pre-miRNA Information
pre-miRNA hsa-mir-4680   
Genomic Coordinates chr10: 110898090 - 110898155
Description Homo sapiens miR-4680 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4680-5p
Sequence 5| AGAACUCUUGCAGUCUUAGAUGU |27
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1274530692 2 dbSNP
rs780271274 5 dbSNP
rs1461423681 7 dbSNP
rs749729920 8 dbSNP
rs1252920446 10 dbSNP
rs201739274 11 dbSNP
rs774971106 19 dbSNP
rs748132091 22 dbSNP
rs773643180 22 dbSNP
rs1235425484 23 dbSNP
Putative Targets

Gene Information
Gene Symbol LACTB   
Synonyms G24, MRPL56
Description lactamase beta
Transcript NM_171846   
Other Transcripts NM_032857   
Expression
Putative miRNA Targets on LACTB
3'UTR of LACTB
(miRNA target sites are highlighted)
>LACTB|NM_171846|3'UTR
   1 ATGAATACCTTCTGCTGTGTCTAGCTATATCGCATCTTAACACTATTTTATTAATTAAAAGTCAAATTTTCTTTGTTTCC
  81 ATTCCAAAATCAACCTGCCACATTTTGGGAGCTTTTCTACATGTCTGTTTTCTCATCTGTAAAGTGAAGGAAGTAAAACA
 161 TGTTTATAAAGTACACTAAGACCCTTTGATGAAAGATAGCAATAATATTAATAATTCAAACATGAATAACTAAACCAAAA
 241 TTGCACCCACCATGAGCATCTGTAATTTGCTCTTTAACCATTCCTTTTTTAGGTTTTAACTAATACTTTGTTTACGTGTT
 321 ATTAGTTTTTAATTGTTTTCATACTGTTTTGAAATAATTTTATACTTATAGAAAAGTTGCAAGAGTAGTACAAAGGATTC
 401 ACATATCCTCTTTACTCAGATTCCCTTAATGTTAGTTTACCGCATTTGCATTACCTTTCTGTCTACATATGTGTTTGTTT
 481 CTGAACCATTTGGAAATAAGTTGTAGACGTGATACCCCTTTACCTATAAATATTTACATGTGTATTTTCTAAAAACAAGG
 561 ACATTCAGGGCCGGGTGCAGTGGCTCACGCCTGTAATCCCAACACTTTGGAAGGCCGAGGTGGGTGGATCACCTGAGGTC
 641 AGGAGTTCAAGACCAGCCTGGCCAATGTGGTGAAATCAACCCTCTCTCTACTAAAAATGCAAAAATTAGCCAGGTGTGGT
 721 GGCGGGTGCCTATAATCCCAGCCACGCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCAGGAGGTGGAGTTGCAGTAAG
 801 CCAAGATCGTGCCCCTGCACTTCAGGCTGGGCGAAAGAGTGAGACTCCATGTCAAAAAAGGAAAAAAAAAAAAAAAAAAA
 881 GGACATTTGGGAAATTAACATAGATACAATGCTTTTATTAAATCTACAGACCTTACTCAAATTTTGCCAGTTGTTCCAAT
 961 AATGTCCTTTATAGCAAAAGAGCAGAAAAACTTTTTTTTCTGGTCTAGGATCTAATCCATGATCTCACATTGCATTTACT
1041 TGTCATATCTATCAGAAGTCACTTGACATCAGTTTGTCCCATTATTGCTGATGGTATTTTAATCACTTTTTGAGGTGGTG
1121 CCTGTCAGGTTATTGTAAAGTTACTATTTTTACTTTATAATTAACAAGTATATTTGGAGGAGATAATTTGAGATGATGTA
1201 AAAATCCTCTTTCTCATCAAACTTTCTACTAGTTTTAGCATCTATCAGTGATTCATGACTGAATCAGTTATTACAGTGAT
1281 GGTTGTCAAATGGTGATTTTCTAATTCCATCATCCATTCTGTATTTATCAGTTGGCATTCTATTATAAGAAGGTGCGGGC
1361 CGGGGCGGTGGCTCACGCCTGTAATCCCATCACTTTGGGAGGCTGAGGTGGGCGGATCACATGAGACCAAGTTTGAGACC
1441 AGCCTGGCCAACATGGCGAAACCCCATCTCTACTGAAAATACAAAAAATCAGCCGGGCATGGTGGCATACACTTGTAATC
1521 TCGGCTGCTCGGGAGTCTGAGGCAGGAGAATCTCTTGAACCCAGGAGGCAGAGGTTGCAGTGAGCCAAGATCATGCCACT
1601 GCACTCCAGCCTGGGCGACAAAGTGAGACTCCATCTCAGAAAAAAAAGTGCTTTCCCTTCTCTCTTATTTATTTATTCAT
1681 ACCAGTATGCACTCATGGATTCTTATTTTAGTCAATGAGTTATAATCTGTCACTGTCATTATTTAATATGTTGCTTTTAA
