pre-miRNA Information
pre-miRNA hsa-mir-216a   
Genomic Coordinates chr2: 55988950 - 55989059
Description Homo sapiens miR-216a stem-loop
Comment This human miRNA was predicted by computational methods using conservation with mouse and Fugu rubripes sequences .
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-216a-5p
Sequence 19| UAAUCUCAGCUGGCAACUGUGA |40
Evidence Experimental
Experiments Cloned
Editing Events in miRNAs
Modification Type Position on miR Chromosome DNA Strand Genomic Position (hg38) List of PMIDs Variant details
A-to-I 15 2 - 55989027 29233923 MiREDiBase
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs757094946 2 dbSNP
rs746980700 8 dbSNP
rs1249388997 12 dbSNP
rs1188616124 15 dbSNP
rs1490501989 19 dbSNP
rs1465789697 20 dbSNP
rs370221981 21 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Biomarker Information
Biomarker ID Name Type Discovered From Mode Level Source Testing Methods
BA0G4V miR-216a Safety Biomarker (SAF) Clinical/Experimental Data Expression Increase Tissue .
BA0G4V miR-216a Safety Biomarker (SAF) Clinical/Experimental Data Expression Increase Plasma MiRNA qPCR analyses
Gene Information
Gene Symbol GP2   
Synonyms ZAP75
Description glycoprotein 2
Transcript NM_001007240   
Other Transcripts NM_001007241 , NM_001007242 , NM_001502   
Expression
Putative miRNA Targets on GP2
3'UTR of GP2
(miRNA target sites are highlighted)
>GP2|NM_001007240|3'UTR
   1 GAGCTCCGCTGAGCATCTGGCCTTGAAGTTTGTGTTCTTCCCTCTGGCAATGGCTCCCTTCAGCACTTCTGCTTTCCACT
  81 CCAATTCACACAGGCTTGGTATTAACAGAATCAAGGCCAGGCTAGGTTAGGAAAAGGGAAGAGCTTTCACCTTCTTTAAA
 161 ACTCTCGGCTGGGCGCAGTGGCTCATGCCTGTAATCCCAGCATTTTGGGAGGCTGAGGCAGGTGGATCACCTGAGGTCAG
 241 CAGTTCAAAATCAGCCTGGCCAAAATGCTGAAACTCCGTCTCTACTAAAAATACAAAAATTAGCCAGGCATGGTGGCAGG
 321 CGCCTGTAATCCCAGCTACTCGGGAGGCCAAGGCAGGAGAATTGCTCGAACTCAGGGGGTGGAGGTTGCAGTGAGTTGAG
 401 ATTGTGCCATTGCACTCCAGCCTGGGCAACAGAGCAAGACTCTGTCTCAGGAAAAAAAAAAAAAAAAAAGAAAAGCAACA
 481 TAGTGGGGTTTCTGTCAATCTGTCCTCGGCTGCCCTTCTCATTTGTTGATGGGACCTTGAAAGCAAGCTTGCTAGGTGCC
 561 CTCTGTGGCTCCAGCCTTTACCGGAAGTGTGGTGCATGTTTTTAACTTCAGGGAAGCGGTATCCTGTCACTGGGGTATGG
 641 GATGAGCATGGAGAAGAGGCACCAGCCACGATTCCTTCCTAAGCATCTCCTGTTCTGACTGCTCATGAATTGAAGAAACT
 721 GACCCTTGTGTTCACTCTGCTTCCTCTGATTGTTTCTATCATGGTTTCCAAAAATTGCCATGGGAACATGTCAAAGGGCC
 801 ACTTTTGGAGACTCTGCTCCAGGAAGAACTAGTCCCCATAGCTCCCCTATCCCCCACCATACCACAGACATGCTGTGACT
 881 TAGAGAACTACACAAACATCCTTGGGACCTAGATGCTGGAGGAATGACTTAATTTGATGCAGAAACTCCATCACCCAAGG
 961 GAGTACCTCTCACTGTAAACAGTGCTGTGCTTGCTCTGAAGGATTAAGCAAGAAGTCCCAACAGAAGCAATGCACCAGTC
1041 CTGCTATGGGAATGAAACTGCAAAGCCTAGGAGATGGGTGAAGTCCCTTTCTGGAGACCTTTAATGAGTACTTCAAAGCA
1121 CCCGACACAGATGCAGCAAATAGGGCATCACACATACACAGGCATTAATACTCACGGGCATATAGATGCTGACATGTGTA
1201 CACTGACTTACGCCCTTCCCACAGCTACAGATAAGGCCTCGCAAAGTTGGCCTCAGAGACACATCAGGAACCAAGGTGGA
1281 CCAGCAGGTGCCGAGCCTGTGTATCTGCTTGGAGGAGACGTTCCAATGTGCTGCCTTGTTCAGAGATGGTGTAGTTGCAA
1361 GAAACAGAAACCCACCACAATTTCTCAGGCAAAAAGGGAGTTAATTATAAGGACATAAGAGCACAAAGTTCCAGTGCAAG
1441 AGATACATCCAGGCTGCACAAGCTCCGGGAGTGGGGCCTGGCAAGCCAAAAGAAACCAAAGTTTGTCTTGCCTTCTGTTC
1521 CTCTTTCTGAAGCCACATAGCCTTTTATGACTGTGTATTTTTGCATCGCTTTTGTTTTCTTTTTATGTCTCTGAAGCCAG
1601 CTTTTCCTGTTCACTCATCCCTTGATTAAATATGGACATTCTAGCTTCA
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' agugUCAACG---GUCGACUCUAAu 5'
              :|||||    ||:||||||| 
Target 5' tggaGGTTGCAGTGAGTTGAGATTg 3'
380 - 404 162.00 -18.60
