pre-miRNA Information
pre-miRNA hsa-mir-452   
Genomic Coordinates chrX: 151959628 - 151959712
Synonyms MIRN452, hsa-mir-452, MIR452
Description Homo sapiens miR-452 stem-loop
Comment The mature sequence shown here represents the most commonly cloned form from large-scale cloning studies . The 5' end of the miRNA may be offset with respect to previous annotations.
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-452-3p
Sequence 58| CUCAUCUGCAAAGAAGUAAGUG |79
Evidence Experimental
Experiments Array-cloned
Editing Events in miRNAs
Modification Type Position on miR Chromosome DNA Strand Genomic Position (hg38) List of PMIDs Variant details
A-to-I 12 X - 151959644 29233923 MiREDiBase
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs757928550 3 dbSNP
rs1324216965 6 dbSNP
rs1390793899 13 dbSNP
rs899383242 17 dbSNP
rs747858567 21 dbSNP
Putative Targets

miRNA Expression profile
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol RANGAP1   
Synonyms Fug1, RANGAP, SD
Description Ran GTPase activating protein 1
Transcript NM_002883   
Expression
Putative miRNA Targets on RANGAP1
3'UTR of RANGAP1
(miRNA target sites are highlighted)
>RANGAP1|NM_002883|3'UTR
   1 ACTCAAAGCCTCTCCCATCCCTTGGCCTGGACCAGTGAGCTGGGGAGGGACTCGGATGAACTGAGGCGCAGCCTACGCCA
  81 TTGCCTTGGACAGGACTCTGGCCACAGGCAGGGCGGGTCTGTGTCCCATGTGTCCTGTCAGTCCCCTGAGTATGTGTGTG
 161 GGTGTGGCGCATGTGCAGGTCTGTGCCTCCTGTCGGGATTTGGGTTTTAACGTCTTCTGCTGGCCCAGCCCTGCTCTGTT
 241 GTGGGGAGTTGGCCCCCAGGGGAAAGGGCTGTGAGCTGCTCCGCCATTAAACTCACCTCCACCTGAGGGCGCTCTGCTGA
 321 TCTCCGCCTGGGCCCTGATGGCCGTCCCCACCCACCTGCCTTCCGGCCCGGCTCCCTGGCGGAGCCAGAACCCAGGGAGT
 401 TGCCCGCGTGCTGTCCTTCCCCTCTGTGTTGTGATTGGGTTGTTTCCTGCCCTGCCTGGGGCTGCTTCTCGTCACCAAGC
 481 CCTGGTCCTGCGGCAGCTGTCACCCCTACCATCCATACCACTGTGCTGACCGCTCAGCCTGAAGAGCAGAGAATGCCATG
 561 GGTGGGACTGTGGGGGTCGGATCGTGGGGTTGTTGGCAGAGGGCAACCCTGGGCCCCACACCGTGTGGACAGGCAGACAC
 641 CAGATTGTCCAGGAGCAGGAGCTGCTGGGACTGCGCTGGCCCCGGACCTAGTGGGCCTTCTCCTGGCTGCTGAGATGTCG
 721 TCTGTGACTGGCCTGGCTGGAGGGGGAGTGTTGACAACCCAAAGCTGTTCTCCAGTCTGGGGAGGGAGAGGCAGGGTCCC
 801 CAATGTCCGAGCTGCATCTGGACGCTGCTCTTAAAGGACCTCCTGGGGCAGGGGAGCGGTAGGGTCTGGACTGGGCAGAT
 881 GCTGTATGACCTCCCTGAGCACCCGTGACTGCCCCATGCTTTCCCCTTTGTGCTCTGTGTGTGTCTGGGCTGTGCCCGGG
 961 GGCTTCACAAATAAAGTCGTGTGGCAGCTTCAGAGACTCAGAAACTCTCACTGAAAGCGGGATAGTCTCGGGGGCCGTTG
1041 TACGTGGAGTCCCACCTCGGCAGAGCATGCGGCCCCGCAGCAGTCTGTGGGGCAGTCAGCCCTGCAGAAGGGCCCGGCCT
1121 CGGCCTCAGGCCACTACCTGGGAAGTGGCAGTCCTGAGTGGGGGCCCATTTTCCTGCCTGGCCACACCTCACCCAGCACC
1201 CTGCCTTTGGGCTGCAGCTCGCTTGGCTTCTGCGTTGCTCCTTCACTATGGAAGCCACCTCCCTTGGGATCCTTTGCTCC
1281 ACTGCCACATATGTGAGGACAGCCCAGCCAACCTTCCTTACCTCCTACCCTACACCATGTATGTGCTTTGGGAGCCCATG
1361 TCCCCCACAAACGGCCTCCAAGAAGTCCCTCCAAGGTTTCTTAGAGGGCAATATTTTCTCATTGGCAGTCGGCCACGTAG
1441 GTGACCAGGTGGCAGAGGATACTGCTGGCCCTGTCCCCTGTCTTCTGTGTGAGTTGATACGGTAGGGGGTGGGTGTGGGG
1521 CTGGCATTAAGTTCTGATGCCAGCTACAACGTGGATGAACTTTGAAAACATGTTAAATGAAATAAGCCAGACACAAAAGG
1601 ACAAATATGATTCCATTTAGATGAGGCATCTAGAATAAGCAAATTCAGAGACAAGAAGGTAGAGGTTGCCAGGGCTAGGG
