miRTarBase - #MIRT477670


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pre-miRNA Information
pre-miRNA hsa-mir-4677   
Genomic Coordinates chr1: 243346176 - 243346255
Description Homo sapiens miR-4677 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4677-3p
Sequence 50| UCUGUGAGACCAAAGAACUACU |71
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1481229343 11 dbSNP
rs771267188 18 dbSNP
rs1254655423 20 dbSNP
Putative Targets

miRNA Expression profile
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol EFHD2   
Synonyms SWS1
Description EF-hand domain family member D2
Transcript NM_024329   
Expression
Putative miRNA Targets on EFHD2
3'UTR of EFHD2
(miRNA target sites are highlighted)		 
>EFHD2|NM_024329|3'UTR
   1 CGGGGGCTGCAGCCGACCGCCCTGCTCCGGCCCCAGTGTGGTGGGCGAGGGTGGCGCATGGGAGGCCGAGCCTGAATCCT
  81 TGCCTGTGTCTGACGGGACCACTACTAAAAACCTAAAAATATCTGTGAATGGAGCAAGTTCAGGGGTCTTATGGAGGTGG
 161 CCCGGCCCCTCCCCGCTCCCTTCCACTCTGCACGAGGCCGCCACACCGGCGCTGGCTCCCTGCCCGGCCCGGCCCTCCCT
 241 GGCAATCCCTGGGCTCTCTTGCACCCCTAACTGCCCCCTGCCTGCTCCGGCACTGCCCCAGGCCCAGCTCCTGGCCCTAG
 321 GTCCCTCCCAGCCCCATGTGCCTGCCGCCTGCCCTCCACACATCCCTGTCCCCCCAACCCGGGAACCCCTGCCCTCCTCC
 401 AGCAGGCCGCACCGCCCCTGGGGCCCCCTGCCAGCCCCTTCCCAGGCTGGGAGACGGCAGAAGAGATAGAATCAGGGCTG
 481 CCCCCACAGAGTGGGACCCAAGGGGCTAATTGGAGGCACGAGGGGACCCCTCCCCAGGGCCTTTTCCTCCTCTGCGTCTT
 561 CCATCTACTGAAATGGGAGAGGGGGTGGGGAGCTTCTGTTCTGGTGAAGGGACCCGGGCAGGCCCCCAGCACCCCATGCT
 641 GACTTGGAGAACCCCAGATCTCTGGGGCCCAGCCAGGCAGGGTGTGGGGGCAGCTGTGCCAATCTACCTCACAGGCCCAC
 721 CCCCTGCCGGGCATGCCGTGGGATCATGGGCAGGGAAGGCTCTGGGGGTCGGAGACACCGCTGCTTAGCACCCCCAGCCA
 801 GAACACCCTGAGGGTCTCGGGGCTCTGGAGAGAGTGGGGCGGGAGGAAGAATTGGCACCTTCCTAGGGAAGGAGACGAGC
 881 GCTTCGCCTTGATTCTCCGAGAAGCCTCCGAGAAGTGCTTTAAGTGTGTTTGCATGCGCCAGGCGGTGGGCAGCGGGGGC
 961 CTGTCCAGCCCTCTCCCGCCATCCTTCCCCAAGTGACGTCCACTGCCTTGTCACCAGCGACCTGCCTGTCATGCCCACCC
1041 CCTGAGGAAGCATGGGGACCCTAACACCCTGGTGCCCTGCACCAGACAGGCCGTGGTCAGGCCCAGGCCACCGGCCGGGT
1121 TCTGCCACAGCTTCCCACGTGCTTGCTGACATGCGTGTGCCTGTGTGTGGTGTCTGTTGCTGTGTCGTGAAACTGTGACC
1201 ATCACTCAGTCCAAACAAGTGAGTGGCCCTCGAGGCCACAGTTATGCAACTTTCAGTGTGTGTCATAACGACGTCACTGC
1281 TTTTTAAACTCGATAACTCTTTATTTTAGTAAAATGCCCAGGAGTCCTGGAAGCTACGCGGACTTGCAGAGGTTTTATTT
1361 TTTGGCCTTAGAATCTGCAGAAATTAGGAGGCACCGAGCCCAGCGCAGCAGCCTCGGACCCGGATTGCGTTTGCCTTAGC
1441 GGATATGTTTATACAGATGAATATAAAATGTTTTTTTCTTTGGGCTTTTTGCTTCTTTTTTCCCCCCCTTCTCACCTTCC
1521 CTTCTCCCCGACCCCACCCCCCAAAAAAGCTACTTCTTCATTCCGTGGTACGATTATTTTTTTTAACTAAAGGAAGATAA
1601 AATTCTATATTCTTATGTGAAAAA
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' ucaucaagaaaccaGAGUGUCu 5'
                        ||||||| 
Target 5' ctgtgccaatctacCTCACAGg 3'
 694 - 715 140.00 -10.90
2 
miRNA  3' ucaUCAAGAAACCAGAGUGUCu 5'