2
miRNA  3' agUGUCAAC--GGUCGACUCUAau 5'
            :||| ||  :|| |||||:|  
Target 5' agGCAGGTGGATCACCTGAGGTca 3'
216 - 239 130.00 -13.60
3
miRNA  3' agUGUCA----ACGGUC--GACU--CUAAu 5'
            |||||    |||: |  ||||  |||| 
Target 5' aaACAGTGCTGTGCTTGCTCTGAAGGATTa 3'
977 - 1006 124.00 -11.40
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN31509801 6 COSMIC
COSN26442068 8 COSMIC
COSN30192443 22 COSMIC
COSN19690845 24 COSMIC
COSN30176414 25 COSMIC
COSN30475072 40 COSMIC
COSN30452734 41 COSMIC
COSN30516030 42 COSMIC
COSN30480408 56 COSMIC
COSN30132935 93 COSMIC
COSN31536369 101 COSMIC
COSN31497948 119 COSMIC
COSN31557995 174 COSMIC
COSN28833290 238 COSMIC
COSN20093091 470 COSMIC
COSN14987529 610 COSMIC
COSN17243460 616 COSMIC
COSN21241240 726 COSMIC
COSN5405284 820 COSMIC
COSN6081339 834 COSMIC
COSN25678038 996 COSMIC
COSN20152256 1211 COSMIC
COSN19536824 1240 COSMIC
COSN7300656 1381 COSMIC
COSN25576152 1414 COSMIC
rs12444232 1078 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs746606123 2 dbSNP
rs779722850 3 dbSNP
rs575694369 4 dbSNP
rs746403673 5 dbSNP
rs779528205 7 dbSNP
rs373559957 8 dbSNP
rs1288623941 13 dbSNP
rs1429325950 15 dbSNP
rs1235350941 16 dbSNP
rs1486669925 19 dbSNP
rs754152225 22 dbSNP
rs778136339 24 dbSNP
rs1469298158 27 dbSNP
rs756308591 34 dbSNP
rs923628535 37 dbSNP
rs981874260 39 dbSNP
rs752870863 40 dbSNP
rs1429310263 41 dbSNP
rs753873896 42 dbSNP
rs767616963 44 dbSNP
rs1190854081 45 dbSNP
rs1185707302 47 dbSNP
rs1449322980 49 dbSNP
rs1167280631 53 dbSNP
rs1427937657 56 dbSNP
rs1338035701 57 dbSNP
rs111297739 61 dbSNP
rs1437581820 62 dbSNP
rs1320937924 66 dbSNP
rs1364203905 67 dbSNP
rs1225972298 79 dbSNP
rs1276537940 84 dbSNP
rs1345679646 91 dbSNP
rs1218105916 94 dbSNP
rs917382594 98 dbSNP
rs1208971444 100 dbSNP
rs11642182 106 dbSNP
rs568081722 117 dbSNP
rs11647569 120 dbSNP
rs1248934976 123 dbSNP
rs773059887 124 dbSNP
rs1478673243 126 dbSNP
rs951234888 141 dbSNP
rs530961892 166 dbSNP
rs1458960489 167 dbSNP
rs1160159826 168 dbSNP
rs1388263925 171 dbSNP
rs995075238 172 dbSNP
rs993548813 174 dbSNP
rs138616491 175 dbSNP
rs1453919592 179 dbSNP
rs565182731 209 dbSNP
rs1156884639 214 dbSNP
rs1015373346 217 dbSNP
rs11553580 220 dbSNP
rs1418263789 222 dbSNP
rs1269285162 242 dbSNP
rs1201324374 246 dbSNP
rs1326690198 248 dbSNP
rs1203734827 260 dbSNP
rs1292500091 261 dbSNP
rs1452657695 268 dbSNP
rs11861170 277 dbSNP
rs890543969 278 dbSNP
rs1473609241 280 dbSNP
rs576966754 283 dbSNP
rs1205790521 286 dbSNP
rs1411477820 290 dbSNP
rs1028796737 292 dbSNP
rs1455861689 293 dbSNP
rs996430231 294 dbSNP
rs893666368 313 dbSNP
rs1053688513 314 dbSNP
rs935267476 317 dbSNP
rs902176048 321 dbSNP
rs1046487846 322 dbSNP
rs1321494158 324 dbSNP
rs775825401 339 dbSNP
rs770204368 341 dbSNP
rs1285509902 342 dbSNP
rs1403501691 345 dbSNP
rs1348190868 355 dbSNP
rs949133453 357 dbSNP
rs914081274 367 dbSNP
rs746355365 368 dbSNP
rs1357475804 372 dbSNP
rs189310662 374 dbSNP
rs568863711 376 dbSNP
rs115321800 379 dbSNP
rs12596974 385 dbSNP
rs969317174 387 dbSNP
rs962309277 391 dbSNP
rs1369329746 401 dbSNP
rs561693248 405 dbSNP
rs1429924229 406 dbSNP
rs1011482410 414 dbSNP
rs1472341276 419 dbSNP
rs1178308305 421 dbSNP
rs1161287362 424 dbSNP
rs917801380 427 dbSNP
rs1306834218 435 dbSNP
rs1368173450 439 dbSNP
rs1240216223 450 dbSNP
rs1397362307 450 dbSNP
rs1381973004 451 dbSNP
rs1339544619 452 dbSNP
rs1428823992 452 dbSNP
