>RPS15A|NM_001019|3'UTR
   1 GGATGTAATACATATATTTACAAATAAAATGCCTCATGGACTCTGGTGCTTCCAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' cgguaGUUUCAAUUUU-CGGu 5' |||| ||||| ||| Target 5' atttaCAAA--TAAAATGCCt 3'	16 - 34	123.00	-5.30

Mutant ID	Mutant Position	Mutant Source
COSN31505969	35	COSMIC
COSN30188787	43	COSMIC
COSN15337707	174	COSMIC
COSN15667544	205	COSMIC
COSN22921223	348	COSMIC
COSN15337706	450	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs777949231	2	dbSNP
rs201061644	3	dbSNP
rs543810121	5	dbSNP
rs1400797893	12	dbSNP
rs781660508	15	dbSNP
rs1463941459	16	dbSNP
rs1424934317	35	dbSNP
rs1238827000	36	dbSNP
rs748007427	37	dbSNP
rs1477040281	43	dbSNP
rs781329726	44	dbSNP
rs1188430408	45	dbSNP
rs1442076202	46	dbSNP
rs768737727	47	dbSNP
rs1483411223	55	dbSNP
rs1381576606	58	dbSNP
rs1300915261	60	dbSNP
rs904945052	61	dbSNP
rs532011624	72	dbSNP
rs1479059643	75	dbSNP
rs1172018936	78	dbSNP
rs1044723646	82	dbSNP
rs56138938	83	dbSNP
rs1427726651	85	dbSNP
rs1178409928	94	dbSNP
rs949051345	99	dbSNP
rs561359874	100	dbSNP
rs1163632163	106	dbSNP
rs982936740	110	dbSNP
rs1338189242	111	dbSNP
rs1401691601	115	dbSNP
rs1046963886	116	dbSNP
rs1344289410	118	dbSNP
rs929918798	118	dbSNP
rs919768775	119	dbSNP
rs866391610	125	dbSNP
rs919009678	126	dbSNP
rs1215472102	133	dbSNP
rs1284268845	134	dbSNP
rs1425235279	135	dbSNP
rs1194920631	136	dbSNP
rs1246634665	146	dbSNP
rs911317761	152	dbSNP
rs1192974710	156	dbSNP
rs986737538	163	dbSNP
rs976175561	168	dbSNP
rs965716483	171	dbSNP
rs1180507982	175	dbSNP
rs1017258950	177	dbSNP
rs955381969	178	dbSNP
rs1318796770	181	dbSNP
rs1483089151	183	dbSNP
rs1253188410	191	dbSNP
rs1207997158	192	dbSNP
rs868834896	198	dbSNP
rs1367730930	201	dbSNP
rs1020732158	202	dbSNP
rs189416901	204	dbSNP
rs967923599	218	dbSNP
rs572597014	221	dbSNP
rs111567159	246	dbSNP
rs892570916	249	dbSNP
rs12926769	251	dbSNP
rs1350942711	252	dbSNP
rs973754073	254	dbSNP
rs1176911955	255	dbSNP
rs1309615795	256	dbSNP
rs1407963851	261	dbSNP
rs1440589703	262	dbSNP
rs1158907068	266	dbSNP
rs1403493768	267	dbSNP
rs545427048	267	dbSNP
rs905219307	268	dbSNP
rs1013782741	269	dbSNP
rs1445401260	273	dbSNP
rs1347759555	278	dbSNP
rs1283935069	280	dbSNP
rs1306506362	280	dbSNP
rs376714102	280	dbSNP
rs56008565	280	dbSNP
rs796546191	280	dbSNP
rs747155768	281	dbSNP
rs896147294	282	dbSNP
rs1047209378	285	dbSNP
rs1187143932	287	dbSNP
rs1196789539	287	dbSNP
rs1458346609	287	dbSNP
rs1419293237	289	dbSNP
rs929873352	292	dbSNP
rs556515417	293	dbSNP
rs1164850465	294	dbSNP
rs1471681079	294	dbSNP
rs898428988	297	dbSNP
rs1038136309	306	dbSNP
rs1465085543	306	dbSNP
rs942553377	308	dbSNP
rs1391544876	309	dbSNP
rs376903576	311	dbSNP
rs1045002604	316	dbSNP
rs1450625819	321	dbSNP
rs1210544767	329	dbSNP
rs941621574	330	dbSNP
rs143662298	331	dbSNP
rs1047717624	332	dbSNP
rs1221195864	340	dbSNP
rs1217359992	342	dbSNP
rs1260031118	347	dbSNP
rs1318699045	350	dbSNP
rs930141547	355	dbSNP
rs989221248	357	dbSNP
rs919029457	362	dbSNP
rs975875440	377	dbSNP
rs1257997594	379	dbSNP
rs1226289345	387	dbSNP