1761 AATAGTATATGAAATAATAAAACTGTAACAGTAAATGGTTATTAGATTGCTTACCTA
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' ugUAGAUUCUGACGUUCUCAAGa 5'
            | ||:||::  ||:|||||| 
Target 5' tcACCTGAGGT--CAGGAGTTCa 3'
629 - 649 149.00 -17.10
2
miRNA  3' uguagaUUCUGACGUUCUCAaga 5'
                || ::|||||||||   
Target 5' tatagaAAAGTTGCAAGAGTagt 3'
367 - 389 129.00 -13.02
3
miRNA  3' ugUAGAUUCUGA--CG--UUCUCAaga 5'
            | :| ||:||  ||  ||||||   
Target 5' gcACTTCAGGCTGGGCGAAAGAGTgag 3'
817 - 843 121.00 -12.52
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSM8850459 4 COSMIC
COSN31576607 19 COSMIC
COSN30184155 22 COSMIC
COSN31900115 24 COSMIC
COSN30166218 29 COSMIC
COSN26982114 33 COSMIC
COSN1681916 61 COSMIC
COSN31583703 72 COSMIC
COSN30107373 94 COSMIC
COSN29802587 832 COSMIC
COSN26811819 1362 COSMIC
COSN8175615 1617 COSMIC
COSN6277792 1737 COSMIC
rs2652822 920 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1234705297 8 dbSNP
rs776186091 9 dbSNP
rs747659368 10 dbSNP
rs1203092532 13 dbSNP
rs769268890 15 dbSNP
rs1261297503 17 dbSNP
rs1466262659 18 dbSNP
rs772952781 20 dbSNP
rs371618594 21 dbSNP
rs767978346 30 dbSNP
rs776131331 31 dbSNP
rs761331959 32 dbSNP
rs200705826 33 dbSNP
rs757380943 34 dbSNP
rs1414857850 41 dbSNP
rs765336354 44 dbSNP
rs1213438509 61 dbSNP
rs934006078 66 dbSNP
rs1251475711 70 dbSNP
rs1466883337 72 dbSNP
rs963619078 72 dbSNP
rs1041730590 76 dbSNP
rs1195040290 84 dbSNP
rs944760416 94 dbSNP
rs879115889 100 dbSNP
rs1335974286 118 dbSNP
rs779091674 120 dbSNP
rs1309411659 126 dbSNP
rs1427398228 133 dbSNP
rs1369365028 135 dbSNP
rs1168317536 151 dbSNP
rs557318270 168 dbSNP
rs1023753021 169 dbSNP
rs755379997 175 dbSNP
rs902469828 192 dbSNP
rs765621335 194 dbSNP
rs1032185796 206 dbSNP
rs530784811 207 dbSNP
rs1470669514 208 dbSNP
rs893604764 212 dbSNP
rs1374692970 231 dbSNP
rs111821958 243 dbSNP
rs577522847 245 dbSNP
rs1163973909 247 dbSNP
rs1222272588 249 dbSNP
rs191740466 251 dbSNP
rs1023829168 253 dbSNP
rs1329521992 259 dbSNP
rs970439129 259 dbSNP
rs1289872480 269 dbSNP
rs1226142370 273 dbSNP
rs1349392711 280 dbSNP
rs567820626 281 dbSNP
rs981776914 283 dbSNP
rs1025223634 284 dbSNP
rs539953669 298 dbSNP
rs553285225 302 dbSNP
rs1361428370 307 dbSNP
rs1414595045 308 dbSNP
rs571364366 316 dbSNP
rs371920917 317 dbSNP
rs199934528 323 dbSNP
rs1192984989 326 dbSNP
rs1489455444 334 dbSNP
rs1244915920 335 dbSNP
rs922412328 337 dbSNP
rs760627566 340 dbSNP
rs182378934 342 dbSNP
rs1271666205 343 dbSNP
rs922714356 365 dbSNP
rs934058457 370 dbSNP
rs777859813 378 dbSNP
rs746952785 386 dbSNP
rs935278243 389 dbSNP
rs1432046744 392 dbSNP
rs1391344912 394 dbSNP