1681 GAAGGGTGGAATAGGGAGTGAGGCTGCAAACAGATTCTCTGGGATGATGAAGATGTTCTGGAAATGGAGAGTGGTGATGG
1761 TTGCATAACATTGTGAATGTACTTAATGCACTGAATTGTACACATAAAAATGGTTAAAATGATAGAAAAAAAAAAAAAA
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' gugaAUGAAGAAACGUCUACUc 5'
              |: |||  | :|||||| 
Target 5' aataTGATTCCATTTAGATGAg 3'
1604 - 1625 138.00 -10.20
2
miRNA  3' gugaaugaaGAAACGUCUACuc 5'
                   ||  |||||||  
Target 5' gggtctggaCTGGGCAGATGct 3'
862 - 883 129.00 -12.80
3
miRNA  3' gugaaugaagaaacGUCUACUc 5'
                        |:||||| 
Target 5' gctggggagggactCGGATGAa 3'
39 - 60 124.00 -7.00
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN15626085 2 COSMIC
COSN30547721 7 COSMIC
COSN231159 24 COSMIC
COSN30510263 30 COSMIC
COSN30136973 36 COSMIC
COSN30135693 67 COSMIC
COSN31564311 68 COSMIC
COSN31959848 76 COSMIC
COSN31586100 168 COSMIC
COSN9166367 376 COSMIC
COSN26323132 481 COSMIC
COSN17005111 623 COSMIC
COSN25906040 805 COSMIC
COSN20650317 815 COSMIC
COSN32063642 928 COSMIC
COSN31961982 941 COSMIC
rs3171692 395 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs776261990 2 dbSNP
rs1345497058 4 dbSNP
rs768691544 8 dbSNP
rs1249057284 9 dbSNP
rs1055919032 10 dbSNP
rs1195791455 12 dbSNP
rs372644088 17 dbSNP
rs1386605684 19 dbSNP
rs779779748 22 dbSNP
rs1448565580 23 dbSNP
rs771712470 24 dbSNP
rs979166295 29 dbSNP
rs370550540 30 dbSNP
rs1486403016 32 dbSNP
rs778657857 36 dbSNP
rs1220937495 37 dbSNP
rs1490978005 38 dbSNP
rs756829159 43 dbSNP
rs1221043738 53 dbSNP
rs1264084373 62 dbSNP
rs1318488608 63 dbSNP
rs950055457 67 dbSNP
rs557412992 68 dbSNP
rs917349786 70 dbSNP
rs1247946500 73 dbSNP
rs913769544 76 dbSNP
rs1186102399 77 dbSNP
rs1415275554 86 dbSNP
rs539022421 99 dbSNP
rs987954175 100 dbSNP
rs989275415 101 dbSNP
rs965823256 105 dbSNP
rs956213028 108 dbSNP
rs926136587 111 dbSNP
rs978915219 114 dbSNP
rs571505287 115 dbSNP
rs1360470746 119 dbSNP
rs953245929 129 dbSNP
rs1027357583 132 dbSNP
rs546983348 135 dbSNP
rs1310832727 137 dbSNP
rs898078378 148 dbSNP
rs1229362019 156 dbSNP
rs534776259 162 dbSNP
rs1014442526 167 dbSNP
rs1159446788 168 dbSNP
rs142951047 169 dbSNP
rs139374732 170 dbSNP
rs1189449972 171 dbSNP
rs745478746 173 dbSNP
rs529878660 178 dbSNP
rs1238710897 181 dbSNP
rs1483259405 186 dbSNP
rs373963890 194 dbSNP
rs568808714 195 dbSNP
rs9611526 196 dbSNP
rs1203308516 201 dbSNP
rs3180782 208 dbSNP
rs757514891 211 dbSNP
rs993230119 212 dbSNP
rs1261066765 213 dbSNP
rs1243729959 214 dbSNP
rs780074492 219 dbSNP
rs532443949 233 dbSNP
rs898906427 234 dbSNP
rs1359829126 255 dbSNP
rs1037531334 262 dbSNP
rs1001991195 270 dbSNP
rs1301357380 272 dbSNP
rs905112493 276 dbSNP
rs564689535 278 dbSNP
rs540244285 282 dbSNP
rs528174736 283 dbSNP
rs1288157494 286 dbSNP
rs1327442872 288 dbSNP
rs1221451446 289 dbSNP
rs1339938148 292 dbSNP
rs561001755 294 dbSNP
rs946015708 308 dbSNP
rs1316892521 310 dbSNP
rs1225982493 311 dbSNP
rs1384397706 321 dbSNP
rs950094713 323 dbSNP
rs1386254985 325 dbSNP
rs73428601 326 dbSNP
rs1250805627 327 dbSNP