rs756530175	390	dbSNP
rs569915836	391	dbSNP
rs554483771	392	dbSNP
rs1282871616	393	dbSNP
rs1349825359	405	dbSNP
rs536010755	409	dbSNP
rs910226876	412	dbSNP
rs985787937	421	dbSNP
rs1364951851	422	dbSNP
rs2606564	428	dbSNP
rs1022195505	430	dbSNP
rs970201377	431	dbSNP
rs1340329248	432	dbSNP
rs988409913	436	dbSNP
rs573846529	449	dbSNP
rs550923812	450	dbSNP
rs896229440	453	dbSNP
rs1232584993	456	dbSNP
rs956577562	457	dbSNP
rs1455940179	459	dbSNP
rs1201280738	460	dbSNP
rs1280700969	460	dbSNP
rs1487848869	461	dbSNP
rs1191312337	465	dbSNP
rs1411883648	465	dbSNP
rs1200129554	466	dbSNP
rs1035241044	474	dbSNP
rs2606565	488	dbSNP
rs905250341	492	dbSNP
rs184652146	502	dbSNP
rs1360224001	503	dbSNP
rs898392923	508	dbSNP
rs1300476233	509	dbSNP
rs1386285653	513	dbSNP
rs1386730793	514	dbSNP
rs1005505715	518	dbSNP
rs888720802	520	dbSNP
rs1206591433	521	dbSNP
rs1328153411	527	dbSNP
rs375916479	528	dbSNP
rs994805019	529	dbSNP
rs1351860375	530	dbSNP
rs1214135409	535	dbSNP
rs1235419107	537	dbSNP
rs549736431	549	dbSNP
rs1028409973	550	dbSNP
rs1300057160	551	dbSNP
rs1038230579	556	dbSNP
rs942647978	560	dbSNP
rs1193781785	563	dbSNP
rs1379273056	566	dbSNP
rs889607073	570	dbSNP
rs1051408011	587	dbSNP
rs1366956800	589	dbSNP
rs1318045664	599	dbSNP
rs934050688	602	dbSNP
rs913314667	613	dbSNP
rs1330807088	615	dbSNP
rs1374920030	617	dbSNP
rs1242611833	620	dbSNP
rs531929839	621	dbSNP
rs988798969	635	dbSNP
rs1243896855	637	dbSNP
rs561600908	638	dbSNP
rs925973396	639	dbSNP
rs1213749148	652	dbSNP
rs1237056787	657	dbSNP
rs980342917	667	dbSNP
rs1178580988	670	dbSNP
rs1468072980	674	dbSNP
rs1423589848	680	dbSNP
rs369648813	680	dbSNP
rs1370668045	682	dbSNP
rs1376379371	683	dbSNP
rs970338677	684	dbSNP
rs62046276	689	dbSNP
rs1461948782	690	dbSNP
rs917385400	691	dbSNP
rs993414186	692	dbSNP
rs1450088015	696	dbSNP
rs1378792794	700	dbSNP
rs1250146500	709	dbSNP
rs1186970627	713	dbSNP
rs1464612152	715	dbSNP
rs1180453793	716	dbSNP
rs1206083240	716	dbSNP
rs1233857652	716	dbSNP
rs1256797914	716	dbSNP
rs1260074775	716	dbSNP
rs1300824571	716	dbSNP
rs1301668078	716	dbSNP
rs1310375753	716	dbSNP
rs1336795331	716	dbSNP
rs1475796215	716	dbSNP
rs1482749687	716	dbSNP
rs71141062	716	dbSNP
rs749155538	716	dbSNP
rs754258726	716	dbSNP
rs756203404	716	dbSNP
rs1338427426	718	dbSNP
rs71382565	718	dbSNP
rs957614688	720	dbSNP
rs1201945190	721	dbSNP
rs1342816974	722	dbSNP
rs1255299446	724	dbSNP
rs1273152762	726	dbSNP
rs1228503028	727	dbSNP
rs1207622140	728	dbSNP
rs960461301	742	dbSNP
rs1025830735	745	dbSNP
rs1033708569	748	dbSNP
rs1486210116	761	dbSNP
rs1193467279	762	dbSNP
rs1343608153	766	dbSNP
rs993952448	771	dbSNP
rs1227262260	777	dbSNP
rs1424589541	778	dbSNP
rs1340677823	780	dbSNP
rs549604794	781	dbSNP
rs1376359045	790	dbSNP
rs1435102944	801	dbSNP
rs1335300171	804	dbSNP
rs1358525774	816	dbSNP
rs1432830286	820	dbSNP
rs1270227133	830	dbSNP
rs527844516	831	dbSNP
rs1217053769	838	dbSNP
rs962339031	847	dbSNP
rs560655981	851	dbSNP
rs1348231681	863	dbSNP
rs1016588578	864	dbSNP
rs1312740346	882	dbSNP