             |||||   |||||:|::| 
Target 5' gcaAGTTCAGGGGTCTTATGGa 3'
 134 - 155 123.00 -18.20
3 
miRNA  3' ucaucaaGAAACCA--GAGUGUCu 5'
                 | | |||  ||| ||| 
Target 5' tcctggcCCTAGGTCCCTCCCAGc 3'
 309 - 332 117.00 -9.00
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30152761 28 COSMIC
COSN28795450 29 COSMIC
COSN30137885 50 COSMIC
COSN31565419 78 COSMIC
COSN1090378 292 COSMIC
COSN1090379 357 COSMIC
COSN5732375 496 COSMIC
COSN29369279 682 COSMIC
COSN26561308 691 COSMIC
COSN31488928 802 COSMIC
COSN16076553 996 COSMIC
COSN28201947 1013 COSMIC
COSN28719899 1019 COSMIC
COSN23887677 1086 COSMIC
COSN22596291 1098 COSMIC
COSN25771771 1114 COSMIC
COSN29467925 1151 COSMIC
COSN26583326 1155 COSMIC
COSN26565612 1156 COSMIC
COSN26586001 1261 COSMIC
COSN31579811 1328 COSMIC
COSN1407829 1333 COSMIC
COSN26555874 1341 COSMIC
rs6695499 457 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs565410583 1 dbSNP
rs77815160 2 dbSNP
rs759964570 3 dbSNP
rs1278098095 5 dbSNP
rs115830229 6 dbSNP
rs751276831 7 dbSNP
rs768726542 9 dbSNP
rs935100897 15 dbSNP
rs756783818 16 dbSNP
rs1282234453 18 dbSNP
rs201530565 19 dbSNP
rs201281899 20 dbSNP
rs755542428 22 dbSNP
rs779295363 23 dbSNP
rs1193294287 24 dbSNP
rs1376509713 25 dbSNP
rs1452218543 28 dbSNP
rs3765372 29 dbSNP
rs372935120 30 dbSNP
rs1273845620 38 dbSNP
rs1048481001 40 dbSNP
rs569804610 41 dbSNP
rs1470641837 43 dbSNP
rs761430989 44 dbSNP
rs1383417639 45 dbSNP
rs1384356906 47 dbSNP
rs375656967 48 dbSNP
rs1330548277 51 dbSNP
rs1454602698 55 dbSNP
rs796420271 56 dbSNP
rs558740986 57 dbSNP
rs994671618 60 dbSNP
rs1283680340 61 dbSNP
rs1349641892 68 dbSNP
rs374763966 69 dbSNP
rs11546436 82 dbSNP
rs952864099 84 dbSNP
rs1398057041 86 dbSNP
rs1407687595 87 dbSNP
rs1329984055 94 dbSNP
rs990830340 95 dbSNP
rs1023560405 96 dbSNP
rs970959355 101 dbSNP
rs11546434 103 dbSNP
rs760237688 105 dbSNP
rs982306355 107 dbSNP
rs368264301 112 dbSNP
rs924125389 113 dbSNP
rs1011310322 120 dbSNP
rs1021411460 123 dbSNP
rs1449731846 124 dbSNP
rs188782434 139 dbSNP
rs989657735 143 dbSNP
rs914994242 147 dbSNP
rs931674251 152 dbSNP
rs1050103418 160 dbSNP
rs928323524 161 dbSNP
rs554608669 164 dbSNP
rs573694208 165 dbSNP
rs1476591824 169 dbSNP
rs1169361367 172 dbSNP
rs915722667 175 dbSNP
rs1462459858 176 dbSNP
rs1389087336 177 dbSNP
rs1378929813 185 dbSNP
rs1386550058 186 dbSNP
rs1036250512 190 dbSNP
rs897688860 194 dbSNP
rs994679085 195 dbSNP
rs372517618 200 dbSNP
rs750955134 201 dbSNP
rs1235098443 202 dbSNP
rs888548217 204 dbSNP
rs1012709774 208 dbSNP
rs556203696 209 dbSNP
rs576149418 210 dbSNP
rs940035592 211 dbSNP
rs545150355 212 dbSNP
rs1393518437 223 dbSNP
rs1041406929 224 dbSNP
rs780476243 225 dbSNP
rs901184766 226 dbSNP