rs1194233482 460 dbSNP
rs1244485944 464 dbSNP
rs992047992 465 dbSNP
rs1229792741 466 dbSNP
rs1448982999 466 dbSNP
rs1202289237 467 dbSNP
rs1479685758 467 dbSNP
rs1257117542 468 dbSNP
rs10653884 470 dbSNP
rs1181459398 470 dbSNP
rs1300272247 470 dbSNP
rs1371310694 470 dbSNP
rs1391786669 470 dbSNP
rs1442115999 470 dbSNP
rs1449958299 470 dbSNP
rs1467131720 470 dbSNP
rs55892430 470 dbSNP
rs879063975 470 dbSNP
rs951183077 470 dbSNP
rs987890676 474 dbSNP
rs1259691671 475 dbSNP
rs1306336026 475 dbSNP
rs954792722 477 dbSNP
rs1235496131 479 dbSNP
rs1031325889 484 dbSNP
rs1256675103 485 dbSNP
rs1029473712 486 dbSNP
rs996289688 489 dbSNP
rs893635036 493 dbSNP
rs963828756 496 dbSNP
rs1222061159 500 dbSNP
rs1032214359 501 dbSNP
rs540217898 507 dbSNP
rs902437154 508 dbSNP
rs143450461 510 dbSNP
rs949093454 517 dbSNP
rs564366463 524 dbSNP
rs372375648 529 dbSNP
rs1467860204 531 dbSNP
rs1051983231 532 dbSNP
rs778827812 535 dbSNP
rs1327836471 537 dbSNP
rs1388974133 540 dbSNP
rs1292749069 551 dbSNP
rs1436272118 556 dbSNP
rs754859938 560 dbSNP
rs545679971 561 dbSNP
rs1360419333 563 dbSNP
rs997771798 568 dbSNP
rs1433793872 571 dbSNP
rs1406729526 580 dbSNP
rs894836133 582 dbSNP
rs1221809844 583 dbSNP
rs1270252283 585 dbSNP
rs1330151283 586 dbSNP
rs753717703 588 dbSNP
rs1052640038 594 dbSNP
rs936394143 600 dbSNP
rs575354538 617 dbSNP
rs925050428 618 dbSNP
rs557188215 621 dbSNP
rs1168317629 626 dbSNP
rs1476473549 634 dbSNP
rs1044841878 637 dbSNP
rs1412235843 638 dbSNP
rs1456389534 640 dbSNP
rs1158747634 646 dbSNP
rs1192541005 651 dbSNP
rs542283815 659 dbSNP
rs1002569597 661 dbSNP
rs917596116 664 dbSNP
rs1365548091 669 dbSNP
rs1403172629 676 dbSNP
rs574572926 683 dbSNP
rs1351272363 692 dbSNP
rs1461281287 698 dbSNP
rs920760659 704 dbSNP
rs973544465 708 dbSNP
rs369968164 710 dbSNP
rs951337586 729 dbSNP
rs918410748 732 dbSNP
rs973905845 746 dbSNP
rs908138257 750 dbSNP
rs963476218 751 dbSNP
rs987763262 752 dbSNP
rs1016737578 753 dbSNP
rs1251911730 754 dbSNP
rs1472035870 759 dbSNP
rs534691325 775 dbSNP
rs953463495 777 dbSNP
rs1425888383 784 dbSNP
rs954859646 786 dbSNP
rs1365445844 792 dbSNP
rs1029027272 802 dbSNP
rs1030377119 810 dbSNP
rs112444798 819 dbSNP
rs559159095 826 dbSNP
rs1309892557 827 dbSNP
rs892753647 829 dbSNP
rs1249328598 838 dbSNP
rs1441630867 839 dbSNP
rs1296637154 842 dbSNP
rs958109873 843 dbSNP
rs537258304 846 dbSNP
rs999375501 849 dbSNP
rs1357106822 857 dbSNP
rs559872710 862 dbSNP
rs1339805791 863 dbSNP
rs1329225197 869 dbSNP
rs1482428211 891 dbSNP
rs138011260 901 dbSNP
rs1013534632 904 dbSNP
rs1427312065 905 dbSNP
rs896136207 916 dbSNP
rs1182740961 926 dbSNP
rs1385042181 927 dbSNP
rs1056090469 933 dbSNP
rs929880874 934 dbSNP
rs1168239180 936 dbSNP
rs1409448583 939 dbSNP
rs1168497588 940 dbSNP
rs540199695 941 dbSNP
rs767119380 943 dbSNP
rs918526972 954 dbSNP
rs1054759782 972 dbSNP
rs941158081 975 dbSNP
rs911060386 977 dbSNP
rs548470755 992 dbSNP
rs1181857991 1000 dbSNP
rs986619175 1003 dbSNP
rs529031268 1006 dbSNP
rs1280137665 1017 dbSNP
rs953523411 1017 dbSNP
rs1209018707 1018 dbSNP
rs1190980524 1022 dbSNP
rs1240944129 1022 dbSNP
rs568151872 1022 dbSNP
rs898258845 1024 dbSNP
rs1030326150 1027 dbSNP
rs976106595 1041 dbSNP
rs1037811391 1046 dbSNP
rs1427390284 1057 dbSNP
rs940843334 1059 dbSNP
rs1031231549 1061 dbSNP
rs12444232 1078 dbSNP
rs1458609010 1083 dbSNP
rs903978374 1085 dbSNP
rs1325720959 1087 dbSNP
rs1428595478 1088 dbSNP
