miRTarBase - #MIRT349304


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pre-miRNA Information
pre-miRNA hsa-mir-3915   
Genomic Coordinates chrX: 32583656 - 32583752
Description Homo sapiens miR-3915 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-3915
Sequence 21| UUGAGGAAAAGAUGGUCUUAUU |42
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs997323565 10 dbSNP
rs1192161547 15 dbSNP
rs1255075246 19 dbSNP
rs1452812574 20 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol ZNF317   
Synonyms -
Description zinc finger protein 317
Transcript NM_020933   
Expression
Putative miRNA Targets on ZNF317
3'UTR of ZNF317
(miRNA target sites are highlighted)		 
>ZNF317|NM_020933|3'UTR
   1 GCGCGCCTGCTTTAGAGACACAGGATGATTCAGACCGGAAACAGACCTCGTGGGTGTAAGAGGAAGCCTCTGTGAGCTCG
  81 CACCTTACTGGGTGCAAAAGAATCCACGGAACTTGGGAGAAGTCCAGTTCCTGTAAAAACTGGGAAGACGAGGCGTTCTC
 161 ATCCCATAGGAGGTTTGTGAGAACTCACGCCGGGGGTGAAAATGTACGTCTGTAGCATGGAGAAGCCTTCAGGGTACATT
 241 CAGCTCTTAACAAACACAGGAGGACTTAATGGCAGCTTGGCATTTAATGTCAAAATCCAAGCCGTGGCATTTAATGTCAA
 321 AATGACTTCAGACCACTTCTAGCCTTCTGGGCCCATGAGTAATAATGAGCACACTAGGGAGCATCTCTGTAAACACAGTG
 401 GCTGGGGAAACCCTTCCTAGTCTCACTTGATTCCTCATGACGGAAATCACACTAAAGAGAGAAATCAGTGAAGTAAGGAA
 481 CGTGGAAGGTCATGAATGGGCCGCAAACCACGGCCAGCTGCTTGTCTTTGTATGGCTTGCCAGCTAACAATAGTGGTTCC
 561 ATCTTTAAGGAAGAAGAATGTTTGATGGAGAAAATTTGTGGCCAATGAAGTCTGAAATACTTCCTGTCATCTGCCCCTTT
 641 CCAGAAAAACTTGGCCGACCCTTGGTCTACAGCACGGGTTCTCAGTCGGGCGACGATTTGGCTGTCTAGGCGTCATTTGG
 721 CAATGTCTAGAGACATTTTTGGTAGTTAGAATGGGGGGAAGATACTCCTGACTTGTAATAAGAAGACATCAGAGATGCTG
 801 CTAAGTCGGCTCCAGCACACAGGAGCCCCCCACAACGAAGAGTTAGTGCCCCCAAACGTCACTGTTGCTGAGGTTGAAAA
 881 TAATCATGCAGTCATTCCTCAATTACTGCCTGCAGCAATTCCTCCATTTTTATGAATCTTGTGAGCACTTACGCTAGGAG
 961 AAATTTCTTTTACAAAACTTTTAAAATACAATTAGTGCTGATAATTCCTATGTGGAAATGATTCCAGCCATGGTCCCCTC
1041 ACTTGAGCATGTGAATATTCTCACGGAGAGAAGCCCCAGCGAGATTTTCCGGTGAATACGGGATTGCACTTACTCTTTCA
1121 TCACGGAAACAGACCCCCCGAGAGAAGCCCCAACGAGATTTTCCGGTGAATACGGGACTGCACGTACTCTCTCATCATGA
1201 AAACAGAGCCCCGTTCATAAATTTTTCATCTTTATTTTTAAGGTTATACTCCTCTAAATAACCCTTAAGCCTCATCAAGA
1281 AAGGTTTGTTTATAGTATTTTTACTATAGCTTCATCCTTGATAACGTCCTAATTTCCTTCTGGACAACCTCCTTGACCAA
1361 TGGCATATTGAGATCTATGTGACATGAGGATATTTCTCAGTACCACTTTGTTACTGGTACCTGATGCACACGGATTGCGA
1441 CCAGAGCATGATGCCTCCATCAAGTGGTAATATGTTTGCAGCCTGCTGTCCAGCCAAGAGTGACAGATACTTCTAGTGAC
1521 TTCCCCGGTATCCACTCTCATCTTCTTCCAATATCAAGAGAATCCAGGTTCTGTCAGATTAGTAAGGTGTGCTAATCTAA
1601 ATTTTAAAAAATCTCTTACAGGTTTTCTTGCAGCTGGTACCATCCATGTCTCACAGCCCTGGCCACTGACAGATCAGCAG
1681 ATGTCACCACATGGGCTTCTGAGAAAGCTCTTGAATGGGGATCGTTCTTAAACATGAATTCCTCCCTGTATGTTTTGTTC
1761 TTTGCTTTACTTTTCACCTTGCAAAGAGATCCAGTACCTAGTATTGGAAGATCCACCTTAACGACCGTGCATATGAAAAC