rs565482388 227 dbSNP
rs893963735 228 dbSNP
rs1457787430 230 dbSNP
rs1031196448 231 dbSNP
rs957130179 232 dbSNP
rs527917769 242 dbSNP
rs1297787781 244 dbSNP
rs541704638 247 dbSNP
rs1416681336 250 dbSNP
rs1310565467 260 dbSNP
rs1339806954 266 dbSNP
rs1239622436 268 dbSNP
rs1262305974 270 dbSNP
rs1245253644 272 dbSNP
rs967492701 274 dbSNP
rs181508240 278 dbSNP
rs1486405819 285 dbSNP
rs953159301 289 dbSNP
rs985851662 290 dbSNP
rs911572095 291 dbSNP
rs944339705 296 dbSNP
rs1258193573 297 dbSNP
rs1036302972 300 dbSNP
rs1266721915 311 dbSNP
rs529701075 312 dbSNP
rs1382594986 315 dbSNP
rs1418224929 322 dbSNP
rs919174555 324 dbSNP
rs11546433 325 dbSNP
rs549820554 331 dbSNP
rs991382998 333 dbSNP
rs760310385 336 dbSNP
rs1401540152 337 dbSNP
rs1048891524 338 dbSNP
rs894278652 348 dbSNP
rs376789696 364 dbSNP
rs879257730 365 dbSNP
rs1239157874 366 dbSNP
rs532250197 371 dbSNP
rs1003495184 375 dbSNP
rs1254931399 375 dbSNP
rs552046598 378 dbSNP
rs940132036 381 dbSNP
rs1438300449 382 dbSNP
rs1178413693 383 dbSNP
rs1031246645 387 dbSNP
rs956984438 388 dbSNP
rs1011535585 390 dbSNP
rs1370510537 393 dbSNP
rs1472123642 409 dbSNP
rs1358706036 410 dbSNP
rs1022477806 412 dbSNP
rs1164796690 413 dbSNP
rs953642406 414 dbSNP
rs1467234982 415 dbSNP
rs565859168 416 dbSNP
rs911624700 421 dbSNP
rs965737719 423 dbSNP
rs1300133769 424 dbSNP
rs1050014567 431 dbSNP
rs781250860 433 dbSNP
rs1228968350 435 dbSNP
rs534561881 448 dbSNP
rs918879464 456 dbSNP
rs6695499 457 dbSNP
rs1198527882 467 dbSNP
rs1254065834 481 dbSNP
rs1489659078 484 dbSNP
rs1189753636 487 dbSNP
rs1424725076 488 dbSNP
rs1278753328 498 dbSNP
rs1049424811 499 dbSNP
rs769858705 501 dbSNP
rs112780652 509 dbSNP
rs948539886 520 dbSNP
rs536216362 521 dbSNP
rs902667842 528 dbSNP
rs1465065978 530 dbSNP
rs868141037 533 dbSNP
rs41270247 536 dbSNP
rs895484182 539 dbSNP
rs1012500964 541 dbSNP
rs1483383468 545 dbSNP
rs1022838557 553 dbSNP
rs1316715361 555 dbSNP
rs117944029 556 dbSNP
rs1003547706 557 dbSNP
rs983992445 558 dbSNP
rs1219836519 565 dbSNP
rs1246436283 575 dbSNP
rs1486330958 578 dbSNP
rs781201108 582 dbSNP
rs6695620 583 dbSNP
rs1165633725 586 dbSNP
rs1415862336 589 dbSNP
rs1403470969 599 dbSNP
rs961215818 602 dbSNP
rs558829394 616 dbSNP
rs1479067432 617 dbSNP
rs1168651504 620 dbSNP
rs1295939592 621 dbSNP
rs1011170387 623 dbSNP
rs1022955686 626 dbSNP
rs1414861937 627 dbSNP
rs922679422 636 dbSNP
rs932643433 638 dbSNP
rs953594876 640 dbSNP
rs1227058985 642 dbSNP
rs1007728279 649 dbSNP
rs1019090893 651 dbSNP
rs572575404 663 dbSNP
rs971784076 680 dbSNP
rs113663027 683 dbSNP
rs951791747 685 dbSNP
rs1284127589 687 dbSNP
rs984750884 691 dbSNP
rs1042626549 697 dbSNP
rs915813511 717 dbSNP
rs879308846 719 dbSNP
rs1239222897 721 dbSNP