rs1053109303 330 dbSNP
rs1471454133 335 dbSNP
rs934764249 338 dbSNP
rs988045915 342 dbSNP
rs944606832 343 dbSNP
rs926022508 344 dbSNP
rs1475286908 347 dbSNP
rs767002434 348 dbSNP
rs985919005 353 dbSNP
rs958831014 356 dbSNP
rs953162488 360 dbSNP
rs978927098 361 dbSNP
rs1448682379 363 dbSNP
rs1275998276 364 dbSNP
rs1367485831 365 dbSNP
rs778184519 367 dbSNP
rs1262289208 369 dbSNP
rs964838317 370 dbSNP
rs961984713 376 dbSNP
rs1466962452 379 dbSNP
rs1275363658 380 dbSNP
rs910817949 381 dbSNP
rs1247021233 382 dbSNP
rs1317427713 387 dbSNP
rs1189332777 389 dbSNP
rs3171692 395 dbSNP
rs752829724 403 dbSNP
rs954964883 404 dbSNP
rs1026427851 405 dbSNP
rs773739578 406 dbSNP
rs767739376 407 dbSNP
rs1349619822 413 dbSNP
rs1434951275 415 dbSNP
rs1300371234 416 dbSNP
rs1034527429 419 dbSNP
rs1296480675 421 dbSNP
rs1337067848 423 dbSNP
rs557534354 425 dbSNP
rs963138419 429 dbSNP
rs1397137164 430 dbSNP
rs141198880 431 dbSNP
rs1002070144 435 dbSNP
rs767576320 436 dbSNP
rs904625353 437 dbSNP
rs112952942 443 dbSNP
rs1395254255 454 dbSNP
rs1371354172 456 dbSNP
rs1165680661 460 dbSNP
rs1002002471 463 dbSNP
rs545336226 470 dbSNP
rs904997540 471 dbSNP
rs1046330179 479 dbSNP
rs891819760 480 dbSNP
rs1452389658 483 dbSNP
rs1041021120 490 dbSNP
rs944659274 491 dbSNP
rs1284415187 492 dbSNP
rs1355467071 493 dbSNP
rs1231188133 494 dbSNP
rs1269989152 499 dbSNP
rs911776292 500 dbSNP
rs1013946622 504 dbSNP
rs371660618 508 dbSNP
rs1053147027 510 dbSNP
rs1444144680 513 dbSNP
rs186662503 518 dbSNP
rs1188578901 520 dbSNP
rs1340137215 526 dbSNP
rs1255992823 528 dbSNP
rs182065081 531 dbSNP
rs1444733276 532 dbSNP
rs1043132874 535 dbSNP
rs943535515 539 dbSNP
rs1457182744 542 dbSNP
rs920368384 558 dbSNP
rs973587908 562 dbSNP
rs879073166 563 dbSNP
rs1304650937 567 dbSNP
rs961790019 575 dbSNP
rs55963927 578 dbSNP
rs529686492 579 dbSNP
rs907576014 583 dbSNP
rs1334805012 584 dbSNP
rs1326432723 585 dbSNP
rs534756849 587 dbSNP
rs35721033 590 dbSNP
rs1258879716 595 dbSNP
rs1347299799 598 dbSNP
rs987643830 603 dbSNP
rs1255499207 604 dbSNP
rs567410846 615 dbSNP
rs960283164 617 dbSNP
rs933602505 622 dbSNP
rs1953 623 dbSNP
rs1180373908 631 dbSNP
rs1379851099 632 dbSNP
rs1396558011 634 dbSNP
rs971707738 635 dbSNP
rs1172992302 641 dbSNP
rs962982449 661 dbSNP
rs1467174527 665 dbSNP
rs1015981511 672 dbSNP
rs980467352 673 dbSNP
rs969148911 674 dbSNP
rs1469386619 675 dbSNP
rs1010775883 677 dbSNP
rs1231451662 680 dbSNP
rs891873435 681 dbSNP
rs73885753 683 dbSNP
rs761451831 684 dbSNP
rs1208753858 685 dbSNP
rs1207637418 688 dbSNP
rs1275619800 689 dbSNP
rs568916592 691 dbSNP
rs1482958784 692 dbSNP
rs1350715853 694 dbSNP
rs1281583953 700 dbSNP
rs1434281024 705 dbSNP
rs890390837 710 dbSNP
rs1393969079 714 dbSNP
rs550764052 719 dbSNP
rs1030887124 720 dbSNP
rs1277453876 723 dbSNP
rs931904411 723 dbSNP
rs1392533594 725 dbSNP
rs1387294737 727 dbSNP
rs998867407 743 dbSNP
rs1368958410 749 dbSNP
rs532276809 762 dbSNP
rs1037533420 774 dbSNP
rs1043058632 777 dbSNP
rs940430439 781 dbSNP
rs943477800 782 dbSNP