1841 CACAGTCTAAGGAAGTGACTGCAGAAAGCTCACAGCGACCCTGGCCTCCCCTGTGGCCTCTTTGAGTGTCTGCAGCAGCC
1921 CTGGACTTCCAGACTTCTATCACATGAGAAAAAATAAAACTGATTATTGGTTTAAGCTGCTAAAAAAAAAAAAAAAAAAA
2001 AAAAA
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' uuAUUCUGGUAGAA--AAGGAGUu 5'
            ||:  :|| |||  ||||||| 
Target 5' ccTAGTCTCA-CTTGATTCCTCAt 3'
 416 - 438 153.00 -10.10
2 
miRNA  3' uuAUUCUGGUAGAAAAGGAGUu 5'
            | | :| :||  ||||||| 
Target 5' aaTCATGCAGTC-ATTCCTCAa 3'
 882 - 902 147.00 -10.00
3 
miRNA  3' uuAUUCUGGUAGAAAAGGAGuu 5'
            ||| | |||   ||||||  
Target 5' ctTAA-A-CATGAATTCCTCcc 3'
 1727 - 1746 130.00 -7.00
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN19668605 4 COSMIC
COSN31512224 4 COSMIC
COSN30504796 5 COSMIC
COSN31574250 33 COSMIC
COSN27006000 37 COSMIC
COSN30504477 38 COSMIC
COSN30179816 39 COSMIC
COSN27005996 51 COSMIC
COSN32078415 51 COSMIC
COSN30516013 55 COSMIC
COSN31566971 64 COSMIC
COSN30453923 80 COSMIC
COSN30505428 127 COSMIC
COSN21085350 128 COSMIC
COSN30522990 132 COSMIC
COSN31527341 147 COSMIC
COSN31554134 208 COSMIC
COSN16680306 337 COSMIC
COSN15291894 605 COSMIC
COSN20093505 636 COSMIC
COSN217043 958 COSMIC
COSN19297418 1010 COSMIC
COSN20115422 1140 COSMIC
COSN21546538 1197 COSMIC
COSN20093506 1552 COSMIC
COSN1773521 1922 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1178959466 2 dbSNP
rs372294186 3 dbSNP
rs746352165 4 dbSNP
rs79077891 5 dbSNP
rs780526352 6 dbSNP
rs181088695 16 dbSNP
rs1174566481 17 dbSNP
rs1405877016 20 dbSNP
rs768134330 22 dbSNP
rs185783954 29 dbSNP
rs747814166 32 dbSNP
rs761290234 34 dbSNP
rs769271843 36 dbSNP
rs768346748 37 dbSNP
rs762840519 38 dbSNP
rs552148193 39 dbSNP
rs773962624 45 dbSNP
rs760953478 50 dbSNP
rs764287714 51 dbSNP
rs1246599258 56 dbSNP
rs564023468 57 dbSNP
rs190495074 68 dbSNP
rs1178410266 73 dbSNP
rs1450658405 76 dbSNP
rs957293259 76 dbSNP
rs1380572076 80 dbSNP
rs778700649 81 dbSNP
rs1156395830 84 dbSNP
rs1241145784 88 dbSNP
rs1367212972 90 dbSNP
rs1322934152 99 dbSNP
rs1287149054 107 dbSNP
rs546344390 109 dbSNP
rs1342825166 110 dbSNP
rs568169657 111 dbSNP
rs1432618097 114 dbSNP
rs1001575779 117 dbSNP
rs1011077186 128 dbSNP
rs893285949 129 dbSNP
rs1348022729 131 dbSNP
rs1164206398 141 dbSNP
rs918929723 145 dbSNP
rs10445619 146 dbSNP
rs117499943 150 dbSNP
rs1378007907 151 dbSNP
rs1239717919 153 dbSNP
rs796195024 155 dbSNP
rs200606986 156 dbSNP
rs975715698 157 dbSNP
rs909476608 158 dbSNP
rs1244433906 170 dbSNP
rs796357895 179 dbSNP
rs938270639 180 dbSNP
rs182973801 183 dbSNP
rs1210762227 185 dbSNP
rs1221054493 187 dbSNP
rs539347937 189 dbSNP
rs1276681227 190 dbSNP
rs1226088833 192 dbSNP
rs953077070 196 dbSNP