rs1298509624 728 dbSNP
rs561595133 729 dbSNP
rs981247382 730 dbSNP
rs939506065 731 dbSNP
rs1057290890 734 dbSNP
rs41270249 738 dbSNP
rs879802376 739 dbSNP
rs939454456 741 dbSNP
rs1434893420 743 dbSNP
rs1012615127 748 dbSNP
rs1022617857 749 dbSNP
rs144211637 750 dbSNP
rs1253868704 751 dbSNP
rs1005446627 752 dbSNP
rs1015484166 756 dbSNP
rs961513096 759 dbSNP
rs976574319 760 dbSNP
rs1201200834 763 dbSNP
rs1280862678 769 dbSNP
rs1440750732 771 dbSNP
rs892496143 772 dbSNP
rs1210657861 777 dbSNP
rs563284280 779 dbSNP
rs946689243 780 dbSNP
rs774229457 781 dbSNP
rs954144477 790 dbSNP
rs985529396 791 dbSNP
rs111823605 792 dbSNP
rs771803732 798 dbSNP
rs1433834943 805 dbSNP
rs552247716 810 dbSNP
rs146569598 814 dbSNP
rs1007776809 818 dbSNP
rs1178257997 819 dbSNP
rs1019143598 820 dbSNP
rs1449578133 824 dbSNP
rs1329757295 836 dbSNP
rs775279196 837 dbSNP
rs1376571374 841 dbSNP
rs760323341 853 dbSNP
rs1234290756 854 dbSNP
rs1276817240 861 dbSNP
rs924181789 868 dbSNP
rs1376138553 877 dbSNP
rs555109030 878 dbSNP
rs1026467022 880 dbSNP
rs528254911 882 dbSNP
rs948499046 886 dbSNP
rs951787424 887 dbSNP
rs1288212494 888 dbSNP
rs1200621371 898 dbSNP
rs548106310 899 dbSNP
rs1168003563 900 dbSNP
rs1425089037 905 dbSNP
rs1467672132 906 dbSNP
rs1169122094 909 dbSNP
rs567966309 911 dbSNP
rs1387706992 927 dbSNP
rs753336552 931 dbSNP
rs1329577913 933 dbSNP
rs536955389 937 dbSNP
rs550499925 938 dbSNP
rs185744822 939 dbSNP
rs1287240524 941 dbSNP
rs953840545 945 dbSNP
rs538682860 946 dbSNP
rs1022359699 947 dbSNP
rs558991078 953 dbSNP
rs988267041 954 dbSNP
rs766747093 955 dbSNP
rs528782923 956 dbSNP
rs1044120885 958 dbSNP
rs1264752028 964 dbSNP
rs535194268 969 dbSNP
rs1454033079 971 dbSNP
rs755269171 978 dbSNP
rs767792664 979 dbSNP
rs1388979880 987 dbSNP
rs1405035110 989 dbSNP
rs1299009058 990 dbSNP
rs948197027 996 dbSNP
rs1044135189 998 dbSNP
rs1350401411 999 dbSNP
rs1341004298 1001 dbSNP
rs1246834853 1002 dbSNP
rs902038509 1008 dbSNP
rs994072125 1011 dbSNP
rs1369573398 1018 dbSNP
rs117492771 1019 dbSNP
rs375854876 1020 dbSNP
rs1310987871 1027 dbSNP
rs1256183877 1028 dbSNP
rs1424936643 1033 dbSNP
rs369118556 1039 dbSNP
rs1285261117 1044 dbSNP
rs1036735596 1053 dbSNP
rs1367140758 1056 dbSNP
rs1348708643 1073 dbSNP
rs1005928641 1074 dbSNP
rs1362694462 1083 dbSNP
rs1418027945 1086 dbSNP
rs575147612 1093 dbSNP
rs969664916 1094 dbSNP
rs1397756098 1102 dbSNP
rs1002774615 1109 dbSNP
rs544119052 1110 dbSNP
rs1035553114 1113 dbSNP
rs373882885 1114 dbSNP
rs1322872847 1117 dbSNP
rs1050979537 1118 dbSNP
rs370335182 1128 dbSNP
rs955911919 1129 dbSNP
rs564019064 1140 dbSNP
rs989041908 1155 dbSNP
rs773588720 1156 dbSNP
rs1254684496 1166 dbSNP
rs1022390678 1173 dbSNP
rs968556382 1176 dbSNP
rs1382499263 1180 dbSNP