rs1202640926 793 dbSNP
rs971658816 797 dbSNP
rs907585623 803 dbSNP
rs992515002 807 dbSNP
rs776647322 808 dbSNP
rs1189913837 809 dbSNP
rs1412310774 812 dbSNP
rs1377215364 814 dbSNP
rs571543946 815 dbSNP
rs57712473 823 dbSNP
rs933465893 824 dbSNP
rs1167806944 825 dbSNP
rs1370032931 836 dbSNP
rs980787299 838 dbSNP
rs1325181290 839 dbSNP
rs1392168877 840 dbSNP
rs1405481771 843 dbSNP
rs773874577 852 dbSNP
rs1437122744 854 dbSNP
rs919518680 855 dbSNP
rs11913689 856 dbSNP
rs528135725 857 dbSNP
rs560964951 858 dbSNP
rs760687346 859 dbSNP
rs1417364091 862 dbSNP
rs540528989 869 dbSNP
rs1244480918 874 dbSNP
rs1271883286 889 dbSNP
rs573520424 890 dbSNP
rs1486659331 893 dbSNP
rs1258915428 896 dbSNP
rs542700457 900 dbSNP
rs1215667717 901 dbSNP
rs969580422 902 dbSNP
rs1248119397 903 dbSNP
rs187859921 904 dbSNP
rs771687486 911 dbSNP
rs1257792577 912 dbSNP
rs1163970461 913 dbSNP
rs956536539 915 dbSNP
rs1458759008 924 dbSNP
rs1159744491 925 dbSNP
rs1428719925 926 dbSNP
rs1304851985 930 dbSNP
rs1380134397 933 dbSNP
rs146895453 935 dbSNP
rs1019633987 945 dbSNP
rs1000806831 946 dbSNP
rs1292230219 957 dbSNP
rs183174209 958 dbSNP
rs1315850836 961 dbSNP
rs1213005083 965 dbSNP
rs1021669335 970 dbSNP
rs1028305718 972 dbSNP
rs774931759 976 dbSNP
rs745557535 978 dbSNP
rs773835727 979 dbSNP
rs889202944 988 dbSNP
rs996531891 991 dbSNP
rs1473445329 996 dbSNP
rs1051823749 1001 dbSNP
rs1407124471 1002 dbSNP
rs1399080032 1003 dbSNP
rs1037942209 1006 dbSNP
rs1359772508 1008 dbSNP
rs564519571 1009 dbSNP
rs1434352206 1010 dbSNP
rs1161114535 1016 dbSNP
rs940482695 1018 dbSNP
rs933499882 1019 dbSNP
rs1410788073 1022 dbSNP
rs1056932581 1027 dbSNP
rs897976037 1029 dbSNP
rs1371835386 1030 dbSNP
rs1221393845 1034 dbSNP
rs578172576 1036 dbSNP
rs6002298 1037 dbSNP
rs909462399 1043 dbSNP
rs1045126798 1044 dbSNP
rs947709673 1057 dbSNP
rs947632361 1058 dbSNP
rs917670356 1059 dbSNP
rs1163034326 1061 dbSNP
rs1476252573 1063 dbSNP
rs1418641953 1068 dbSNP
rs991898233 1070 dbSNP
rs575316078 1071 dbSNP
rs573651082 1076 dbSNP
rs1192791926 1077 dbSNP
rs1426031743 1078 dbSNP
rs1019727320 1081 dbSNP
rs555350258 1083 dbSNP
rs1372618072 1085 dbSNP
rs1216977573 1088 dbSNP
rs1328635576 1090 dbSNP
rs986869462 1097 dbSNP
rs979251156 1112 dbSNP
rs967995667 1115 dbSNP
rs537110517 1121 dbSNP
rs899096890 1122 dbSNP
rs1016156707 1136 dbSNP
rs1300869116 1158 dbSNP
rs1336371954 1164 dbSNP
rs375930033 1165 dbSNP
rs1343887299 1168 dbSNP
rs1214755639 1171 dbSNP
rs1018164824 1174 dbSNP
rs1435852892 1182 dbSNP
rs1223761591 1193 dbSNP
rs1253513389 1194 dbSNP
rs1468128933 1199 dbSNP
rs1007981052 1215 dbSNP
rs953378028 1218 dbSNP
rs371174688 1220 dbSNP
rs1450326378 1221 dbSNP
rs1271799260 1223 dbSNP
rs748620053 1225 dbSNP
rs557009492 1233 dbSNP
rs1393422674 1234 dbSNP
rs1324831519 1240 dbSNP
rs897902459 1248 dbSNP
rs1439284044 1249 dbSNP
rs1036525173 1257 dbSNP
rs1006303935 1261 dbSNP
rs1324199025 1275 dbSNP
rs1463235646 1279 dbSNP
rs1366658434 1288 dbSNP
rs570153142 1289 dbSNP
rs1395449262 1292 dbSNP
rs117983667 1296 dbSNP