rs1289854147 197 dbSNP
rs1450363195 200 dbSNP
rs1200056834 201 dbSNP
rs1365715847 208 dbSNP
rs1293207881 209 dbSNP
rs984532874 216 dbSNP
rs896616222 223 dbSNP
rs551929763 227 dbSNP
rs1438470291 231 dbSNP
rs773399756 233 dbSNP
rs1429694435 235 dbSNP
rs1360062546 243 dbSNP
rs1178732152 244 dbSNP
rs1431843498 245 dbSNP
rs909003603 252 dbSNP
rs1176427309 256 dbSNP
rs1198321800 263 dbSNP
rs148696681 270 dbSNP
rs572870789 270 dbSNP
rs1002276507 274 dbSNP
rs1473030762 275 dbSNP
rs771039338 276 dbSNP
rs1256553495 278 dbSNP
rs1411617291 284 dbSNP
rs572863348 287 dbSNP
rs1032332052 290 dbSNP
rs533951917 294 dbSNP
rs1007472305 303 dbSNP
rs141816800 304 dbSNP
rs905881302 305 dbSNP
rs975814855 307 dbSNP
rs937376042 309 dbSNP
rs1446081261 313 dbSNP
rs760032770 320 dbSNP
rs1025994360 326 dbSNP
rs1409708528 336 dbSNP
rs1329589855 344 dbSNP
rs950451407 345 dbSNP
rs1403497493 349 dbSNP
rs1305164109 353 dbSNP
rs11543149 358 dbSNP
rs1464848977 370 dbSNP
rs765527463 374 dbSNP
rs908877092 376 dbSNP
rs1054466918 378 dbSNP
rs1457460948 397 dbSNP
rs1413480038 406 dbSNP
rs1179343230 407 dbSNP
rs1418049347 411 dbSNP
rs1256755511 413 dbSNP
rs893242575 415 dbSNP
rs1246036865 428 dbSNP
rs938266962 434 dbSNP
rs1283968347 437 dbSNP
rs1010807029 441 dbSNP
rs1221008847 443 dbSNP
rs1209546579 444 dbSNP
rs753073748 447 dbSNP
rs918105511 449 dbSNP
rs1456946142 454 dbSNP
rs1315361495 456 dbSNP
rs1341208061 456 dbSNP
rs949509032 477 dbSNP
rs902067249 478 dbSNP
rs1042561584 483 dbSNP
rs761583327 485 dbSNP
rs574062399 489 dbSNP
rs146304669 503 dbSNP
rs534251535 504 dbSNP
rs1054235487 507 dbSNP
rs750092607 512 dbSNP
rs367984270 513 dbSNP
rs1452421076 521 dbSNP
rs1368548901 522 dbSNP
rs889754011 529 dbSNP
rs1007897434 530 dbSNP
rs961835548 531 dbSNP
rs1466127516 533 dbSNP
rs1366515655 541 dbSNP
rs1246411232 549 dbSNP
rs139466257 552 dbSNP
rs1357069775 554 dbSNP
rs1171341349 561 dbSNP
rs901699611 570 dbSNP
rs917759827 581 dbSNP
rs1465213753 592 dbSNP
rs1168586111 602 dbSNP
rs755633286 604 dbSNP
rs578219193 606 dbSNP
rs980647297 612 dbSNP
rs926580191 620 dbSNP
rs950511604 634 dbSNP
rs1396815040 637 dbSNP
rs545676800 652 dbSNP
rs144345141 656 dbSNP
rs1054412806 657 dbSNP
rs753721414 658 dbSNP
rs554081103 659 dbSNP
rs946168455 662 dbSNP
rs1192681802 674 dbSNP
rs991498144 676 dbSNP
rs1279439430 677 dbSNP
rs1490222695 679 dbSNP
rs1042245930 687 dbSNP
rs1231260260 688 dbSNP
rs918195836 689 dbSNP
rs1270005892 690 dbSNP
rs902003087 692 dbSNP
rs997726072 693 dbSNP
rs978290438 695 dbSNP
rs754903171 696 dbSNP
rs1364488607 704 dbSNP
rs11543150 707 dbSNP
rs1431574537 712 dbSNP
rs1199534509 713 dbSNP
rs889400793 716 dbSNP
rs1053841649 718 dbSNP
rs540203801 725 dbSNP