rs1217139461	883	dbSNP
rs1246144069	891	dbSNP
rs1487539802	892	dbSNP
rs1006758463	894	dbSNP
rs889701866	900	dbSNP
rs1050913372	901	dbSNP
rs998440461	902	dbSNP
rs891650274	913	dbSNP
rs545564345	914	dbSNP
rs1402303982	922	dbSNP
rs1405554872	922	dbSNP
rs1392172794	925	dbSNP
rs1053600717	926	dbSNP
rs1166765907	927	dbSNP
rs1327378735	928	dbSNP
rs1475238846	929	dbSNP
rs1239016634	946	dbSNP
rs1307445489	955	dbSNP
rs1353306808	963	dbSNP
rs1289790123	973	dbSNP
rs1369224701	976	dbSNP
rs1189404225	977	dbSNP
rs1253733005	979	dbSNP
rs1457449093	986	dbSNP
rs1440414199	993	dbSNP
rs578027935	997	dbSNP
rs1158996641	1003	dbSNP
rs1412936622	1007	dbSNP
rs1459854193	1008	dbSNP
rs936105104	1019	dbSNP
rs1394584460	1026	dbSNP
rs1205859948	1031	dbSNP
rs1445507895	1032	dbSNP
rs1483976117	1033	dbSNP
rs925942487	1035	dbSNP
rs1226964342	1036	dbSNP
rs1356651916	1039	dbSNP
rs1285518729	1040	dbSNP
rs1247457449	1042	dbSNP
rs1339134593	1043	dbSNP
rs1284029109	1046	dbSNP
rs562776075	1049	dbSNP
rs1273813533	1068	dbSNP
rs1317384883	1072	dbSNP
rs1411018744	1075	dbSNP
rs948917400	1089	dbSNP
rs1306288298	1090	dbSNP
rs1409415277	1093	dbSNP
rs1391729553	1097	dbSNP
rs544558580	1100	dbSNP
rs1474147247	1104	dbSNP
rs917504778	1107	dbSNP
rs1418562423	1109	dbSNP
rs1464647120	1110	dbSNP
rs1173002679	1114	dbSNP
rs1165694811	1118	dbSNP
rs1165161098	1125	dbSNP
rs992990551	1131	dbSNP
rs950927825	1137	dbSNP
rs919460243	1139	dbSNP
rs1416982464	1142	dbSNP
rs972884666	1144	dbSNP
rs1340515845	1150	dbSNP
rs1253194291	1155	dbSNP
rs1340260611	1155	dbSNP
rs1473544332	1184	dbSNP
rs1277582991	1187	dbSNP
rs752060543	1199	dbSNP
rs1249478590	1204	dbSNP
rs1484560700	1205	dbSNP
rs576280979	1206	dbSNP
rs376998991	1207	dbSNP
rs1451618108	1215	dbSNP
rs1477484543	1216	dbSNP
rs1190339359	1217	dbSNP
rs1374332309	1219	dbSNP
rs537198112	1227	dbSNP
rs536132109	1231	dbSNP
rs953934666	1232	dbSNP
rs571957476	1245	dbSNP
rs1360422872	1246	dbSNP
rs998142295	1247	dbSNP
rs553530120	1250	dbSNP
rs1327118056	1251	dbSNP
rs4780766	1258	dbSNP
rs1232701987	1264	dbSNP
rs538390593	1274	dbSNP
rs1410863646	1275	dbSNP
rs1052996222	1279	dbSNP
rs571289230	1287	dbSNP
rs1280814071	1290	dbSNP
rs1000240616	1292	dbSNP
rs904614639	1295	dbSNP
rs1044387570	1320	dbSNP
rs1170307837	1321	dbSNP
rs948716671	1322	dbSNP
rs1197622919	1331	dbSNP
rs549535027	1347	dbSNP
rs917282760	1348	dbSNP
rs1455347074	1354	dbSNP
rs1174604405	1355	dbSNP
rs537804869	1362	dbSNP
rs1452181608	1368	dbSNP
rs567876714	1386	dbSNP
rs1386395750	1394	dbSNP
rs1386249883	1396	dbSNP
rs1324022529	1401	dbSNP
rs1373404748	1403	dbSNP
rs1235335427	1406	dbSNP
rs2650658	1407	dbSNP
rs1303784177	1412	dbSNP
rs1316129773	1413	dbSNP
rs41461745	1421	dbSNP
rs929611038	1421	dbSNP
rs1212501155	1423	dbSNP
rs527984685	1425	dbSNP
rs973545996	1427	dbSNP
rs1403859760	1433	dbSNP
rs941080990	1434	dbSNP
rs1417700432	1435	dbSNP
rs560694575	1438	dbSNP
rs1364854320	1455	dbSNP
rs1457860091	1458	dbSNP
rs1159667173	1464	dbSNP
rs1162826682	1472	dbSNP
rs551986953	1478	dbSNP
rs1441839593	1486	dbSNP
rs953700589	1488	dbSNP
