSNP
rs1404136316 2022 dbSNP
rs1269818459 2025 dbSNP
rs1413115562 2028 dbSNP
rs1410688345 2029 dbSNP
rs1178424268 2050 dbSNP
rs1381229812 2052 dbSNP
rs1159590524 2058 dbSNP
rs1163228488 2062 dbSNP
rs1422089749 2062 dbSNP
rs1349785069 2066 dbSNP
rs1458008061 2067 dbSNP
rs1056506102 2069 dbSNP
rs939573809 2073 dbSNP
rs768312955 2075 dbSNP
rs574438069 2077 dbSNP
rs150734978 2079 dbSNP
rs192752194 2091 dbSNP
rs1243714907 2092 dbSNP
rs34947813 2093 dbSNP
rs12674 2096 dbSNP
rs1322250176 2097 dbSNP
rs1222476527 2102 dbSNP
rs1267239055 2118 dbSNP
rs1456610058 2121 dbSNP
rs1198199165 2123 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 9110.0
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... "PAR-CLIP data was present in GSM714644. RNA binding protein: AGO2. Condition:completeT1 ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' auguagguuuucuAGUGUAAc 5'
                       ||||||| 
Target 5' -------------UCACAUUg 3'
1 - 8
2
miRNA  3' auGUAGGUUUUCU----AGUGUAAc 5'
            :|||| :|| |     ||| || 
Target 5' cuUAUCCUGAACACUUGACACCUUg 3'
12 - 36
Article - Kishore S; Jaskiewicz L; Burger L; Hausser et al.
- Nature methods, 2011
Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.
LinkOut: [PMID: 21572407]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions TZM-bl
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... PAR-CLIP data was present in GSM1462574. RNA binding protein: AGO2. Condition:TZM-bl ami 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 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 GSM714644
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repA
Location of target site ENST00000579925.1 | 3UTR | UCACAUUGCUUCUUAUCCUGAACACUUGACACCUUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000579925.1 | 3UTR | UCACAUUGCUUCUUAUCCUGAACACUUGACACCUUG
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
92 hsa-miR-8066 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT060588 CCND1 cyclin D1 2 2
MIRT067440 RIMKLB ribosomal modification protein rimK like family member B 2 2
MIRT078862 WBP2 WW domain binding protein 2 2 2
MIRT088062 UBXN2A UBX domain protein 2A 2 4
MIRT088214 NUP50 nucleoporin 50 2 2
MIRT103494 HOXA3 homeobox A3 2 8
MIRT135196 TMBIM6 transmembrane BAX inhibitor motif containing 6 2 4
MIRT177727 REEP3 receptor accessory protein 3 2 2
MIRT179439 TBRG1 transforming growth factor beta regulator 1 2 4
MIRT191647 SLC39A9 solute carrier family 39 member 9 2 2
MIRT192342 KLF13 Kruppel like factor 13 2 2
MIRT212035 RAPGEF2 Rap guanine nucleotide exchange factor 2 2 2
MIRT215387 CREBRF CREB3 regulatory factor 2 2
MIRT235001 IER2 immediate early response 2 2 2
MIRT238793 TPD52L1 tumor protein D52 like 1 2 2
MIRT273384 SMARCD1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1 2 4
MIRT280473 UBR7 ubiquitin protein ligase E3 component n-recognin 7 (putative) 2 2
MIRT298320 SLC5A3 solute carrier family 5 member 3 2 2
MIRT309180 SPATA5 spermatogenesis associated 5 2 2
MIRT354483 LRRC58 leucine rich repeat containing 58 2 2
MIRT354710 SLC25A36 solute carrier family 25 member 36 2 2
MIRT361004 CDC5L cell division cycle 5 like 2 4
MIRT366247 VMA21 VMA21, vacuolar ATPase assembly factor 2 2
MIRT405774 EIF5 eukaryotic translation initiation factor 5 2 2
MIRT442640 TBC1D12 TBC1 domain family member 12 2 2
MIRT443928 ZNF99 zinc finger protein 99 2 2
MIRT454287 FXN frataxin 2 2
MIRT454367 ASAH2 N-acylsphingosine amidohydrolase 2 2 2
MIRT463574 ZBTB39 zinc finger and BTB domain containing 39 2 6