rs1379576029 743 dbSNP
rs889796505 745 dbSNP
rs1194090149 747 dbSNP
rs150638564 754 dbSNP
rs1252640625 755 dbSNP
rs1207859659 758 dbSNP
rs556801596 761 dbSNP
rs1191195398 765 dbSNP
rs747984654 776 dbSNP
rs758158353 777 dbSNP
rs997378922 778 dbSNP
rs1288459611 780 dbSNP
rs1344267703 780 dbSNP
rs118007221 782 dbSNP
rs1172233295 804 dbSNP
rs886241283 805 dbSNP
rs550451295 809 dbSNP
rs568667290 810 dbSNP
rs1015994717 812 dbSNP
rs770930630 813 dbSNP
rs1412748895 819 dbSNP
rs1421943301 822 dbSNP
rs1299181890 828 dbSNP
rs532971628 837 dbSNP
rs1471679804 839 dbSNP
rs551231830 846 dbSNP
rs1232800121 852 dbSNP
rs781108071 853 dbSNP
rs367898567 857 dbSNP
rs566404651 858 dbSNP
rs926527623 859 dbSNP
rs1331217118 863 dbSNP
rs776709111 873 dbSNP
rs1253933048 874 dbSNP
rs1229678575 883 dbSNP
rs747831358 888 dbSNP
rs1348006918 892 dbSNP
rs1448684763 894 dbSNP
rs1341988704 895 dbSNP
rs990531759 897 dbSNP
rs971007956 900 dbSNP
rs914579587 901 dbSNP
rs978300118 903 dbSNP
rs139916130 906 dbSNP
rs1399023517 910 dbSNP
rs1407359142 918 dbSNP
rs1041803737 923 dbSNP
rs923376304 927 dbSNP
rs564881339 932 dbSNP
rs933465079 933 dbSNP
rs1465674026 939 dbSNP
rs1050597451 940 dbSNP
rs1210214575 941 dbSNP
rs1282967961 951 dbSNP
rs989989128 951 dbSNP
rs1192881337 952 dbSNP
rs889348711 953 dbSNP
rs149818985 954 dbSNP
rs1041057602 955 dbSNP
rs770068165 963 dbSNP
rs746396591 967 dbSNP
rs567598493 972 dbSNP
rs1324246291 977 dbSNP
rs933248989 980 dbSNP
rs1047611658 983 dbSNP
rs1450406288 985 dbSNP
rs77605489 992 dbSNP
rs993608458 1003 dbSNP
rs1484705840 1009 dbSNP
rs1241202083 1010 dbSNP
rs1024707213 1022 dbSNP
rs1006077452 1026 dbSNP
rs1452032258 1036 dbSNP
rs906318734 1044 dbSNP
rs776121405 1050 dbSNP
rs1033490022 1058 dbSNP
rs1342541099 1060 dbSNP
rs894929424 1063 dbSNP
rs957908977 1065 dbSNP
rs1012001883 1068 dbSNP
rs989407392 1072 dbSNP
rs1275720701 1081 dbSNP
rs556703850 1082 dbSNP
rs1021330828 1092 dbSNP
rs577330531 1101 dbSNP
rs958511239 1105 dbSNP
rs1168740724 1106 dbSNP
rs1375852634 1110 dbSNP
rs977856723 1110 dbSNP
rs989691630 1111 dbSNP
rs1191479255 1112 dbSNP
rs923322429 1114 dbSNP
rs1266173380 1118 dbSNP
rs911369885 1120 dbSNP
rs578191620 1121 dbSNP
rs933409799 1125 dbSNP
rs1483361006 1126 dbSNP
rs3834986 1134 dbSNP
rs397841009 1134 dbSNP
rs1202162066 1137 dbSNP
rs986260879 1140 dbSNP
rs910732633 1141 dbSNP
rs1221167676 1151 dbSNP
rs942226646 1154 dbSNP
rs1410557088 1155 dbSNP
rs1488112680 1159 dbSNP
rs1297024719 1161 dbSNP
rs907814109 1165 dbSNP
rs1037952928 1166 dbSNP
rs1176268977 1170 dbSNP
rs1209375247 1174 dbSNP
rs898094573 1175 dbSNP
rs1251227189 1183 dbSNP
rs1472664726 1184 dbSNP
rs1459092673 1187 dbSNP
rs1045354 1192 dbSNP
rs1037580260 1195 dbSNP