rs1269224891 1296 dbSNP
rs1045290667 1298 dbSNP
rs1169832408 1305 dbSNP
rs9637339 1325 dbSNP
rs1273524358 1330 dbSNP
rs1408222208 1332 dbSNP
rs1044454845 1334 dbSNP
rs567364018 1338 dbSNP
rs780485954 1339 dbSNP
rs1447646068 1358 dbSNP
rs914822058 1362 dbSNP
rs1056520887 1368 dbSNP
rs1474008557 1370 dbSNP
rs6002297 1372 dbSNP
rs1187612592 1373 dbSNP
rs562754629 1377 dbSNP
rs751813958 1379 dbSNP
rs1390287514 1382 dbSNP
rs1251497682 1392 dbSNP
rs1382266965 1396 dbSNP
rs1195834792 1410 dbSNP
rs571444094 1411 dbSNP
rs967840031 1422 dbSNP
rs1265591297 1430 dbSNP
rs1231434820 1431 dbSNP
rs912768957 1433 dbSNP
rs911142955 1436 dbSNP
rs6002296 1437 dbSNP
rs955453633 1440 dbSNP
rs534921594 1441 dbSNP
rs1444377946 1443 dbSNP
rs1030363080 1445 dbSNP
rs962774118 1448 dbSNP
rs1229029737 1450 dbSNP
rs997920321 1459 dbSNP
rs780084513 1462 dbSNP
rs567230951 1465 dbSNP
rs756986914 1467 dbSNP
rs1453613386 1470 dbSNP
rs1442751472 1471 dbSNP
rs549015382 1476 dbSNP
rs1382056042 1479 dbSNP
rs1415829092 1480 dbSNP
rs1297810217 1483 dbSNP
rs950607189 1485 dbSNP
rs1290194510 1491 dbSNP
rs1035529813 1500 dbSNP
rs1336304462 1500 dbSNP
rs1006356417 1501 dbSNP
rs905625442 1510 dbSNP
rs1044121986 1513 dbSNP
rs1171789743 1514 dbSNP
rs1484923705 1517 dbSNP
rs1207766594 1526 dbSNP
rs1379180843 1530 dbSNP
rs758635155 1543 dbSNP
rs1393765058 1546 dbSNP
rs1361616496 1550 dbSNP
rs887921079 1554 dbSNP
rs1011728219 1555 dbSNP
rs1045621369 1558 dbSNP
rs1374458229 1561 dbSNP
rs1432431797 1562 dbSNP
rs1299699592 1571 dbSNP
rs753644433 1572 dbSNP
rs763951476 1578 dbSNP
rs1396865173 1584 dbSNP
rs1390762583 1587 dbSNP
rs186968705 1599 dbSNP
rs1332947316 1607 dbSNP
rs1267680258 1608 dbSNP
rs1176259484 1609 dbSNP
rs1218459247 1615 dbSNP
rs1302699712 1616 dbSNP
rs1346030269 1619 dbSNP
rs1230797639 1625 dbSNP
rs563426992 1627 dbSNP
rs1479401670 1630 dbSNP
rs1480500926 1633 dbSNP
rs1194656317 1638 dbSNP
rs1270061491 1640 dbSNP
rs1469460930 1656 dbSNP
rs1193745958 1659 dbSNP
rs896722075 1666 dbSNP
rs767167696 1668 dbSNP
rs934923602 1669 dbSNP
rs1373490947 1672 dbSNP
rs1461292682 1676 dbSNP
rs912776027 1683 dbSNP
rs1051223440 1689 dbSNP
rs1396624242 1691 dbSNP
rs932807839 1695 dbSNP
rs141090986 1698 dbSNP
rs1325304007 1702 dbSNP
rs1368801331 1703 dbSNP
rs1205208165 1714 dbSNP
rs921421552 1727 dbSNP
rs533620137 1735 dbSNP
rs1225676564 1744 dbSNP
rs1278027250 1746 dbSNP
rs1056172149 1749 dbSNP
rs758902325 1752 dbSNP
rs1312554390 1754 dbSNP
rs6002295 1757 dbSNP
rs1187969062 1759 dbSNP
rs1261968269 1761 dbSNP
rs541286064 1770 dbSNP
rs1427504168 1773 dbSNP
rs574007715 1774 dbSNP
rs1190799317 1780 dbSNP
rs1389866389 1782 dbSNP
rs1375736960 1786 dbSNP
rs946551286 1787 dbSNP
rs911083007 1798 dbSNP
rs1164107663 1803 dbSNP
rs908579930 1805 dbSNP
rs1455380543 1822 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HeLa
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... HITS-CLIP data was present in Chi_ControlB_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell Control B ...

