ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gaCCUCUCUC---UCUCCGAGUCa 5' ||||:|:| | ||||||| Target 5' agGGAGGGGGTTCATTGGCTCAGc 3'	216 - 239	159.00	-24.20
2	miRNA 3' gaccucUCUCUC-UCCGAGUca 5' | ||:| |||||| Target 5' ccacccATAGGGCTGGCTCAca 3'	876 - 897	127.00	-10.50
3	miRNA 3' gaccucucUCUCUCCGAGUCa 5' || |:||| ||| Target 5' ttgtgcccAG-GGGGCCCAGt 3'	118 - 137	116.00	-12.00

Mutant ID	Mutant Position	Mutant Source
COSN30498173	9	COSMIC
COSN31550109	85	COSMIC
COSN31550988	248	COSMIC
COSN30138332	264	COSMIC
COSN26649292	320	COSMIC
COSN28877307	322	COSMIC
COSN30570116	328	COSMIC
COSM9854633	381	COSMIC
COSM7518037	395	COSMIC
COSM2918619	406	COSMIC
COSM7607579	414	COSMIC
COSM7576673	442	COSMIC
COSM4819354	471	COSMIC
COSM4600533	492	COSMIC
COSN31539502	517	COSMIC
COSN30133660	535	COSMIC
COSN30138106	552	COSMIC
COSN30511179	574	COSMIC
COSN28866289	643	COSMIC
COSN17413868	795	COSMIC
COSN4765106	878	COSMIC
rs3743879	794	GWAS

Mutant ID	Mutant Position	Mutant Source
rs1336131342	2	dbSNP
rs1394043250	6	dbSNP
rs949680262	10	dbSNP
rs1172170899	18	dbSNP
rs916719438	20	dbSNP
rs1425793133	28	dbSNP
rs771290246	29	dbSNP
rs377266331	31	dbSNP
rs1477559693	34	dbSNP
rs1238536090	38	dbSNP
rs1190252126	40	dbSNP
rs376750878	41	dbSNP
rs375031338	42	dbSNP
rs1198825455	44	dbSNP
rs1319546981	48	dbSNP
rs116377490	49	dbSNP
rs1376038226	50	dbSNP
rs1435395089	59	dbSNP
rs1317798755	61	dbSNP
rs950728375	64	dbSNP
rs1468463279	65	dbSNP
rs1343651383	66	dbSNP
rs1414428903	69	dbSNP
rs1370661282	70	dbSNP
rs527708863	70	dbSNP
rs1047583640	71	dbSNP
rs560591101	72	dbSNP
rs1349306111	74	dbSNP
rs898911537	75	dbSNP
rs79822720	78	dbSNP
rs1484163792	83	dbSNP
rs1243249167	85	dbSNP
rs1448236009	87	dbSNP
rs1018244785	91	dbSNP
rs1202446664	92	dbSNP
rs943034819	92	dbSNP
rs1195319646	95	dbSNP
rs1321028900	115	dbSNP
rs1006722012	116	dbSNP
rs113827075	122	dbSNP
rs1240290845	130	dbSNP
rs934230243	131	dbSNP
rs779789227	132	dbSNP
rs1402554097	136	dbSNP
rs1319191093	137	dbSNP
rs1394082748	138	dbSNP
rs1439137278	140	dbSNP
rs566943213	141	dbSNP
rs1238886519	142	dbSNP
rs1372187564	142	dbSNP
rs1278318256	144	dbSNP
rs1305233073	145	dbSNP
rs1223894441	148	dbSNP
rs1398329063	150	dbSNP
rs1272123696	152	dbSNP
rs766186232	158	dbSNP
rs1215332482	160	dbSNP
rs966801593	167	dbSNP
rs1457167334	169	dbSNP
rs9926058	174	dbSNP
rs999703453	177	dbSNP
rs562788031	182	dbSNP
rs543101631	184	dbSNP
rs1046494297	189	dbSNP
rs959658343	197	dbSNP
rs1159275464	202	dbSNP
rs1417408883	209	dbSNP
rs1217446999	217	dbSNP
rs1356493128	219	dbSNP
rs1285829850	221	dbSNP
rs575763571	225	dbSNP
rs1339581612	233	dbSNP
rs756142692	236	dbSNP
rs1013797592	238	dbSNP
rs1448794363	243	dbSNP
rs748426105	248	dbSNP
rs1329618593	250	dbSNP
rs1465127482	251	dbSNP
rs1414667767	255	dbSNP
rs895399447	256	dbSNP
rs1472105670	267	dbSNP
rs1368457198	274	dbSNP
rs1055337088	276	dbSNP
rs560916674	280	dbSNP
rs1391211182	284	dbSNP
rs1179653854	287	dbSNP
rs942189726	290	dbSNP
rs779102377	302	dbSNP
rs1235950130	307	dbSNP
rs1207958652	308	dbSNP
rs1197646266	310	dbSNP
rs1451634727	316	dbSNP
rs749886084	317	dbSNP
rs1003901451	320	dbSNP
rs1291406781	322	dbSNP
rs1226477576	325	dbSNP
rs909408439	326	dbSNP
rs1355539184	332	dbSNP
rs1309974741	334	dbSNP
rs1242023266	337	dbSNP
rs1374415945	338	dbSNP
rs767101229	341	dbSNP
rs929390598	343	dbSNP
rs1350485684	348	dbSNP
rs1325598252	350	dbSNP
rs760838438	351	dbSNP
rs1403745488	352	dbSNP
rs1390602386	357	dbSNP
rs761339296	360	dbSNP
rs923257952	361	dbSNP
rs751213654	367	dbSNP
rs1026190330	368	dbSNP
rs1177546180	373	dbSNP