rs1023842980 1097 dbSNP
rs1367671788 1099 dbSNP
rs867361737 1108 dbSNP
rs1052438356 1120 dbSNP
rs10852240 1122 dbSNP
rs1243150233 1123 dbSNP
rs544327401 1124 dbSNP
rs1285399236 1130 dbSNP
rs11864405 1131 dbSNP
rs1249015814 1132 dbSNP
rs1478377854 1136 dbSNP
rs1198869020 1138 dbSNP
rs1427441957 1140 dbSNP
rs184978734 1150 dbSNP
rs1473700082 1157 dbSNP
rs374812278 1168 dbSNP
rs1384005810 1169 dbSNP
rs116859174 1175 dbSNP
rs978197328 1176 dbSNP
rs966933824 1183 dbSNP
rs1350467715 1185 dbSNP
rs941327112 1196 dbSNP
rs1024844206 1202 dbSNP
rs1013918964 1203 dbSNP
rs959321763 1211 dbSNP
rs538534354 1212 dbSNP
rs1350381557 1218 dbSNP
rs932042361 1225 dbSNP
rs563528576 1232 dbSNP
rs372162086 1233 dbSNP
rs12922283 1237 dbSNP
rs1266907379 1240 dbSNP
rs777712024 1241 dbSNP
rs1003999119 1242 dbSNP
rs923939062 1243 dbSNP
rs1409318165 1244 dbSNP
rs1160855123 1246 dbSNP
rs1414365277 1248 dbSNP
rs980088707 1262 dbSNP
rs1300700377 1264 dbSNP
rs1469076159 1265 dbSNP
rs772241127 1268 dbSNP
rs574635715 1271 dbSNP
rs886602175 1276 dbSNP
rs1237312966 1291 dbSNP
rs192045099 1293 dbSNP
rs1049732283 1297 dbSNP
rs1245922653 1305 dbSNP
rs748285606 1319 dbSNP
rs541030350 1320 dbSNP
rs1196527150 1323 dbSNP
rs1250068276 1324 dbSNP
rs1039031820 1327 dbSNP
rs1189282281 1328 dbSNP
rs929541997 1334 dbSNP
rs80260134 1341 dbSNP
rs1161571226 1346 dbSNP
rs993881042 1347 dbSNP
rs925304480 1358 dbSNP
rs1429818284 1360 dbSNP
rs1166866836 1363 dbSNP
rs1393794704 1364 dbSNP
rs978165897 1365 dbSNP
rs1336508362 1376 dbSNP
rs1383965813 1378 dbSNP
rs966859383 1379 dbSNP
rs1348494010 1381 dbSNP
rs896824379 1384 dbSNP
rs1313553368 1392 dbSNP
rs1345011671 1394 dbSNP
rs1228172097 1398 dbSNP
rs1250837123 1401 dbSNP
rs1337651558 1404 dbSNP
rs1287413573 1405 dbSNP
rs559003722 1407 dbSNP
rs116595845 1409 dbSNP
rs992013808 1414 dbSNP
rs1249797866 1415 dbSNP
rs1301570646 1418 dbSNP
rs1005870081 1421 dbSNP
rs959523342 1422 dbSNP
rs386789648 1423 dbSNP
rs576645463 1424 dbSNP
rs1399400353 1463 dbSNP
rs1033538796 1466 dbSNP
rs1177580293 1467 dbSNP
rs1469600669 1473 dbSNP
rs1160581814 1481 dbSNP
rs146386325 1481 dbSNP
rs367855523 1481 dbSNP
rs919538194 1482 dbSNP
rs922439731 1484 dbSNP
rs1189145093 1485 dbSNP
rs1487965573 1488 dbSNP
rs1040440204 1500 dbSNP
rs78425396 1501 dbSNP
rs1463443798 1503 dbSNP
rs1263985002 1507 dbSNP
rs1267501162 1509 dbSNP
rs1323163347 1511 dbSNP
rs536835232 1514 dbSNP
rs1204027451 1516 dbSNP
rs1015251444 1528 dbSNP
rs1325484121 1533 dbSNP
rs923929249 1537 dbSNP
rs1218828613 1540 dbSNP
rs558285213 1542 dbSNP
rs1004328266 1543 dbSNP
rs1434396511 1547 dbSNP
rs868559500 1549 dbSNP
rs1428094757 1550 dbSNP
rs189903712 1551 dbSNP
rs916814071 1552 dbSNP
rs4780282 1559 dbSNP
rs1288764339 1562 dbSNP
rs997711224 1564 dbSNP
rs900697409 1567 dbSNP
rs570397540 1568 dbSNP
rs1284012522 1579 dbSNP
rs545261275 1585 dbSNP
rs993871150 1595 dbSNP
rs1290501234 1601 dbSNP
rs1039293109 1602 dbSNP
rs1338002495 1610 dbSNP
rs1317262261 1614 dbSNP
rs936942810 1622 dbSNP
rs1238154110 1624 dbSNP
rs551868554 1630 dbSNP
rs1404301151 1631 dbSNP
rs1175834411 1641 dbSNP
rs1042395062 1647 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HEK293S
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 GSM1084041. RNA binding protein: AGO2. Condition:CLIP_arsenite_rep1 HITS-CLIP data was present in GSM1084046. RNA binding protein: AGO2. Condition:CLIP_noarsenite_rep4 ...