- Chi SW; Zang JB; Mele A; Darnell RB, 2009, Nature.

Article - Chi SW; Zang JB; Mele A; Darnell RB
- Nature, 2009
MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets-Ago-miRNA and Ago-mRNA binding sites-that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.
LinkOut: [PMID: 19536157]
CLIP-seq Support 1 for dataset Chi_ControlB_2A8_130_50
Method / RBP HITS-CLIP / AGO
Cell line / Condition HeLa / HeLa cell Control B
Location of target site ENST00000405486.1 | 3UTR | UUAGGAGUGAGGAAAAGAUGAAU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 19536157 / Chi_HITSCLIP
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
GSE42095 Differentiated embryonic stem cells 0.338 5.7e-2 0.332 6.1e-2 23 Click to see details
GSE28544 Breast cancer 0.268 1.0e-1 0.410 2.3e-2 24 Click to see details
GSE17498 Multiple myeloma -0.204 1.0e-1 -0.023 4.4e-1 40 Click to see details
GSE27834 Pluripotent stem cells -0.267 1.6e-1 -0.421 5.2e-2 16 Click to see details
GSE19350 CNS germ cell tumors -0.276 1.9e-1 0.280 1.9e-1 12 Click to see details
GSE21849 B cell lymphoma -0.114 2.8e-1 0.178 1.8e-1 29 Click to see details
GSE32688 Pancreatic cancer 0.102 2.9e-1 -0.135 2.3e-1 32 Click to see details
GSE21687 Ependynoma primary tumors -0.07 2.9e-1 -0.080 2.6e-1 64 Click to see details
GSE34608 Pulmonary tuberculosis and sarcoidosis 0.079 3.7e-1 0.398 4.1e-2 20 Click to see details
GSE38974 Chronic obstructive pulmonary disease -0.057 3.9e-1 0.009 4.8e-1 25 Click to see details
GSE14794 Lymphoblastoid cells -0.024 4.1e-1 -0.024 4.1e-1 90 Click to see details
GSE38226 Liver fibrosis 0.044 4.2e-1 -0.069 3.8e-1 21 Click to see details
GSE26953 Aortic valvular endothelial cells 0.039 4.3e-1 -0.071 3.7e-1 24 Click to see details
GSE17306 Multiple myeloma 0.022 4.4e-1 0.478 2.6e-4 49 Click to see details
GSE28260 Renal cortex and medulla -0.036 4.5e-1 -0.033 4.6e-1 13 Click to see details
GSE28260 Renal cortex and medulla -0.036 4.5e-1 -0.033 4.6e-1 13 Click to see details
GSE28260 Renal cortex and medulla -0.036 4.5e-1 -0.033 4.6e-1 13 Click to see details
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
LUSC 0.375 0.01 0.227 0.09 38 Click to see details
STAD 0.386 0.02 0.394 0.02 29 Click to see details
PRAD 0.293 0.02 0.240 0.05 48 Click to see details
LIHC 0.282 0.02 0.266 0.03 49 Click to see details
KIRP 0.277 0.07 0.256 0.08 31 Click to see details
HNSC 0.223 0.08 0.184 0.12 42 Click to see details
BLCA 0.242 0.17 0.267 0.15 17 Click to see details
UCEC 0.22 0.18 0.153 0.27 19 Click to see details
ESCA 0.33 0.19 0.250 0.26 9 Click to see details
BRCA 0.078 0.25 0.048 0.34 79 Click to see details
PAAD 0.498 0.25 0.400 0.3 4 Click to see details
KICH 0.139 0.26 0.063 0.38 24 Click to see details
THCA -0.085 0.26 -0.015 0.46 59 Click to see details
KIRC -0.068 0.3 -0.137 0.14 65 Click to see details
LUAD 0.097 0.39 0.155 0.32 11 Click to see details
CESC 0.202 0.44 0.500 0.33 3 Click to see details
CHOL 0.032 0.47 -0.050 0.45 9 Click to see details
CHOL 0.032 0.47 -0.050 0.45 9 Click to see details
CHOL 0.032 0.47 -0.050 0.45 9 Click to see details
CHOL 0.032 0.47 -0.050 0.45 9 Click to see details
87 hsa-miR-452-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT150000 MIDN midnolin 2 10