rs1205761862 1197 dbSNP
rs1046497890 1198 dbSNP
rs1262809603 1205 dbSNP
rs1379869957 1207 dbSNP
rs1318882098 1211 dbSNP
rs3764602 1213 dbSNP
rs1391340067 1222 dbSNP
rs1377537573 1234 dbSNP
rs1167314350 1244 dbSNP
rs1380293799 1248 dbSNP
rs1369615516 1249 dbSNP
rs1046150739 1250 dbSNP
rs906216468 1259 dbSNP
rs186873375 1264 dbSNP
rs1324399547 1265 dbSNP
rs145797654 1278 dbSNP
rs1033437600 1284 dbSNP
rs1446815402 1286 dbSNP
rs3088289 1293 dbSNP
rs192266709 1307 dbSNP
rs1011180730 1308 dbSNP
rs765834971 1324 dbSNP
rs894089891 1326 dbSNP
rs1313141458 1327 dbSNP
rs753338234 1337 dbSNP
rs1242758656 1345 dbSNP
rs1209603222 1349 dbSNP
rs1486856983 1352 dbSNP
rs967044879 1362 dbSNP
rs977425553 1376 dbSNP
rs1030339530 1379 dbSNP
rs1242517718 1390 dbSNP
rs1322821085 1396 dbSNP
rs1317843879 1397 dbSNP
rs1244228566 1402 dbSNP
rs1018453847 1404 dbSNP
rs1335597258 1414 dbSNP
rs529074464 1415 dbSNP
rs1297979547 1421 dbSNP
rs964154388 1422 dbSNP
rs1386439993 1427 dbSNP
rs986207169 1432 dbSNP
rs1452487039 1433 dbSNP
rs976825781 1436 dbSNP
rs765198948 1439 dbSNP
rs942193741 1440 dbSNP
rs974008498 1442 dbSNP
rs561722503 1450 dbSNP
rs1189403564 1452 dbSNP
rs1430556393 1454 dbSNP
rs1259965451 1462 dbSNP
rs749399382 1464 dbSNP
rs528887091 1468 dbSNP
rs1479778806 1491 dbSNP
rs1184022644 1495 dbSNP
rs1220916065 1499 dbSNP
rs941961758 1504 dbSNP
rs1298838462 1505 dbSNP
rs1257320177 1509 dbSNP
rs1230126065 1519 dbSNP
rs1327807147 1524 dbSNP
rs544257401 1527 dbSNP
rs929564043 1528 dbSNP
rs1046005984 1531 dbSNP
rs1422694412 1544 dbSNP
rs1364693526 1545 dbSNP
rs1168959696 1548 dbSNP
rs562261499 1550 dbSNP
rs184048941 1553 dbSNP
rs1371549013 1557 dbSNP
rs937719716 1561 dbSNP
rs78029020 1568 dbSNP
rs1433783423 1569 dbSNP
rs1470682215 1577 dbSNP
rs1271164076 1589 dbSNP
rs906307647 1590 dbSNP
rs1168417636 1598 dbSNP
rs1276032091 1606 dbSNP
rs935058940 1610 dbSNP
rs1399507895 1619 dbSNP
rs893577299 1620 dbSNP
rs868020790 1628 dbSNP
rs1042632021 1631 dbSNP
rs566367885 1632 dbSNP
rs1249194031 1634 dbSNP
rs1226256102 1637 dbSNP
rs1345542933 1640 dbSNP
rs998519280 1653 dbSNP
rs1402605945 1657 dbSNP
rs893421828 1663 dbSNP
rs527578797 1669 dbSNP
rs1011172062 1671 dbSNP
rs1018920225 1674 dbSNP
rs1385242969 1682 dbSNP
rs900078428 1691 dbSNP
rs10129 1692 dbSNP
rs1181326135 1696 dbSNP
rs1247430267 1698 dbSNP
rs187726894 1711 dbSNP
rs1174337378 1713 dbSNP
rs1480183824 1714 dbSNP
rs1225484922 1716 dbSNP
rs1007587634 1724 dbSNP
rs1184609699 1725 dbSNP
rs1436375467 1736 dbSNP
rs1017688275 1739 dbSNP
rs141873513 1742 dbSNP
rs1323770159 1757 dbSNP
rs1266056664 1758 dbSNP
rs1478426795 1766 dbSNP
rs1221144781 1779 dbSNP
rs1322219679 1782 dbSNP
rs1016946038 1792 dbSNP