rs1485281829 402 dbSNP
rs757260172 402 dbSNP
rs1456973667 404 dbSNP
rs1184234953 411 dbSNP
rs1178426248 418 dbSNP
rs1054091183 421 dbSNP
rs575335754 425 dbSNP
rs1012474119 431 dbSNP
rs1012523084 435 dbSNP
rs1023418170 441 dbSNP
rs187869211 443 dbSNP
rs1415407112 445 dbSNP
rs1003211542 447 dbSNP
rs554859093 450 dbSNP
rs956772403 468 dbSNP
rs1309956869 499 dbSNP
rs989871343 501 dbSNP
rs951095095 503 dbSNP
rs1367966487 504 dbSNP
rs983785473 509 dbSNP
rs1434840536 510 dbSNP
rs975278635 513 dbSNP
rs1290746877 519 dbSNP
rs922446744 520 dbSNP
rs1017631424 521 dbSNP
rs139740798 524 dbSNP
rs376585578 527 dbSNP
rs1291965862 532 dbSNP
rs908270707 540 dbSNP
rs1430395661 549 dbSNP
rs941063449 554 dbSNP
rs564916437 557 dbSNP
rs144440329 559 dbSNP
rs1186524923 566 dbSNP
rs1448674766 568 dbSNP
rs1256532895 570 dbSNP
rs955450632 573 dbSNP
rs376807695 574 dbSNP
rs745722488 577 dbSNP
rs1254969192 587 dbSNP
rs977476471 589 dbSNP
rs73444395 590 dbSNP
rs1213162716 594 dbSNP
rs1287542034 601 dbSNP
rs1228253267 602 dbSNP
rs936025962 606 dbSNP
rs1315241147 607 dbSNP
rs775131854 608 dbSNP
rs1054448014 609 dbSNP
rs1045309543 610 dbSNP
rs1210145367 612 dbSNP
rs1308804742 614 dbSNP
rs1411748729 615 dbSNP
rs113265850 617 dbSNP
rs748887698 618 dbSNP
rs947996401 619 dbSNP
rs1182259521 622 dbSNP
rs1044882743 624 dbSNP
rs1166638888 631 dbSNP
rs192500968 638 dbSNP
rs1160625285 649 dbSNP
rs549058999 650 dbSNP
rs1182366169 655 dbSNP
rs1010962994 666 dbSNP
rs1022271881 672 dbSNP
rs963975485 680 dbSNP
rs996751972 685 dbSNP
rs1434181042 692 dbSNP
rs185649160 695 dbSNP
rs1321431335 699 dbSNP
rs528768067 700 dbSNP
rs190520918 701 dbSNP
rs1005662334 709 dbSNP
rs1016596054 714 dbSNP
rs1307465638 717 dbSNP
rs1390816937 719 dbSNP
rs908339672 722 dbSNP
rs1221727933 724 dbSNP
rs964646613 725 dbSNP
rs1416838112 727 dbSNP
rs996788185 728 dbSNP
rs1353878879 734 dbSNP
rs1159510019 741 dbSNP
rs571849551 742 dbSNP
rs1232902377 743 dbSNP
rs761202724 746 dbSNP
rs1444095880 747 dbSNP
rs1451624479 748 dbSNP
rs539209315 751 dbSNP
rs1210647831 768 dbSNP
rs1208538445 770 dbSNP
rs766966179 771 dbSNP
rs915586600 772 dbSNP
rs1479530330 780 dbSNP
rs117074183 788 dbSNP
rs955503717 792 dbSNP
rs1287874906 795 dbSNP
rs1238991570 796 dbSNP
rs1234072021 803 dbSNP
rs977570952 809 dbSNP
rs568933922 810 dbSNP
rs924718855 811 dbSNP
rs1393511401 813 dbSNP
rs192067117 814 dbSNP
rs1458541318 819 dbSNP
rs1386021110 821 dbSNP
rs1157566884 822 dbSNP
rs184613743 827 dbSNP
rs139120249 830 dbSNP
rs915875417 832 dbSNP
rs947978446 833 dbSNP
rs1170291668 834 dbSNP
rs1044935902 836 dbSNP
rs1190889178 841 dbSNP
rs1353180233 842 dbSNP
rs68054050 843 dbSNP
rs1332996040 847 dbSNP
rs1377214395 849 dbSNP