- Karginov FV; Hannon GJ, 2013, Genes & development.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' agugucaacggucGACUCUAAu 5'
                       :||||||| 
Target 5' -------------UUGAGAUUg 3'
1 - 9
Article - Karginov FV; Hannon GJ
- Genes & development, 2013
When adapting to environmental stress, cells attenuate and reprogram their translational output. In part, these altered translation profiles are established through changes in the interactions between RNA-binding proteins and mRNAs. The Argonaute 2 (Ago2)/microRNA (miRNA) machinery has been shown to participate in stress-induced translational up-regulation of a particular mRNA, CAT-1; however, a detailed, transcriptome-wide understanding of the involvement of Ago2 in the process has been lacking. Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by cross-linking immunoprecipitation (CLIP) followed by high-throughput sequencing (CLIP-seq). Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3' untranslated region (UTR) and coding sequence (CDS) sites exhibiting stronger interaction. Interestingly, target sites that were destined for release from Ago2 upon stress were depleted in miRNA complementarity signatures, suggesting an alternative mode of interaction. To compare the changes in Ago2-binding patterns across transcripts with changes in their translational states, we measured mRNA profiles on ribosome/polysome gradients by RNA sequencing (RNA-seq). Increased Ago2 occupancy correlated with stronger repression of translation for those mRNAs, as evidenced by a shift toward lighter gradient fractions upon stress, while release of Ago2 was associated with the limited number of transcripts that remained translated. Taken together, these data point to a role for Ago2 and the mammalian miRNAs in mediating the translational component of the stress response.
LinkOut: [PMID: 23824327]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions Prostate Tissue
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 SRX1760631. RNA binding protein: AGO2. Condition:AGO-CLIP-22RV1_B ...

- Hamilton MP; Rajapakshe KI; Bader DA; Cerne et al., 2016, Neoplasia (New York, N.Y.).

Article - Hamilton MP; Rajapakshe KI; Bader DA; Cerne et al.
- Neoplasia (New York, N.Y.), 2016
MicroRNA (miRNA) deregulation in prostate cancer (PCa) contributes to PCa initiation and metastatic progression. To comprehensively define the cancer-associated changes in miRNA targeting and function in commonly studied models of PCa, we performed photoactivatable ribonucleoside-enhanced cross-linking immunoprecipitation of the Argonaute protein in a panel of PCa cell lines modeling different stages of PCa progression. Using this comprehensive catalogue of miRNA targets, we analyzed miRNA targeting on known drivers of PCa and examined tissue-specific and stage-specific pathway targeting by miRNAs. We found that androgen receptor is the most frequently targeted PCa oncogene and that miR-148a targets the largest number of known PCa drivers. Globally, tissue-specific and stage-specific changes in miRNA targeting are driven by homeostatic response to active oncogenic pathways. Our findings indicate that, even in advanced PCa, the miRNA pool adapts to regulate continuing alterations in the cancer genome to balance oncogenic molecular changes. These findings are important because they are the first to globally characterize miRNA changes in PCa and demonstrate how the miRNA target spectrum responds to staged tumorigenesis.
LinkOut: [PMID: 27292025]
CLIP-seq Support 1 for dataset GSM1084041
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_arsenite_rep1
Location of target site ENST00000302555.5 | 3UTR | AGGUUGCAGUGAGUUGAGAUUGUGCCAUUGCACUCC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1084046
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noarsenite_rep4
Location of target site ENST00000302555.5 | 3UTR | UUGAGAUUGUGCCAUUGCACUCCAGCCUGGGCAACA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
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
GSE32688 Pancreatic cancer 0.857 1.9e-10 0.701 3.9e-6 32 Click to see details
GSE42095 Differentiated embryonic stem cells 0.812 1.3e-6 0.723 4.9e-5 23 Click to see details