rs757450090 1793 dbSNP
rs1333723877 1794 dbSNP
rs1327902366 1798 dbSNP
rs191301727 1801 dbSNP
rs1408556461 1805 dbSNP
rs950961366 1823 dbSNP
rs1176357030 1824 dbSNP
rs571747347 1827 dbSNP
rs1160749432 1828 dbSNP
rs1432675866 1843 dbSNP
rs916524739 1848 dbSNP
rs1462984320 1849 dbSNP
rs1244594872 1858 dbSNP
rs1341121475 1870 dbSNP
rs982319587 1872 dbSNP
rs1460442251 1873 dbSNP
rs551814480 1877 dbSNP
rs539170395 1878 dbSNP
rs1348424329 1880 dbSNP
rs947938265 1881 dbSNP
rs981973450 1882 dbSNP
rs927777665 1884 dbSNP
rs182438047 1886 dbSNP
rs1052586995 1887 dbSNP
rs1345824044 1890 dbSNP
rs1220993030 1891 dbSNP
rs187077257 1892 dbSNP
rs1399081295 1897 dbSNP
rs914976294 1903 dbSNP
rs1384858521 1904 dbSNP
rs1164858417 1905 dbSNP
rs1347423356 1908 dbSNP
rs946400966 1909 dbSNP
rs1181324898 1917 dbSNP
rs946461712 1926 dbSNP
rs536906519 1933 dbSNP
rs1242387695 1936 dbSNP
rs900127671 1941 dbSNP
rs1444847566 1945 dbSNP
rs1283389371 1950 dbSNP
rs1223151049 1966 dbSNP
rs998390478 1970 dbSNP
rs1288616492 1971 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' uuAUUCUGGUAGAAAAGGAGUu 5'
            | | :| :||  ||||||| 
Target 5' aaUCAUGCAGUC-AUUCCUCAa 3'
 		6 - 26
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 ENST00000247956.6 | 3UTR | AAAAUAAUCAUGCAGUCAUUCCUCAAUUACUGCCUG
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
111 hsa-miR-3915 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT059544 PIP5K1A phosphatidylinositol-4-phosphate 5-kinase type 1 alpha 2 2
MIRT081703 ZNF507 zinc finger protein 507 2 2
MIRT083311 ZCCHC3 zinc finger CCHC-type containing 3 2 6
MIRT119046 SFT2D3 SFT2 domain containing 3 2 2
MIRT189381 TXLNA taxilin alpha 2 4
MIRT195895 C16ORF72 chromosome 16 open reading frame 72 2 6
MIRT223807 OXR1 oxidation resistance 1 2 2
MIRT292954 ZNF146 zinc finger protein 146 2 4
MIRT293949 RPL13A ribosomal protein L13a 2 6
MIRT300900 KREMEN1 kringle containing transmembrane protein 1 2 2
MIRT339332 SESN2 sestrin 2 2 2
MIRT349304 ZNF317 zinc finger protein 317 2 2
MIRT364736 TOR1B torsin family 1 member B 2 2
MIRT366233 VMA21 VMA21, vacuolar ATPase assembly factor 2 2
MIRT384605 CLIC4 chloride intracellular channel 4 2 2
MIRT401745 HLA-DRA major histocompatibility complex, class II, DR alpha 2 2
MIRT443169 UBL3 ubiquitin like 3 2 2
MIRT444215 METTL12 methyltransferase like 12 2 2
MIRT444375 SH3TC2 SH3 domain and tetratricopeptide repeats 2 2 2
MIRT445340 TCEANC transcription elongation factor A N-terminal and central domain containing 2 2
MIRT445474 KDM6A lysine demethylase 6A 2 2
MIRT445598 CAMK2N1 calcium/calmodulin dependent protein kinase II inhibitor 1 2 2
MIRT445630 TMEM50A transmembrane protein 50A 2 2