rs188547979 850 dbSNP
rs1436867806 854 dbSNP
rs1231065800 857 dbSNP
rs1370140802 860 dbSNP
rs888346378 861 dbSNP
rs1011411380 862 dbSNP
rs1170289637 862 dbSNP
rs142946511 862 dbSNP
rs1491073548 862 dbSNP
rs201338310 862 dbSNP
rs34509023 862 dbSNP
rs765672600 862 dbSNP
rs867323854 863 dbSNP
rs1448077460 868 dbSNP
rs201472257 870 dbSNP
rs190235801 871 dbSNP
rs201227866 871 dbSNP
rs1043780652 872 dbSNP
rs56399509 873 dbSNP
rs1005260698 874 dbSNP
rs1258409838 874 dbSNP
rs1448383142 875 dbSNP
rs1341875072 876 dbSNP
rs1366354688 882 dbSNP
rs182846531 883 dbSNP
rs1191905369 885 dbSNP
rs1248541687 886 dbSNP
rs1038450770 887 dbSNP
rs1478388868 895 dbSNP
rs1186512218 896 dbSNP
rs1417952578 897 dbSNP
rs1370591292 900 dbSNP
rs899470801 900 dbSNP
rs899882314 903 dbSNP
rs996784509 906 dbSNP
rs1029562777 908 dbSNP
rs955482441 910 dbSNP
rs1164187129 915 dbSNP
rs2652822 920 dbSNP
rs1015844295 923 dbSNP
rs1187450215 928 dbSNP
rs1394121333 934 dbSNP
rs750131481 936 dbSNP
rs1029945427 937 dbSNP
rs752989962 938 dbSNP
rs372242227 947 dbSNP
rs955597886 950 dbSNP
rs1207254713 952 dbSNP
rs962539859 955 dbSNP
rs999058684 957 dbSNP
rs9788649 965 dbSNP
rs1358121001 973 dbSNP
rs1282100352 974 dbSNP
rs1232248609 975 dbSNP
rs957689185 979 dbSNP
rs1350623632 991 dbSNP
rs915663357 992 dbSNP
rs1332392119 995 dbSNP
rs1354480327 999 dbSNP
rs1436539194 1000 dbSNP
rs969737641 1006 dbSNP
rs1388969144 1008 dbSNP
rs1164546507 1011 dbSNP
rs981092669 1015 dbSNP
rs764193654 1018 dbSNP
rs990220265 1030 dbSNP
rs112492528 1043 dbSNP
rs118066038 1045 dbSNP
rs1222164747 1052 dbSNP
rs575328436 1053 dbSNP
rs1271012091 1068 dbSNP
rs1212725379 1074 dbSNP
rs1329411695 1079 dbSNP
rs1289771289 1095 dbSNP
rs970054938 1121 dbSNP
rs981395001 1125 dbSNP
rs927917483 1147 dbSNP
rs181310525 1183 dbSNP
rs149901777 1185 dbSNP
rs116900717 1193 dbSNP
rs1212118488 1197 dbSNP
rs1052662671 1205 dbSNP
rs1348547261 1214 dbSNP
rs1325642561 1235 dbSNP
rs1276595872 1236 dbSNP
rs547002333 1241 dbSNP
rs1292286277 1245 dbSNP
rs1458016336 1257 dbSNP
rs1452293927 1263 dbSNP
rs1391120014 1272 dbSNP
rs1157127447 1277 dbSNP
rs545888435 1293 dbSNP
rs914065882 1308 dbSNP
rs373266214 1310 dbSNP
rs1240391772 1319 dbSNP
rs1479092352 1322 dbSNP
rs1191746671 1324 dbSNP
rs1478950198 1338 dbSNP
rs368392011 1341 dbSNP
rs1465127900 1345 dbSNP
rs1038101648 1354 dbSNP
rs565546024 1356 dbSNP
rs751713578 1357 dbSNP
rs532764768 1362 dbSNP
rs1050741910 1363 dbSNP
rs1221500853 1366 dbSNP
rs551150010 1367 dbSNP
rs1004543582 1368 dbSNP
rs891423691 1375 dbSNP
rs1317055958 1377 dbSNP
rs1357992696 1378 dbSNP
rs569020509 1380 dbSNP
rs535955788 1382 dbSNP
rs1359856845 1383 dbSNP
rs1178318354 1393 dbSNP