GSE19350 CNS germ cell tumors 0.857 1.8e-4 0.705 5.2e-3 12 Click to see details
GSE26953 Aortic valvular endothelial cells 0.39 3.0e-2 0.333 5.6e-2 24 Click to see details
GSE21849 B cell lymphoma -0.241 1.0e-1 0.364 2.6e-2 29 Click to see details
GSE38226 Liver fibrosis 0.222 1.7e-1 -0.022 4.6e-1 21 Click to see details
GSE17306 Multiple myeloma 0.141 1.7e-1 0.492 1.7e-4 49 Click to see details
GSE17498 Multiple myeloma -0.156 1.7e-1 -0.118 2.3e-1 40 Click to see details
GSE28260 Renal cortex and medulla 0.267 1.9e-1 0.133 3.3e-1 13 Click to see details
GSE35602 Colorectal cancer stromal tissue -0.168 2.1e-1 0.388 2.8e-2 25 Click to see details
GSE21687 Ependynoma primary tumors -0.069 2.9e-1 -0.052 3.4e-1 64 Click to see details
GSE34608 Pulmonary tuberculosis and sarcoidosis 0.085 3.6e-1 -0.035 4.4e-1 20 Click to see details
GSE28544 Breast cancer 0.046 4.2e-1 0.006 4.9e-1 24 Click to see details
GSE38974 Chronic obstructive pulmonary disease 0.007 4.9e-1 -0.024 4.5e-1 25 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
PAAD 0.977 0.01 1.000 0.5 4 Click to see details
HNSC -0.332 0.06 0.058 0.4 23 Click to see details
LIHC 0.184 0.11 0.228 0.07 45 Click to see details
KIRC 0.223 0.12 -0.077 0.35 29 Click to see details
UCEC -0.315 0.19 0.085 0.41 10 Click to see details
KICH -0.283 0.2 -0.609 0.02 11 Click to see details
CHOL 0.321 0.22 0.190 0.33 8 Click to see details
BRCA 0.16 0.22 0.153 0.23 25 Click to see details
ESCA 0.49 0.26 0.400 0.3 4 Click to see details
KIRP -0.123 0.31 -0.055 0.41 18 Click to see details
LUAD -0.185 0.32 -0.083 0.42 9 Click to see details
THCA 0.064 0.33 0.174 0.12 47 Click to see details
LUSC -0.077 0.37 -0.143 0.27 20 Click to see details
STAD 0.046 0.42 0.033 0.45 20 Click to see details
PRAD -0.032 0.43 0.088 0.32 31 Click to see details
BLCA -0.005 0.49 0.136 0.35 10 Click to see details
BLCA -0.005 0.49 0.136 0.35 10 Click to see details
BLCA -0.005 0.49 0.136 0.35 10 Click to see details
148 hsa-miR-216a-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT000534 PTEN phosphatase and tensin homolog 4 3
MIRT005018 SIRT1 sirtuin 1 3 1
MIRT005964 CDC42 cell division cycle 42 2 1
MIRT005969 CD44 CD44 molecule (Indian blood group) 2 1
MIRT007154 SMAD7 SMAD family member 7 1 1
MIRT054887 BECN1 beclin 1 5 3
MIRT067588 METAP2 methionyl aminopeptidase 2 2 6
MIRT099144 MYLIP myosin regulatory light chain interacting protein 2 12
MIRT162313 TGFBR2 transforming growth factor beta receptor 2 2 2
MIRT230668 DFFA DNA fragmentation factor subunit alpha 2 2
MIRT256274 PHAX phosphorylated adaptor for RNA export 2 2
MIRT386817 RAD51L3-RFFL RAD51L3-RFFL readthrough 2 2
MIRT386825 RFFL ring finger and FYVE like domain containing E3 ubiquitin protein ligase 2 2
MIRT438816 HNF4A hepatocyte nuclear factor 4 alpha 1 1
MIRT464699 UBE2V1 ubiquitin conjugating enzyme E2 V1 2 2
MIRT465962 TMEM189-UBE2V1 TMEM189-UBE2V1 readthrough 2 2
MIRT466046 TMEM189 transmembrane protein 189 2 2
MIRT466482 TECPR2 tectonin beta-propeller repeat containing 2 2 7
MIRT472209 NGFRAP1 brain expressed X-linked 3 2 4
MIRT472562 NACC1 nucleus accumbens associated 1 2 4
MIRT478921 CPS1 carbamoyl-phosphate synthase 1 2 2
MIRT480121 CALR calreticulin 2 2
MIRT497754 OXGR1 oxoglutarate receptor 1 2 2
MIRT497967 TWISTNB TWIST neighbor 2 2
MIRT502882 CDK4 cyclin dependent kinase 4 2 8
MIRT510191 MON1B MON1 homolog B, secretory trafficking associated 2 4
MIRT512407 CD84 CD84 molecule 2 2
MIRT513739 PSD3 pleckstrin and Sec7 domain containing 3 2 4
MIRT526257 DROSHA drosha ribonuclease III 2 2
MIRT528968 FAM19A3 family with sequence similarity 19 member A3, C-C motif chemokine like 2 2
MIRT529599 C6orf132 chromosome 6 open reading frame 132 2 2
MIRT529776 ZNF486 zinc finger protein 486 2 2
MIRT530110 PSAPL1 prosaposin like 1 (gene/pseudogene) 2 2
MIRT530504 FADS6 fatty acid desaturase 6 2 2
MIRT531437 PAK1 p21 (RAC1) activated kinase 1 2 2
MIRT534445 SDR16C5 short chain dehydrogenase/reductase family 16C member 5 2 2
MIRT537286 GABPB1 GA binding protein transcription factor beta subunit 1 2 2
MIRT538451 CNNM2 cyclin and CBS domain divalent metal cation transport mediator 2 2 2
MIRT543085 ACTB actin beta 2 2
MIRT550982 ZNF254 zinc finger protein 254 2 2