MIRT330600 ZWINT ZW10 interacting kinetochore protein 2 2
MIRT358701 SUB1 SUB1 homolog, transcriptional regulator 2 4
MIRT362854 EIF4H eukaryotic translation initiation factor 4H 2 2
MIRT447215 ATXN7 ataxin 7 2 2
MIRT466655 TAF1D TATA-box binding protein associated factor, RNA polymerase I subunit D 2 6
MIRT483979 PANK1 pantothenate kinase 1 2 8
MIRT485118 SF3B3 splicing factor 3b subunit 3 2 2
MIRT488864 AUTS8 Autism, susceptibility to, 8 2 2
MIRT492293 SH2B3 SH2B adaptor protein 3 2 2
MIRT492976 NCK2 NCK adaptor protein 2 2 2
MIRT497410 LRRC40 leucine rich repeat containing 40 2 2
MIRT511143 MRPL17 mitochondrial ribosomal protein L17 2 6
MIRT512650 MAP3K2 mitogen-activated protein kinase kinase kinase 2 2 2
MIRT513017 NSFL1C NSFL1 cofactor 2 6
MIRT520445 TSPAN2 tetraspanin 2 2 6
MIRT527995 NDNF neuron derived neurotrophic factor 2 2
MIRT528667 PDE4DIP phosphodiesterase 4D interacting protein 2 2
MIRT533512 TRIM71 tripartite motif containing 71 2 2
MIRT537404 FBXO47 F-box protein 47 2 2
MIRT538161 DCP2 decapping mRNA 2 2 2
MIRT539124 ARHGEF17 Rho guanine nucleotide exchange factor 17 2 2
MIRT540666 MIS18A MIS18 kinetochore protein A 2 4
MIRT542948 GDF11 growth differentiation factor 11 2 2
MIRT547534 MAML3 mastermind like transcriptional coactivator 3 2 2
MIRT559033 C20orf24 chromosome 20 open reading frame 24 2 4
MIRT559554 ARF6 ADP ribosylation factor 6 2 2
MIRT570177 RCBTB1 RCC1 and BTB domain containing protein 1 2 2
MIRT573149 ITGA9 integrin subunit alpha 9 2 2
MIRT575849 Rab1 RAB1A, member RAS oncogene family 1 1
MIRT611034 RRP1B ribosomal RNA processing 1B 2 2
MIRT616281 HMGB1 high mobility group box 1 2 2
MIRT618372 PRKG2 protein kinase, cGMP-dependent, type II 2 2
MIRT619540 PIWIL2 piwi like RNA-mediated gene silencing 2 2 2
MIRT622303 SGIP1 SH3 domain GRB2 like endophilin interacting protein 1 2 2
MIRT622590 PRRG4 proline rich and Gla domain 4 2 2
MIRT624441 CAMK2N1 calcium/calmodulin dependent protein kinase II inhibitor 1 2 2
MIRT637089 KLRD1 killer cell lectin like receptor D1 2 2
MIRT639084 ADCYAP1 adenylate cyclase activating polypeptide 1 2 2
MIRT639334 NINJ1 ninjurin 1 2 2
MIRT639798 EIF3E eukaryotic translation initiation factor 3 subunit E 2 2
MIRT640851 RAB3B RAB3B, member RAS oncogene family 2 2
MIRT641628 KIAA1244 ARFGEF family member 3 1 1
MIRT642634 EPPIN epididymal peptidase inhibitor 2 2
MIRT643053 EPPIN-WFDC6 EPPIN-WFDC6 readthrough 2 2
MIRT643416 ERVMER34-1 endogenous retrovirus group MER34 member 1, envelope 2 2
MIRT645586 SAR1A secretion associated Ras related GTPase 1A 2 2
MIRT647393 FAM181B family with sequence similarity 181 member B 2 2
MIRT649411 CDC14B cell division cycle 14B 2 2
MIRT649477 CLDN16 claudin 16 2 2
MIRT651307 ZDHHC20 zinc finger DHHC-type containing 20 2 2
MIRT651387 ZBTB16 zinc finger and BTB domain containing 16 2 2
MIRT653411 SLC7A2 solute carrier family 7 member 2 2 2
MIRT654084 RSPH4A radial spoke head 4 homolog A 2 2
MIRT654613 PTPRM protein tyrosine phosphatase, receptor type M 2 2
MIRT655338 PCP4L1 Purkinje cell protein 4 like 1 2 2
MIRT656173 MRPL44 mitochondrial ribosomal protein L44 2 2
MIRT657272 HS3ST3B1 heparan sulfate-glucosamine 3-sulfotransferase 3B1 2 2
MIRT657881 GFPT1 glutamine--fructose-6-phosphate transaminase 1 2 2