rs1412777249 1398 dbSNP
rs1393200631 1399 dbSNP
rs1401776341 1410 dbSNP
rs1278750046 1414 dbSNP
rs7162715 1415 dbSNP
rs898362942 1416 dbSNP
rs1485339940 1422 dbSNP
rs1286222445 1423 dbSNP
rs117973093 1429 dbSNP
rs1022750587 1430 dbSNP
rs1223366505 1436 dbSNP
rs1280273057 1440 dbSNP
rs781261778 1444 dbSNP
rs893280173 1449 dbSNP
rs751937496 1452 dbSNP
rs565283406 1453 dbSNP
rs1381931419 1454 dbSNP
rs970107330 1457 dbSNP
rs1218076792 1458 dbSNP
rs1257399770 1459 dbSNP
rs1484925370 1472 dbSNP
rs1374878317 1474 dbSNP
rs981445674 1478 dbSNP
rs1430301896 1481 dbSNP
rs1391859372 1484 dbSNP
rs1190077835 1489 dbSNP
rs1035769116 1493 dbSNP
rs558397229 1495 dbSNP
rs1472923420 1496 dbSNP
rs144925121 1500 dbSNP
rs558437410 1504 dbSNP
rs1256165693 1512 dbSNP
rs1206552431 1521 dbSNP
rs1484319149 1522 dbSNP
rs908391791 1523 dbSNP
rs1227159849 1524 dbSNP
rs914138046 1531 dbSNP
rs755922637 1532 dbSNP
rs779779650 1534 dbSNP
rs1394165477 1536 dbSNP
rs1410421165 1542 dbSNP
rs932740608 1545 dbSNP
rs1340788508 1574 dbSNP
rs755498985 1575 dbSNP
rs1350198108 1579 dbSNP
rs1288114776 1581 dbSNP
rs1307343020 1588 dbSNP
rs932388192 1590 dbSNP
rs1416613724 1595 dbSNP
rs372000762 1597 dbSNP
rs11635238 1599 dbSNP
rs1182250069 1600 dbSNP
rs576679061 1604 dbSNP
rs573601203 1617 dbSNP
rs1249076834 1618 dbSNP
rs1050752084 1633 dbSNP
rs768401296 1635 dbSNP
rs891153474 1640 dbSNP
rs1267576914 1658 dbSNP
rs537693850 1660 dbSNP
rs1289161417 1661 dbSNP
rs199541205 1663 dbSNP
rs768892470 1665 dbSNP
rs1257313311 1669 dbSNP
rs890762018 1674 dbSNP
rs934917842 1679 dbSNP
rs1053395892 1683 dbSNP
rs893364599 1684 dbSNP
rs555928101 1686 dbSNP
rs898400699 1694 dbSNP
rs542771024 1699 dbSNP
rs1393293640 1700 dbSNP
rs781564222 1703 dbSNP
rs781632481 1714 dbSNP
rs575365863 1717 dbSNP
rs1158746858 1718 dbSNP
rs1393887610 1719 dbSNP
rs1464496971 1725 dbSNP
rs1434254617 1732 dbSNP
rs527659456 1734 dbSNP
rs1192166863 1740 dbSNP
rs542736581 1742 dbSNP
rs950697570 1743 dbSNP
rs1269039726 1747 dbSNP
rs771416834 1750 dbSNP
rs1002633385 1757 dbSNP
rs1260186693 1761 dbSNP
rs1238323851 1766 dbSNP
rs149033546 1771 dbSNP
rs1305459604 1786 dbSNP
rs1438482964 1800 dbSNP
rs1369910170 1811 dbSNP
rs1035439124 1814 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions BCBL-1
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 GSM1015448. RNA binding protein: AGO2. Condition:BCBL-1 mRNA ...

- Haecker I; Gay LA; Yang Y; Hu J; Morse AM; et al., 2012, PLoS pathogens.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' ugUAGAUUCUGACGUUCUCAAGa 5'
            | ||:||::  ||:|||||| 
Target 5' ucACCUGAGGU--CAGGAGUUCa 3'
15 - 35
Article - Haecker I; Gay LA; Yang Y; Hu J; Morse AM; et al.