MIRT446012 VNN1 vanin 1 2 2
MIRT446115 ASTN1 astrotactin 1 2 2
MIRT446248 ELP2 elongator acetyltransferase complex subunit 2 2 2
MIRT446382 SYNCRIP synaptotagmin binding cytoplasmic RNA interacting protein 2 2
MIRT446940 ZMAT3 zinc finger matrin-type 3 2 2
MIRT446967 SLCO4C1 solute carrier organic anion transporter family member 4C1 2 2
MIRT447178 PGRMC2 progesterone receptor membrane component 2 2 2
MIRT447209 APBB2 amyloid beta precursor protein binding family B member 2 2 2
MIRT447237 IHH indian hedgehog 2 2
MIRT447807 EMX1 empty spiracles homeobox 1 2 2
MIRT447853 RRP8 ribosomal RNA processing 8 2 4
MIRT448054 MMP15 matrix metallopeptidase 15 2 2
MIRT448094 RASD2 RASD family member 2 2 2
MIRT448704 KLHL11 kelch like family member 11 2 2
MIRT448851 FEM1C fem-1 homolog C 2 2
MIRT449488 ZBTB4 zinc finger and BTB domain containing 4 2 2
MIRT449785 C1orf109 chromosome 1 open reading frame 109 2 2
MIRT450774 PDE3A phosphodiesterase 3A 2 2
MIRT451124 ZNF99 zinc finger protein 99 2 2
MIRT452676 GPR156 G protein-coupled receptor 156 2 2
MIRT452888 PSD4 pleckstrin and Sec7 domain containing 4 2 2
MIRT453188 ACSF2 acyl-CoA synthetase family member 2 2 2
MIRT453353 ZNF3 zinc finger protein 3 2 2
MIRT454502 ZFYVE27 zinc finger FYVE-type containing 27 2 2
MIRT454629 FAM83H family with sequence similarity 83 member H 2 2
MIRT455183 AGTRAP angiotensin II receptor associated protein 2 2
MIRT458204 FOXL2 forkhead box L2 2 2
MIRT458723 CES2 carboxylesterase 2 2 2
MIRT458942 SAMD4B sterile alpha motif domain containing 4B 2 2
MIRT460304 FLCN folliculin 2 2
MIRT460989 SYT7 synaptotagmin 7 2 2
MIRT461697 ZNF426 zinc finger protein 426 2 2
MIRT461903 NECAB3 N-terminal EF-hand calcium binding protein 3 2 2
MIRT462193 NDUFS1 NADH:ubiquinone oxidoreductase core subunit S1 2 2
MIRT462290 PPM1H protein phosphatase, Mg2+/Mn2+ dependent 1H 2 2
MIRT463795 XPOT exportin for tRNA 2 2
MIRT464649 UBE2V1 ubiquitin conjugating enzyme E2 V1 2 4
MIRT465911 TMEM189-UBE2V1 TMEM189-UBE2V1 readthrough 2 4
MIRT465992 TMEM189 transmembrane protein 189 2 4
MIRT466302 TIMM22 translocase of inner mitochondrial membrane 22 2 2
MIRT466575 TBC1D2B TBC1 domain family member 2B 2 2
MIRT470558 POU2F1 POU class 2 homeobox 1 2 2
MIRT471333 PERP PERP, TP53 apoptosis effector 2 2
MIRT471659 PALM2 paralemmin 2 2 2
MIRT472363 TSPAN1 tetraspanin 1 2 2
MIRT473468 MCFD2 multiple coagulation factor deficiency 2 2 2
MIRT474702 KIF3A kinesin family member 3A 2 2
MIRT476067 GRIN2A glutamate ionotropic receptor NMDA type subunit 2A 2 2
MIRT476077 GRB2 growth factor receptor bound protein 2 2 2
MIRT476423 GBA2 glucosylceramidase beta 2 2 2
MIRT476463 GATAD2B GATA zinc finger domain containing 2B 2 2