rs576750492 1182 dbSNP
rs115472852 1187 dbSNP
rs565170894 1196 dbSNP
rs1378330911 1208 dbSNP
rs1467635192 1211 dbSNP
rs1301085555 1212 dbSNP
rs1405281767 1216 dbSNP
rs1447361079 1217 dbSNP
rs757237620 1221 dbSNP
rs992438998 1227 dbSNP
rs1239045749 1232 dbSNP
rs943335855 1233 dbSNP
rs1313512439 1241 dbSNP
rs1425531280 1244 dbSNP
rs1162700502 1246 dbSNP
rs969533356 1247 dbSNP
rs11546437 1250 dbSNP
rs1238523999 1254 dbSNP
rs984965923 1255 dbSNP
rs1240455767 1256 dbSNP
rs909378842 1268 dbSNP
rs778690128 1270 dbSNP
rs777997158 1271 dbSNP
rs1332720776 1273 dbSNP
rs771753949 1274 dbSNP
rs1048362488 1275 dbSNP
rs532616854 1279 dbSNP
rs1006395179 1285 dbSNP
rs1044109317 1290 dbSNP
rs1397921411 1291 dbSNP
rs1441207443 1292 dbSNP
rs905559730 1293 dbSNP
rs1002491580 1294 dbSNP
rs1340560678 1295 dbSNP
rs1219833962 1298 dbSNP
rs1260534681 1317 dbSNP
rs1316513606 1318 dbSNP
rs1204272262 1320 dbSNP
rs1266353129 1327 dbSNP
rs942590535 1336 dbSNP
rs796949201 1337 dbSNP
rs141287039 1338 dbSNP
rs190553677 1339 dbSNP
rs11546435 1340 dbSNP
rs561534724 1341 dbSNP
rs896496791 1343 dbSNP
rs968568849 1348 dbSNP
rs530662659 1350 dbSNP
rs1351362386 1351 dbSNP
rs550435983 1353 dbSNP
rs1456100336 1358 dbSNP
rs969648593 1358 dbSNP
rs910639485 1360 dbSNP
rs570443809 1361 dbSNP
rs1436339180 1364 dbSNP
rs1204057815 1386 dbSNP
rs1237910710 1392 dbSNP
rs1484105516 1393 dbSNP
rs984995645 1395 dbSNP
rs532506277 1396 dbSNP
rs552314073 1397 dbSNP
rs566121292 1399 dbSNP
rs751655259 1401 dbSNP
rs923230665 1403 dbSNP
rs918297317 1405 dbSNP
rs1409046179 1406 dbSNP
rs1475058723 1413 dbSNP
rs929564324 1417 dbSNP
rs1360164473 1419 dbSNP
rs116128102 1423 dbSNP
rs555142720 1425 dbSNP
rs768388492 1428 dbSNP
rs1355418368 1429 dbSNP
rs1295846908 1430 dbSNP
rs757487870 1441 dbSNP
rs866187971 1442 dbSNP
rs942193697 1444 dbSNP
rs1303924904 1447 dbSNP
rs1381882498 1456 dbSNP
rs200639825 1471 dbSNP
rs1314734435 1472 dbSNP
rs1354712757 1476 dbSNP
rs181021774 1478 dbSNP
rs1043644968 1482 dbSNP
rs760654236 1486 dbSNP
rs1214266529 1492 dbSNP
rs1282292670 1492 dbSNP
rs903700410 1496 dbSNP
rs761208479 1497 dbSNP
rs537670210 1501 dbSNP
rs1182768469 1502 dbSNP
rs557671339 1502 dbSNP
rs891432860 1504 dbSNP
rs1380638762 1506 dbSNP
rs577489138 1507 dbSNP
rs1010599245 1508 dbSNP
rs1013617132 1509 dbSNP
rs1451039901 1510 dbSNP
rs1336516672 1521 dbSNP
rs1378065305 1524 dbSNP
rs1256486284 1530 dbSNP
rs1277987600 1531 dbSNP
rs1488602639 1537 dbSNP
rs1021524652 1542 dbSNP
rs1195708827 1543 dbSNP
rs1321355213 1543 dbSNP
rs1238615317 1544 dbSNP
rs1023622685 1554 dbSNP
rs905185039 1559 dbSNP
rs1478120499 1561 dbSNP
rs566696026 1563 dbSNP
rs904396708 1565 dbSNP
rs1422393079 1566 dbSNP
rs545736660 1569 dbSNP
rs184321296 1572 dbSNP