- PLoS pathogens, 2012
KSHV is the etiological agent of Kaposi's sarcoma (KS), primary effusion lymphoma (PEL), and a subset of multicentricCastleman's disease (MCD). The fact that KSHV-encoded miRNAs are readily detectable in all KSHV-associated tumors suggests a potential role in viral pathogenesis and tumorigenesis. MiRNA-mediated regulation of gene expression is a complex network with each miRNA having many potential targets, and to date only few KSHV miRNA targets have been experimentally determined. A detailed understanding of KSHV miRNA functions requires high-through putribonomics to globally analyze putative miRNA targets in a cell type-specific manner. We performed Ago HITS-CLIP to identify viral and cellular miRNAs and their cognate targets in two latently KSHV-infected PEL cell lines. Ago HITS-CLIP recovered 1170 and 950 cellular KSHV miRNA targets from BCBL-1 and BC-3, respectively. Importantly, enriched clusters contained KSHV miRNA seed matches in the 3'UTRs of numerous well characterized targets, among them THBS1, BACH1, and C/EBPbeta. KSHV miRNA targets were strongly enriched for genes involved in multiple pathways central for KSHV biology, such as apoptosis, cell cycle regulation, lymphocyte proliferation, and immune evasion, thus further supporting a role in KSHV pathogenesis and potentially tumorigenesis. A limited number of viral transcripts were also enriched by HITS-CLIP including vIL-6 expressed only in a subset of PEL cells during latency. Interestingly, Ago HITS-CLIP revealed extremely high levels of Ago-associated KSHV miRNAs especially in BC-3 cells where more than 70% of all miRNAs are of viral origin. This suggests that in addition to seed match-specific targeting of cellular genes, KSHV miRNAs may also function by hijacking RISCs, thereby contributing to a global de-repression of cellular gene expression due to the loss of regulation by human miRNAs. In summary, we provide an extensive list of cellular and viral miRNA targets representing an important resource to decipher KSHV miRNA function.
LinkOut: [PMID: 22927820]
Experimental Support 2 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 GSM1084043. RNA binding protein: AGO2. Condition:CLIP_arsenite_rep2 HITS-CLIP data was present in GSM1084064. RNA binding protein: AGO2. Condition:CLIP_noemetine_AbnovaAb ...

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

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]
CLIP-seq Support 1 for dataset GSM1015448
Method / RBP HITS-CLIP / AGO2
Cell line / Condition BCBL-1 / BCBL-1 mRNA
Location of target site ENST00000413507.2 | 3UTR | CCGAGGUGGGUGGAUCACCUGAGGUCAGGAGUUCAAGACC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 22927820 / GSE41357
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1084043
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_arsenite_rep2
Location of target site ENST00000413507.2 | 3UTR | GAAGGCCGAGGUGGGUGGAUCACCUGAGGUCAGGAGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM1084064
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noemetine_AbnovaAb
Location of target site ENST00000413507.2 | 3UTR | GGAAGGCCGAGGUGGGUGGAUCACCUGAGGUCAGGAGU
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
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
133 hsa-miR-4680-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT378771 MACC1 MACC1, MET transcriptional regulator 2 2
MIRT393867 ZDHHC21 zinc finger DHHC-type containing 21 2 4
MIRT446684 C2CD2 C2 calcium dependent domain containing 2 2 2
MIRT447600 MRPL3 mitochondrial ribosomal protein L3 2 2
MIRT450708 RNF152 ring finger protein 152 2 2
MIRT450784 PAPOLG poly(A) polymerase gamma 2 2