MIRT659875 CAPRIN1 cell cycle associated protein 1 2 2
MIRT662381 ICA1L islet cell autoantigen 1 like 2 4
MIRT666308 SLC22A3 solute carrier family 22 member 3 2 2
MIRT667274 NAV1 neuron navigator 1 2 2
MIRT667614 LIMCH1 LIM and calponin homology domains 1 2 2
MIRT674242 NUP62 nucleoporin 62 2 4
MIRT690386 PARP15 poly(ADP-ribose) polymerase family member 15 2 2
MIRT693402 NUDT16 nudix hydrolase 16 2 2
MIRT702503 KDELR1 KDEL endoplasmic reticulum protein retention receptor 1 2 2
MIRT708632 STMN4 stathmin 4 2 2
MIRT708839 SCAND3 zinc finger BED-type containing 9 1 1
MIRT709016 HSBP1 heat shock factor binding protein 1 2 2
MIRT709235 RANGAP1 Ran GTPase activating protein 1 2 2
MIRT710885 PARL presenilin associated rhomboid like 2 2
MIRT712262 PPP1CB protein phosphatase 1 catalytic subunit beta 2 2
MIRT712573 ATP2B4 ATPase plasma membrane Ca2+ transporting 4 2 2
MIRT715046 PRPF38A pre-mRNA processing factor 38A 2 2
MIRT718905 GALR1 galanin receptor 1 2 2
MIRT719368 FEM1A fem-1 homolog A 2 2
MIRT719495 SEC24B SEC24 homolog B, COPII coat complex component 2 2
MIRT719601 PRKX protein kinase, X-linked 2 2
MIRT719891 RRP36 ribosomal RNA processing 36 2 2
MIRT720063 ZNF449 zinc finger protein 449 2 2
MIRT721679 CMTM4 CKLF like MARVEL transmembrane domain containing 4 2 2
MIRT721724 VTI1A vesicle transport through interaction with t-SNAREs 1A 2 2
MIRT723370 ZNF470 zinc finger protein 470 2 2
MIRT724941 TXNL1 thioredoxin like 1 2 2
MIRT725302 NLRC5 NLR family CARD domain containing 5 2 2
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-452 Formaldehyde NULL 712 Microarray Human lung epithelial cells (A549) 21147603 2011 down-regulated
miR-452 Phenethyl isothiocyanate(PEITC) NULL 16741 Microarray neonatal mice liver 20145010 2010 up-regulated
miR-452 Tert-butyl hydroperoxide (t-BHP) NULL 6410 Microarray mouse auditory cells 20510889 2010 down-regulated
miR-452 Reversine NULL 210332 Microarray C2C12 myoblast cells 24513286 2014 down-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-452 Cisplatin 5460033 NSC119875 approved resistant High Gastric Cancer cell line (BGC823)
hsa-mir-452 Cisplatin 5460033 NSC119875 approved resistant High Ovarian Cancer cell line (A2780CP20)
hsa-mir-452 Cisplatin 5460033 NSC119875 approved resistant cell line (CP20)
hsa-mir-452 Ceritinib 57379345 NSC776422 approved sensitive cell line (H3122)
hsa-mir-452 Cisplatin 5460033 NSC119875 approved resistant cell line (BGC-823)
hsa-miR-452-3p Fluorouracil 3385 NSC19893 approved resistant cell line (KM12C) (72 h)
hsa-miR-452-3p Sunitinib 5329102 NSC750690 approved resistant tissue (CardB)
hsa-miR-452-3p Paclitaxel 36314 NSC125973 approved sensitive cell line (SKOV3)
hsa-miR-452-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (HCT8)
hsa-miR-452-3p Oxaliplatin 6857599 NSC266046 approved resistant cell line (IGROV-1)
hsa-miR-452-3p Oxaliplatin 6857599 NSC266046 approved resistant cell line (IGROV-1)
hsa-miR-452-3p Cisplatin 5460033 NSC119875 approved resistant cell line (IGROV-1)
hsa-miR-452-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-452-3p Neoadjuvant chemotherapy sensitive tissue (breast cancer)
hsa-miR-452-3p Ceritinib 57379345 NSC776422 approved sensitive cell line (H3122)

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