rs962243475 1573 dbSNP
rs1018087481 1574 dbSNP
rs1327190647 1576 dbSNP
rs1335411082 1576 dbSNP
rs1172186979 1577 dbSNP
rs1276727929 1577 dbSNP
rs1375190242 1590 dbSNP
rs1222889922 1599 dbSNP
rs1258629871 1608 dbSNP
rs1319827020 1613 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' ucaucaagaaaccaGAGUGUCu 5'
                        ||||||| 
Target 5' -----ccaaucuacCUCACAGg 3'
 		1 - 17
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 ENST00000375980.4 | 3UTR | CCAAUCUACCUCACAGGCCCACCCCCUGCCGGGCAUG
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
61 hsa-miR-4677-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT277530 HSP90AA1 heat shock protein 90 alpha family class A member 1 2 2
MIRT296646 RPS21 ribosomal protein S21 2 4
MIRT306961 THRB thyroid hormone receptor beta 2 2
MIRT439091 MYC MYC proto-oncogene, bHLH transcription factor 0 1
MIRT443953 LRIT3 leucine rich repeat, Ig-like and transmembrane domains 3 2 2
MIRT445487 KLF12 Kruppel like factor 12 2 2
MIRT446637 SDC3 syndecan 3 2 2
MIRT448594 PCP4L1 Purkinje cell protein 4 like 1 2 2
MIRT449822 FNBP1 formin binding protein 1 2 2
MIRT450422 BCL2L14 BCL2 like 14 2 2
MIRT454907 SEPT8 septin 8 2 17
MIRT466442 TFAM transcription factor A, mitochondrial 2 6
MIRT474198 LEPRE1 prolyl 3-hydroxylase 1 1 1
MIRT474486 KLHDC8B kelch domain containing 8B 2 2
MIRT474900 KCTD21 potassium channel tetramerization domain containing 21 2 2
MIRT477670 EFHD2 EF-hand domain family member D2 2 2
MIRT483912 GNB1L G protein subunit beta 1 like 2 2
MIRT484163 FAM71B family with sequence similarity 71 member B 2 2
MIRT487565 LOXL2 lysyl oxidase like 2 2 2
MIRT489678 CYP1A1 cytochrome P450 family 1 subfamily A member 1 2 2
MIRT491482 APC2 APC2, WNT signaling pathway regulator 2 6
MIRT492745 PER1 period circadian clock 1 2 10
MIRT499212 CHRDL1 chordin like 1 2 4
MIRT501197 SUMO1 small ubiquitin-like modifier 1 2 2
MIRT522622 MAP7D1 MAP7 domain containing 1 2 4
MIRT523971 DVL3 dishevelled segment polarity protein 3 2 2
MIRT541017 WIPI2 WD repeat domain, phosphoinositide interacting 2 2 2
MIRT554741 RHOC ras homolog family member C 2 2
MIRT558910 CBX5 chromobox 5 2 2
MIRT561466 TCEB3 elongin A 2 2
MIRT564039 BIRC5 baculoviral IAP repeat containing 5 2 2
MIRT564508 DUSP3 dual specificity phosphatase 3 2 2
MIRT566854 LRRC58 leucine rich repeat containing 58 2 2
MIRT574110 SPINT2 serine peptidase inhibitor, Kunitz type 2 2 2
MIRT611056 DAB2 DAB2, clathrin adaptor protein 2 2
MIRT615578 NCS1 neuronal calcium sensor 1 2 2
MIRT615742 EIF4EBP1 eukaryotic translation initiation factor 4E binding protein 1 2 2
MIRT626785 IL18RAP interleukin 18 receptor accessory protein 2 2
MIRT627338 TTLL7 tubulin tyrosine ligase like 7 2 2