MIRT454623 COL23A1 collagen type XXIII alpha 1 chain 2 8
MIRT461620 PTCD3 pentatricopeptide repeat domain 3 2 2
MIRT462695 SNRPD3 small nuclear ribonucleoprotein D3 polypeptide 2 2
MIRT475530 HOXA3 homeobox A3 2 8
MIRT475739 HERPUD1 homocysteine inducible ER protein with ubiquitin like domain 1 2 4
MIRT489676 CYP1A1 cytochrome P450 family 1 subfamily A member 1 2 2
MIRT490610 SLC47A1 solute carrier family 47 member 1 2 2
MIRT493628 HIC2 HIC ZBTB transcriptional repressor 2 2 2
MIRT496152 RPS15A ribosomal protein S15a 2 2
MIRT499232 VAV3 vav guanine nucleotide exchange factor 3 2 4
MIRT501496 PRICKLE2 prickle planar cell polarity protein 2 2 2
MIRT507163 GAS2L3 growth arrest specific 2 like 3 2 2
MIRT512389 MTRNR2L1 MT-RNR2-like 1 2 4
MIRT514626 MTRNR2L7 MT-RNR2-like 7 2 2
MIRT517474 PEX26 peroxisomal biogenesis factor 26 2 2
MIRT525332 CNGB1 cyclic nucleotide gated channel beta 1 2 2
MIRT526685 BAK1 BCL2 antagonist/killer 1 2 2
MIRT527317 CCR2 C-C motif chemokine receptor 2 2 2
MIRT527608 EYS eyes shut homolog (Drosophila) 2 2
MIRT528794 RAB32 RAB32, member RAS oncogene family 2 2
MIRT531048 TIPARP TCDD inducible poly(ADP-ribose) polymerase 2 2
MIRT532254 TBPL2 TATA-box binding protein like 2 2 2
MIRT533801 TMED7 transmembrane p24 trafficking protein 7 2 4
MIRT535887 MLEC malectin 2 2
MIRT540704 PDPK1 3-phosphoinositide dependent protein kinase 1 2 4
MIRT544645 PHF8 PHD finger protein 8 2 4
MIRT545760 HS3ST1 heparan sulfate-glucosamine 3-sulfotransferase 1 2 2
MIRT555310 PPP2R5C protein phosphatase 2 regulatory subunit B'gamma 2 2
MIRT555877 PAFAH1B2 platelet activating factor acetylhydrolase 1b catalytic subunit 2 2 4
MIRT559507 ARID5B AT-rich interaction domain 5B 2 2
MIRT560448 SLC30A7 solute carrier family 30 member 7 2 2
MIRT561262 ZIK1 zinc finger protein interacting with K protein 1 2 2
MIRT561795 PAWR pro-apoptotic WT1 regulator 2 2
MIRT567007 KLHL15 kelch like family member 15 2 2
MIRT569298 SURF6 surfeit 6 2 2
MIRT570606 MTRNR2L11 MT-RNR2-like 11 2 2
MIRT572888 ADCY2 adenylate cyclase 2 2 2
MIRT573119 ADAMTS18 ADAM metallopeptidase with thrombospondin type 1 motif 18 2 2
MIRT608332 ZNF670 zinc finger protein 670 2 6
MIRT614942 KCNK5 potassium two pore domain channel subfamily K member 5 2 2
MIRT615324 ERN1 endoplasmic reticulum to nucleus signaling 1 2 2
MIRT618441 ZNF800 zinc finger protein 800 2 2
MIRT620110 HARBI1 harbinger transposase derived 1 2 2
MIRT626008 ZNF517 zinc finger protein 517 2 2
MIRT626626 SLC30A6 solute carrier family 30 member 6 2 2
MIRT627842 POU3F1 POU class 3 homeobox 1 2 2
MIRT628386 CACNB2 calcium voltage-gated channel auxiliary subunit beta 2 2 2
MIRT629305 PTPLAD2 3-hydroxyacyl-CoA dehydratase 4 1 1
MIRT629864 GATAD1 GATA zinc finger domain containing 1 2 2
MIRT630444 IDE insulin degrading enzyme 2 2
MIRT631854 PIGG phosphatidylinositol glycan anchor biosynthesis class G 2 2
MIRT633173 AGO3 argonaute 3, RISC catalytic component 2 2
MIRT633477 ZNF724P zinc finger protein 724 2 2
MIRT634395 PLSCR1 phospholipid scramblase 1 2 2
MIRT635538 TRIM72 tripartite motif containing 72 2 2
MIRT635821 OPA3 OPA3, outer mitochondrial membrane lipid metabolism regulator 2 2
MIRT636169 TIMM8A translocase of inner mitochondrial membrane 8A 2 2
MIRT636797 CYB5D1 cytochrome b5 domain containing 1 2 2
MIRT637952 IVD isovaleryl-CoA dehydrogenase 2 2
MIRT645136 HES2 hes family bHLH transcription factor 2 2 2
MIRT645667 ADK adenosine kinase 2 2
MIRT646148 FLVCR1 feline leukemia virus subgroup C cellular receptor 1 2 2
MIRT647004 NCR3LG1 natural killer cell cytotoxicity receptor 3 ligand 1 2 2
MIRT648187 C2orf68 chromosome 2 open reading frame 68 2 2