MIRT556259 MAPRE2 microtubule associated protein RP/EB family member 2 2 2
MIRT556639 LAMC1 laminin subunit gamma 1 2 2
MIRT559127 C11orf57 chromosome 11 open reading frame 57 2 2
MIRT561405 TUBB2A tubulin beta 2A class IIa 2 2
MIRT569677 SEC23B Sec23 homolog B, coat complex II component 2 4
MIRT574660 KLHL15 kelch like family member 15 2 2
MIRT575030 Tecpr2 tectonin beta-propeller repeat containing 2 2 5
MIRT617683 JRKL JRK like 2 2
MIRT618540 SEMA5A semaphorin 5A 2 2
MIRT620805 C1orf27 chromosome 1 open reading frame 27 2 2
MIRT621569 ZBTB7A zinc finger and BTB domain containing 7A 2 2
MIRT622133 SP4 Sp4 transcription factor 2 2
MIRT624913 CTCFL CCCTC-binding factor like 2 2
MIRT625010 PAK4 p21 (RAC1) activated kinase 4 2 2
MIRT626644 ZNF551 zinc finger protein 551 2 2
MIRT626646 ATP5A1 ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle 2 2
MIRT626672 NOM1 nucleolar protein with MIF4G domain 1 2 2
MIRT627945 NNT nicotinamide nucleotide transhydrogenase 2 2
MIRT627963 NLK nemo like kinase 2 2
MIRT628767 SRSF7 serine and arginine rich splicing factor 7 2 2
MIRT629261 KDM2B lysine demethylase 2B 2 2
MIRT629422 ADM2 adrenomedullin 2 2 2
MIRT630238 SORD sorbitol dehydrogenase 2 2
MIRT631272 CENPM centromere protein M 2 4
MIRT631793 CLK4 CDC like kinase 4 2 2
MIRT632058 ATF7IP activating transcription factor 7 interacting protein 2 2
MIRT632485 RPS15A ribosomal protein S15a 2 2
MIRT632611 PDP2 pyruvate dehyrogenase phosphatase catalytic subunit 2 2 2
MIRT632708 MTA3 metastasis associated 1 family member 3 2 2
MIRT632815 INO80 INO80 complex subunit 2 2
MIRT635956 PLA2G12A phospholipase A2 group XIIA 2 2
MIRT636152 UBXN2A UBX domain protein 2A 2 2
MIRT636899 C5orf45 MRN complex interacting protein 2 4
MIRT636930 AGAP9 ArfGAP with GTPase domain, ankyrin repeat and PH domain 9 2 2
MIRT637457 ZNF324B zinc finger protein 324B 2 2
MIRT637900 SLC19A3 solute carrier family 19 member 3 2 2
MIRT639826 ZNF638 zinc finger protein 638 2 2
MIRT640445 ERVMER34-1 endogenous retrovirus group MER34 member 1, envelope 2 2
MIRT640681 ARSK arylsulfatase family member K 2 2
MIRT641611 CAPN7 calpain 7 2 2
MIRT641676 AKR7A2 aldo-keto reductase family 7 member A2 2 2
MIRT646786 IL23R interleukin 23 receptor 2 2
MIRT648352 A2ML1 alpha-2-macroglobulin like 1 2 2
MIRT649144 SPATA5 spermatogenesis associated 5 2 2
MIRT649254 TRIM65 tripartite motif containing 65 2 2
MIRT652491 TMEM178B transmembrane protein 178B 2 2
MIRT653308 SMU1 DNA replication regulator and spliceosomal factor 2 2
MIRT653945 SEPSECS Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase 2 2
MIRT654212 RNF19B ring finger protein 19B 2 2
MIRT654839 PPM1L protein phosphatase, Mg2+/Mn2+ dependent 1L 2 2
MIRT655159 PHF21A PHD finger protein 21A 2 2
MIRT655316 PDCD11 programmed cell death 11 2 2
MIRT655375 PAX3 paired box 3 2 2
MIRT657301 HOXB5 homeobox B5 2 2
MIRT657593 GRIN2A glutamate ionotropic receptor NMDA type subunit 2A 2 2
MIRT658460 FAM117B family with sequence similarity 117 member B 2 2
MIRT658716 ELOVL4 ELOVL fatty acid elongase 4 2 2
MIRT661640 UGT2B28 UDP glucuronosyltransferase family 2 member B28 2 2
MIRT661712 MTO1 mitochondrial tRNA translation optimization 1 2 4
MIRT661833 ZNF793 zinc finger protein 793 2 2
MIRT663805 BET1L Bet1 golgi vesicular membrane trafficking protein like 2 2
MIRT663884 CXorf56 chromosome X open reading frame 56 2 2
MIRT664672 L2HGDH L-2-hydroxyglutarate dehydrogenase 2 2
MIRT665814 TMEM168 transmembrane protein 168 2 2
MIRT668159 GDE1 glycerophosphodiester phosphodiesterase 1 2 2
MIRT668430 FAM20B FAM20B, glycosaminoglycan xylosylkinase 2 2
MIRT672306 GP2 glycoprotein 2 2 2
MIRT673101 SYNPO2L synaptopodin 2 like 2 2
MIRT673437 APAF1 apoptotic peptidase activating factor 1 2 2
MIRT673584 KDELC2 KDEL motif containing 2 2 2
MIRT673718 SLU7 SLU7 homolog, splicing factor 2 2
MIRT673777 MRPL17 mitochondrial ribosomal protein L17 2 2
MIRT674316 IMP4 IMP4, U3 small nucleolar ribonucleoprotein 2 2
MIRT674820 FAM229B family with sequence similarity 229 member B 2 2
MIRT675179 BPTF bromodomain PHD finger transcription factor 2 2
MIRT675586 WWC1 WW and C2 domain containing 1 2 2
MIRT675812 MED28 mediator complex subunit 28 2 2