MIRT477877 DYNLL2 dynein light chain LC8-type 2 2 2
MIRT478240 DDX3X DEAD-box helicase 3, X-linked 2 4
MIRT479460 CDK6 cyclin dependent kinase 6 2 2
MIRT481030 BAZ2A bromodomain adjacent to zinc finger domain 2A 2 2
MIRT491496 HLA-DOA major histocompatibility complex, class II, DO alpha 2 2
MIRT497585 SLC23A1 solute carrier family 23 member 1 2 2
MIRT498542 TMEM30B transmembrane protein 30B 2 2
MIRT499263 NBPF11 NBPF member 11 2 2
MIRT504698 ZNF117 zinc finger protein 117 2 2
MIRT511288 KLHL15 kelch like family member 15 2 4
MIRT523121 HSP90B1 heat shock protein 90 beta family member 1 2 4
MIRT529601 H1F0 H1 histone family member 0 2 2
MIRT533481 TRIM71 tripartite motif containing 71 2 2
MIRT535571 NUP37 nucleoporin 37 2 4
MIRT537869 EDA2R ectodysplasin A2 receptor 2 2
MIRT538010 DNAJC10 DnaJ heat shock protein family (Hsp40) member C10 2 2
MIRT552681 YWHAZ tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta 2 4
MIRT554986 RAB39B RAB39B, member RAS oncogene family 2 2
MIRT556659 KMT2D lysine methyltransferase 2D 2 4
MIRT557437 GTPBP2 GTP binding protein 2 2 2
MIRT560813 CRTAP cartilage associated protein 2 2
MIRT562115 IGFBP5 insulin like growth factor binding protein 5 2 2
MIRT563103 IFRD2 interferon related developmental regulator 2 2 2
MIRT574199 LMNB1 lamin B1 2 2
MIRT623920 FMNL3 formin like 3 2 2
MIRT626551 NMNAT2 nicotinamide nucleotide adenylyltransferase 2 2 2
MIRT645458 ANKS6 ankyrin repeat and sterile alpha motif domain containing 6 2 2
MIRT649082 CACNA1B calcium voltage-gated channel subunit alpha1 B 2 2
MIRT659477 CLDN1 claudin 1 2 2
MIRT667950 HMGCS1 3-hydroxy-3-methylglutaryl-CoA synthase 1 2 2
MIRT701981 MIER3 MIER family member 3 2 2
MIRT708694 TFDP2 transcription factor Dp-2 2 2
MIRT709649 DFFB DNA fragmentation factor subunit beta 2 2
MIRT710090 FAM229B family with sequence similarity 229 member B 2 2
MIRT718396 ALDH1A3 aldehyde dehydrogenase 1 family member A3 2 2
MIRT724972 TNS1 tensin 1 2 2
MIRT756050 HRH4 histamine receptor H4 2 1
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-3915 Paclitaxel 36314 NSC125973 approved resistant High Prostate Cancer cell line (DU-145, PC-3)
hsa-miR-3915 Cisplatin + Decitabine sensitive High Non-Small Cell Lung Cancer cell line (A549)
hsa-mir-3915 Cisplatin 5460033 NSC119875 approved sensitive cell line (BxPC3)
hsa-miR-3915 Tripterygium wilfordii Hook F sensitive tissue
hsa-miR-3915 Cisplatin 5460033 NSC119875 approved resistant cell line (A549)
hsa-miR-3915 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-3915 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)

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