MIRT464484 UGCG UDP-glucose ceramide glucosyltransferase 2 2
MIRT466866 STX6 syntaxin 6 2 2
MIRT467283 SPNS1 sphingolipid transporter 1 (putative) 2 2
MIRT470298 PPTC7 PTC7 protein phosphatase homolog 2 2
MIRT471630 PAPD7 poly(A) RNA polymerase D7, non-canonical 2 2
MIRT472802 MTMR4 myotubularin related protein 4 2 4
MIRT474708 KIF3A kinesin family member 3A 2 2
MIRT478256 DDX3X DEAD-box helicase 3, X-linked 2 2
MIRT479330 CERS2 ceramide synthase 2 2 2
MIRT480658 BSCL2 BSCL2, seipin lipid droplet biogenesis associated 2 2
MIRT481954 ANKRD11 ankyrin repeat domain 11 2 2
MIRT482895 IAH1 isoamyl acetate-hydrolyzing esterase 1 homolog 2 4
MIRT493634 HIC2 HIC ZBTB transcriptional repressor 2 2 2
MIRT500847 SYPL1 synaptophysin like 1 2 4
MIRT502035 LRIG2 leucine rich repeats and immunoglobulin like domains 2 2 2
MIRT502185 IGSF3 immunoglobulin superfamily member 3 2 4
MIRT502605 DNAJB9 DnaJ heat shock protein family (Hsp40) member B9 2 10
MIRT502977 CCNL1 cyclin L1 2 8
MIRT504725 PLEKHA6 pleckstrin homology domain containing A6 2 10
MIRT504778 CLEC2D C-type lectin domain family 2 member D 2 4
MIRT505786 SATB1 SATB homeobox 1 2 4
MIRT510090 PPWD1 peptidylprolyl isomerase domain and WD repeat containing 1 2 4
MIRT520010 YY1 YY1 transcription factor 2 4
MIRT532552 TXNL1 thioredoxin like 1 2 2
MIRT533433 TRPS1 transcriptional repressor GATA binding 1 2 2
MIRT537459 FAM84B family with sequence similarity 84 member B 2 2
MIRT541825 SV2B synaptic vesicle glycoprotein 2B 2 2
MIRT543222 TMEM117 transmembrane protein 117 2 2
MIRT551088 DDX52 DExD-box helicase 52 2 2
MIRT551500 UGT2B4 UDP glucuronosyltransferase family 2 member B4 2 2
MIRT552326 ZNF791 zinc finger protein 791 2 2
MIRT553213 TXLNG taxilin gamma 2 2
MIRT554590 RRAGC Ras related GTP binding C 2 2
MIRT559004 CA8 carbonic anhydrase 8 2 2
MIRT559134 BTG3 BTG anti-proliferation factor 3 2 4
MIRT559409 GDNF glial cell derived neurotrophic factor 2 4
MIRT560678 SRFBP1 serum response factor binding protein 1 2 2
MIRT560954 POTED POTE ankyrin domain family member D 2 2
MIRT562856 C17orf58 chromosome 17 open reading frame 58 2 2
MIRT563003 MOCS2 molybdenum cofactor synthesis 2 2 2
MIRT564545 CCDC80 coiled-coil domain containing 80 2 2
MIRT566272 PTAR1 protein prenyltransferase alpha subunit repeat containing 1 2 2
MIRT566510 PAWR pro-apoptotic WT1 regulator 2 2
MIRT572103 EFNB2 ephrin B2 2 2
MIRT574576 NLGN4X neuroligin 4, X-linked 2 4
MIRT576574 Serpine1 serine (or cysteine) peptidase inhibitor, clade E, member 1 2 2
MIRT610815 POT1 protection of telomeres 1 2 2
MIRT624589 BCL11B B-cell CLL/lymphoma 11B 2 2
MIRT627567 SMAD6 SMAD family member 6 2 2
MIRT632675 MTX3 metaxin 3 2 2
MIRT689265 WDR83OS WD repeat domain 83 opposite strand 2 2
MIRT694310 COPB2 coatomer protein complex subunit beta 2 2 2
MIRT697721 USP8 ubiquitin specific peptidase 8 2 2
MIRT700209 RFWD3 ring finger and WD repeat domain 3 2 2
MIRT704399 CTSS cathepsin S 2 2
MIRT710665 CSTF2T cleavage stimulation factor subunit 2 tau variant 2 2
MIRT711953 SLC7A14 solute carrier family 7 member 14 2 2
MIRT712596 ADCYAP1 adenylate cyclase activating polypeptide 1 2 2
MIRT712692 TNFAIP2 TNF alpha induced protein 2 2 2
MIRT714171 PPP1R2 protein phosphatase 1 regulatory inhibitor subunit 2 2 2
MIRT715964 CES4A carboxylesterase 4A 2 2
MIRT722781 PDE3A phosphodiesterase 3A 2 2
MIRT724505 MSMO1 methylsterol monooxygenase 1 2 2

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