MIRT677632 ALG1 ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase 2 2
MIRT683914 PSMB9 proteasome subunit beta 9 2 2
MIRT687135 QPCTL glutaminyl-peptide cyclotransferase like 2 2
MIRT691973 PLCXD1 phosphatidylinositol specific phospholipase C X domain containing 1 2 2
MIRT693078 AS3MT arsenite methyltransferase 2 2
MIRT694084 RNASEH2B ribonuclease H2 subunit B 2 2
MIRT696292 IER3IP1 immediate early response 3 interacting protein 1 2 2
MIRT696541 C3 complement C3 2 2
MIRT701955 MITF melanogenesis associated transcription factor 2 2
MIRT703276 GNG12 G protein subunit gamma 12 2 2
MIRT706852 DNAJB13 DnaJ heat shock protein family (Hsp40) member B13 2 2
MIRT706993 XPO5 exportin 5 2 2
MIRT710716 KRTAP6-1 keratin associated protein 6-1 2 2
MIRT711305 ACOX1 acyl-CoA oxidase 1 2 2
MIRT711514 ESCO1 establishment of sister chromatid cohesion N-acetyltransferase 1 2 2
MIRT711648 LIPG lipase G, endothelial type 2 2
MIRT711772 CCDC59 coiled-coil domain containing 59 2 2
MIRT714280 COQ7 coenzyme Q7, hydroxylase 2 2
MIRT715048 PRPF38A pre-mRNA processing factor 38A 2 2
MIRT716934 INCENP inner centromere protein 2 2
MIRT717220 OTUD3 OTU deubiquitinase 3 2 2
MIRT717865 BICD2 BICD cargo adaptor 2 2 2
MIRT718836 SNX20 sorting nexin 20 2 2
MIRT720243 GPBP1 GC-rich promoter binding protein 1 2 2
MIRT721969 MCM8 minichromosome maintenance 8 homologous recombination repair factor 2 2
MIRT724000 LMTK2 lemur tyrosine kinase 2 2 2
MIRT725193 SDAD1 SDA1 domain containing 1 2 2
MIRT731669 CBL Cbl proto-oncogene 3 1
MIRT732776 AQP4 aquaporin 4 3 0
MIRT733158 ITGA5 integrin subunit alpha 5 1 0
MIRT735623 TLR4 toll like receptor 4 4 0
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-216a Curcumin NULL 969516 Quantitative real-time PCR Y79 RB cells. 22510010 2012 down-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-216a Cisplatin 5460033 NSC119875 approved resistant cell line (CIS)
hsa-miR-216a-5p Cisplatin 5460033 NSC119875 approved resistant High Ovarian Cancer cell line (SKOV3, 2008, OVCAR10, OVCAR3, HeLa, MCF7, MDA-MB-468)
hsa-miR-216a-5p Doxorubicin 31703 NSC123127 approved resistant High Breast Cancer cell line (MCF-7)
hsa-miR-216a-5p Verapamil 2520 NSC272366 approved resistant High Breast Cancer cell line (MCF-7)
hsa-miR-216a-5p Doxorubicin 31703 NSC123127 approved sensitive High Small Cell Lung Cancer cell line (NCI-H69)
hsa-miR-216a-5p Sorafenib 216239 NSC747971 approved resistant Low Hepatocellular Carcinoma tissue and cell line (HepG2, Hep3B, Huh-7, PLC/PRF/5, HCCLM3, Bel-7404, HLE, SK-HEP-1, SNU-449)
hsa-miR-216a-5p Fluorouracil 3385 NSC19893 approved resistant High Colorectal Cancer tissue
hsa-miR-216a-5p Oxaliplatin 6857599 NSC266046 approved resistant High Colorectal Cancer tissue
hsa-miR-216a-5p Sorafenib 216239 NSC747971 approved resistant High Hepatocellular Carcinoma cell line (Huh-7)
hsa-miR-216a-5p Doxorubicin 31703 NSC123127 approved resistant Low Small Cell Lung Cancer cell line (H69, H446)
hsa-miR-216a-5p Cisplatin 5460033 NSC119875 approved resistant Low Ovarian Cancer cell line (SKOV3, OVCA433)
hsa-miR-216a-5p Oxaliplatin 6857599 NSC266046 approved resistant Low Gastric Cancer cell line (MGC, SGC)
hsa-miR-216a-5p Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-216a-5p Osimertinib 71496458 NSC779217 approved sensitive cell line (HCC827)
hsa-miR-216a-5p Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-216a-5p Vemurafenib 42611257 NSC761431 approved sensitive cell line (LM16)
hsa-miR-216a-5p Vemurafenib 42611257 NSC761431 approved resistant cell line (LM11)
hsa-miR-216a-5p Vemurafenib 42611257 NSC761431 approved sensitive cell line (LM17)
hsa-miR-216a-5p Vemurafenib 42611257 NSC761431 approved resistant cell line (LM47)
hsa-miR-216a-5p Vemurafenib 42611257 NSC761431 approved resistant cell line (LM43)
hsa-miR-216a-5p Exemestane 60198 NSC713563 approved sensitive cell line (MCF-7)
hsa-miR-216a-5p Testosterone+Tamoxifen sensitive cell line (MCF-7)
hsa-miR-216a-5p Cisplatin 5460033 NSC119875 approved resistant cell line (RPMI2650)
hsa-miR-216a-5p Tamoxifen 2733525 NSC180973 approved sensitive cell line (TamR8)
hsa-miR-216a-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)

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