MIRT629039 KLLN killin, p53-regulated DNA replication inhibitor 2 2
MIRT637643 RASGRP1 RAS guanyl releasing protein 1 2 2
MIRT641769 ZNF207 zinc finger protein 207 2 2
MIRT645719 PTPRF protein tyrosine phosphatase, receptor type F 2 2
MIRT652155 TRIM71 tripartite motif containing 71 2 2
MIRT659216 CXXC5 CXXC finger protein 5 2 2
MIRT661995 EFTUD2 elongation factor Tu GTP binding domain containing 2 2 2
MIRT662711 C10orf111 chromosome 10 open reading frame 111 2 4
MIRT663216 ZNF277 zinc finger protein 277 2 2
MIRT668715 DIP2C disco interacting protein 2 homolog C 2 2
MIRT675132 FSD2 fibronectin type III and SPRY domain containing 2 2 2
MIRT686180 ZNHIT6 zinc finger HIT-type containing 6 2 2
MIRT695993 SNX19 sorting nexin 19 2 2
MIRT702346 KLHL7 kelch like family member 7 2 2
MIRT702702 IPO9 importin 9 2 2
MIRT708232 PPP1R26 protein phosphatase 1 regulatory subunit 26 2 2
MIRT713311 SNRNP25 small nuclear ribonucleoprotein U11/U12 subunit 25 2 2
MIRT713528 PAFAH2 platelet activating factor acetylhydrolase 2 2 2
MIRT714651 FSTL1 follistatin like 1 2 2
MIRT715549 FPGS folylpolyglutamate synthase 2 2
MIRT724289 KCNMB1 potassium calcium-activated channel subfamily M regulatory beta subunit 1 2 2
MIRT724433 TFCP2L1 transcription factor CP2 like 1 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-4677 Doxorubicin 31703 NSC123127 approved resistant High Triple-Negative Breast Cancer cell line (MDA-MB-231, MDA-MB-468)
hsa-mir-4677 Ceritinib 57379345 NSC776422 approved resistant High Non-Small Cell Lung Cancer cell line (H3122, H2228)
hsa-mir-4677 Ceritinib 57379345 NSC776422 approved resistant cell line (H3122)
hsa-miR-4677-3p Ceritinib 57379345 NSC776422 approved resistant High Non-Small Cell Lung Cancer cell line (H3122, H2228)
hsa-miR-4677-3p Etoposide 36462 NSC141540 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-4677-3p Doxorubicin 31703 NSC123127 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-4677-3p Vinorelbine 44424639 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-4677-3p Vincristine 5978 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-4677-3p Paclitaxel 36314 NSC125973 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-4677-3p Gefitinib 123631 NSC715055 approved resistant cell line (HCC827)
hsa-miR-4677-3p Prednisone/Azathioprine/Methotrexate/Cyclophosphamide/Mycophenolate mofetil resistant tissue (myasthenia gravis)
hsa-miR-4677-3p Cisplatin 5460033 NSC119875 approved resistant cell line (A2780)
hsa-miR-4677-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (A2780)
hsa-miR-4677-3p Ceritinib 57379345 NSC776422 approved resistant cell line (H3122)

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