rs1176606264	1489	dbSNP
rs1371540469	1493	dbSNP
rs1478312424	1500	dbSNP
rs1247988728	1514	dbSNP
rs1196107256	1515	dbSNP
rs1467772604	1516	dbSNP
rs1232636415	1519	dbSNP
rs1029363897	1534	dbSNP
rs1336325036	1537	dbSNP
rs1268327010	1538	dbSNP
rs977071477	1539	dbSNP
rs1250380376	1540	dbSNP
rs533280174	1541	dbSNP
rs1479481834	1544	dbSNP
rs1179268032	1553	dbSNP
rs1331603847	1556	dbSNP
rs955984699	1561	dbSNP
rs1475127051	1568	dbSNP
rs1186436002	1573	dbSNP
rs1266615932	1575	dbSNP
rs1223784065	1578	dbSNP
rs1462031025	1580	dbSNP
rs1346292763	1585	dbSNP
rs1031886891	1587	dbSNP
rs1434343520	1588	dbSNP
rs1000041846	1592	dbSNP
rs1299631296	1597	dbSNP
rs1373793688	1599	dbSNP
rs1414029017	1600	dbSNP
rs904582112	1605	dbSNP
rs1437530772	1614	dbSNP
rs2650657	1618	dbSNP
rs1357331779	1620	dbSNP
rs1233339065	1623	dbSNP
rs1294257903	1624	dbSNP
rs1305357317	1626	dbSNP
rs1023035273	1629	dbSNP
rs1013036381	1638	dbSNP
rs1485539331	1655	dbSNP
rs1386269064	1661	dbSNP
rs1475850106	1662	dbSNP
rs150846261	1664	dbSNP
rs1057174706	1665	dbSNP
rs1430457663	1666	dbSNP
rs1171413184	1677	dbSNP
rs1427121453	1679	dbSNP
rs1433834014	1695	dbSNP
rs1170332374	1699	dbSNP
rs1453199484	1700	dbSNP
rs1377142743	1701	dbSNP
rs1415354688	1703	dbSNP
rs929510253	1705	dbSNP
rs1359268546	1711	dbSNP
rs1215870812	1713	dbSNP

- PLoS pathogens, 2012

Epstein-Barr virus (EBV) is a ubiquitous human herpesvirus linked to a number of B cell cancers and lymphoproliferative disorders. During latent infection, EBV expresses 25 viral pre-microRNAs (miRNAs) and induces the expression of specific host miRNAs, such as miR-155 and miR-21, which potentially play a role in viral oncogenesis. To date, only a limited number of EBV miRNA targets have been identified; thus, the role of EBV miRNAs in viral pathogenesis and/or lymphomagenesis is not well defined. Here, we used photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) combined with deep sequencing and computational analysis to comprehensively examine the viral and cellular miRNA targetome in EBV strain B95-8-infected lymphoblastoid cell lines (LCLs). We identified 7,827 miRNA-interaction sites in 3,492 cellular 3'UTRs. 531 of these sites contained seed matches to viral miRNAs. 24 PAR-CLIP-identified miRNA:3'UTR interactions were confirmed by reporter assays. Our results reveal that EBV miRNAs predominantly target cellular transcripts during latent infection, thereby manipulating the host environment. Furthermore, targets of EBV miRNAs are involved in multiple cellular processes that are directly relevant to viral infection, including innate immunity, cell survival, and cell proliferation. Finally, we present evidence that myc-regulated host miRNAs from the miR-17/92 cluster can regulate latent viral gene expression. This comprehensive survey of the miRNA targetome in EBV-infected B cells represents a key step towards defining the functions of EBV-encoded miRNAs, and potentially, identifying novel therapeutic targets for EBV-associated malignancies.