MIRT650090 TERF2 telomeric repeat binding factor 2 2 2
MIRT650329 RTN2 reticulon 2 2 2
MIRT654224 RNF165 ring finger protein 165 2 2
MIRT654545 RAB1A RAB1A, member RAS oncogene family 2 2
MIRT656457 MAPK14 mitogen-activated protein kinase 14 2 2
MIRT656828 KLF8 Kruppel like factor 8 2 2
MIRT657112 ITPRIPL2 inositol 1,4,5-trisphosphate receptor interacting protein like 2 2 2
MIRT657930 GATSL2 cytosolic arginine sensor for mTORC1 subunit 2 2 2
MIRT659375 CREG2 cellular repressor of E1A stimulated genes 2 2 2
MIRT659833 CARHSP1 calcium regulated heat stable protein 1 2 2
MIRT662108 LACTB lactamase beta 2 4
MIRT662789 TBC1D25 TBC1 domain family member 25 2 2
MIRT669501 ARL3 ADP ribosylation factor like GTPase 3 2 2
MIRT669759 ZNF101 zinc finger protein 101 2 4
MIRT669800 GAN gigaxonin 2 2
MIRT670050 RPP14 ribonuclease P/MRP subunit p14 2 2
MIRT670299 RBBP4 RB binding protein 4, chromatin remodeling factor 2 2
MIRT670388 EMP2 epithelial membrane protein 2 2 2
MIRT672862 C22orf29 retrotransposon Gag like 10 2 2
MIRT672890 FXN frataxin 2 2
MIRT673210 C10orf76 chromosome 10 open reading frame 76 2 2
MIRT674001 KCNN3 potassium calcium-activated channel subfamily N member 3 2 2
MIRT674163 BLOC1S3 biogenesis of lysosomal organelles complex 1 subunit 3 2 2
MIRT674502 TIRAP TIR domain containing adaptor protein 2 2
MIRT675470 NUBPL nucleotide binding protein like 2 2
MIRT675671 TMOD2 tropomodulin 2 2 2
MIRT676006 CRKL CRK like proto-oncogene, adaptor protein 2 2
MIRT676074 TIMM50 translocase of inner mitochondrial membrane 50 2 2
MIRT676386 SEC24D SEC24 homolog D, COPII coat complex component 2 2
MIRT676764 SNX2 sorting nexin 2 2 2
MIRT676896 GABPB1 GA binding protein transcription factor beta subunit 1 2 2
MIRT676978 ZNF708 zinc finger protein 708 2 2
MIRT677236 C15orf40 chromosome 15 open reading frame 40 2 2
MIRT677369 HSPA4L heat shock protein family A (Hsp70) member 4 like 2 2
MIRT677464 PDLIM3 PDZ and LIM domain 3 2 2
MIRT678081 EIF2A eukaryotic translation initiation factor 2A 2 2
MIRT678093 ATCAY ATCAY, caytaxin 2 2
MIRT678324 FBLIM1 filamin binding LIM protein 1 2 2
MIRT678417 ANKRD36 ankyrin repeat domain 36 2 2
MIRT678521 ZNF347 zinc finger protein 347 2 2
MIRT678700 TRIP11 thyroid hormone receptor interactor 11 2 2
MIRT678829 PDE6A phosphodiesterase 6A 2 2
MIRT679991 RUNDC1 RUN domain containing 1 2 2
MIRT680751 PSD4 pleckstrin and Sec7 domain containing 4 2 2
MIRT681249 ZNF383 zinc finger protein 383 2 2
MIRT681422 GTF3C6 general transcription factor IIIC subunit 6 2 2
MIRT681948 SLC19A3 solute carrier family 19 member 3 2 2
MIRT689278 C5AR2 complement component 5a receptor 2 2 2
MIRT690389 PARP15 poly(ADP-ribose) polymerase family member 15 2 2
MIRT691845 OSCAR osteoclast associated, immunoglobulin-like receptor 2 2
MIRT693863 IYD iodotyrosine deiodinase 2 2
MIRT696002 DNAJC10 DnaJ heat shock protein family (Hsp40) member C10 2 2
MIRT701930 MLLT1 MLLT1, super elongation complex subunit 2 2
MIRT702341 KLHL7 kelch like family member 7 2 2
MIRT703557 FKBP14 FK506 binding protein 14 2 2
MIRT705033 CACUL1 CDK2 associated cullin domain 1 2 2
MIRT706341 STAC2 SH3 and cysteine rich domain 2 2 2
MIRT709671 RGP1 RGP1 homolog, RAB6A GEF complex partner 1 2 2
MIRT711212 EFHB EF-hand domain family member B 2 2
MIRT718342 PURA purine rich element binding protein A 2 2
MIRT722755 SIRPB2 signal regulatory protein beta 2 2 2
MIRT723535 NFATC2IP nuclear factor of activated T-cells 2 interacting protein 2 2
MIRT724498 BFAR bifunctional apoptosis regulator 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-4680-5p Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (1500 ng/ml)

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