rs868781716	375	dbSNP
rs769581493	376	dbSNP
rs1218738103	380	dbSNP
rs898962094	386	dbSNP
rs1450589446	388	dbSNP
rs745592127	394	dbSNP
rs542229434	395	dbSNP
rs1351151521	396	dbSNP
rs781212878	398	dbSNP
rs757105096	399	dbSNP
rs957836762	406	dbSNP
rs1332382377	407	dbSNP
rs1276875568	410	dbSNP
rs1321012863	411	dbSNP
rs888791829	414	dbSNP
rs1032188098	415	dbSNP
rs999247593	418	dbSNP
rs966863246	421	dbSNP
rs1024764134	424	dbSNP
rs373457082	425	dbSNP
rs370212981	426	dbSNP
rs894842198	427	dbSNP
rs1477385990	430	dbSNP
rs187219600	432	dbSNP
rs1325546915	434	dbSNP
rs1195684530	435	dbSNP
rs1006446419	438	dbSNP
rs1487261948	439	dbSNP
rs763857887	441	dbSNP
rs759918872	442	dbSNP
rs139307060	444	dbSNP
rs572158496	445	dbSNP
rs114887633	446	dbSNP
rs758741011	447	dbSNP
rs938098305	450	dbSNP
rs1401989764	455	dbSNP
rs943334462	456	dbSNP
rs1288838219	457	dbSNP
rs372974584	458	dbSNP
rs766733051	459	dbSNP
rs982130919	461	dbSNP
rs1468979164	467	dbSNP
rs970665674	468	dbSNP
rs761134807	474	dbSNP
rs1476575732	475	dbSNP
rs1262354698	480	dbSNP
rs773754897	481	dbSNP
rs1484091072	485	dbSNP
rs556432276	489	dbSNP
rs1235530624	491	dbSNP
rs141970551	492	dbSNP
rs1461029622	496	dbSNP
rs1326765217	506	dbSNP
rs75586002	507	dbSNP
rs1220513626	508	dbSNP
rs1025131168	510	dbSNP
rs1295443777	517	dbSNP
rs549474512	518	dbSNP
rs535851149	519	dbSNP
rs1231718134	521	dbSNP
rs1301445344	525	dbSNP
rs773138294	526	dbSNP
rs1452449327	529	dbSNP
rs1400530332	534	dbSNP
rs75157109	535	dbSNP
rs1006390642	550	dbSNP
rs902818063	551	dbSNP
rs1042637599	558	dbSNP
rs1362660297	559	dbSNP
rs888027497	564	dbSNP
rs368091910	567	dbSNP
rs1290235026	568	dbSNP
rs1385283321	570	dbSNP
rs1427598031	571	dbSNP
rs182059870	573	dbSNP
rs945605374	574	dbSNP
rs748252038	576	dbSNP
rs779051131	580	dbSNP
rs938134541	581	dbSNP
rs550288128	583	dbSNP
rs902035569	585	dbSNP
rs926719813	593	dbSNP
rs1040837713	599	dbSNP
rs1213301985	601	dbSNP
rs768871142	606	dbSNP
rs919236068	607	dbSNP
rs889083926	609	dbSNP
rs368701831	610	dbSNP
rs936024690	623	dbSNP
rs191993608	629	dbSNP
rs978061989	630	dbSNP
rs1160733061	635	dbSNP
rs1303508830	636	dbSNP
rs945184384	637	dbSNP
rs917776035	638	dbSNP
rs1302526011	641	dbSNP
rs985975417	642	dbSNP
rs1422481611	644	dbSNP
rs1398405208	647	dbSNP
rs953301614	648	dbSNP
rs185808733	649	dbSNP
rs137924642	650	dbSNP
rs902872120	650	dbSNP
rs997198931	650	dbSNP
rs1019897135	654	dbSNP
rs1337365827	672	dbSNP
rs1009799108	677	dbSNP
rs959117829	679	dbSNP
rs1033429479	686	dbSNP
rs138797785	687	dbSNP
rs1251838128	691	dbSNP
rs529467251	693	dbSNP
rs560786251	694	dbSNP
rs1054395961	701	dbSNP
rs1002383218	704	dbSNP
rs951744329	707	dbSNP
rs1026966195	709	dbSNP
rs1308581174	719	dbSNP
rs376890530	721	dbSNP
rs527287076	722	dbSNP
rs1291645081	732	dbSNP
rs901981997	735	dbSNP
rs1229244713	746	dbSNP
rs779956213	753	dbSNP
rs949419761	754	dbSNP
rs560136441	756	dbSNP
rs1007607196	760	dbSNP
rs919287896	762	dbSNP
rs545308573	764	dbSNP
rs941980595	768	dbSNP
rs1054577188	770	dbSNP
rs1472881792	775	dbSNP
rs1224177496	779	dbSNP
rs1417063021	793	dbSNP
rs3743879	794	dbSNP
rs903206343	796	dbSNP
rs371528613	797	dbSNP
rs1042674614	800	dbSNP
rs1434169478	802	dbSNP
rs945325938	813	dbSNP
rs181252644	814	dbSNP
rs1329300795	815	dbSNP
rs1019948459	821	dbSNP
rs1056224950	822	dbSNP
rs1360265237	823	dbSNP
rs937881518	831	dbSNP
rs926362922	832	dbSNP
rs1207833994	843	dbSNP
rs984530452	845	dbSNP
rs957225070	852	dbSNP
rs544389323	854	dbSNP
rs3743878	855	dbSNP
rs1469835724	857	dbSNP
rs114569898	858	dbSNP
rs1486710706	858	dbSNP
rs756775677	865	dbSNP
rs534347287	866	dbSNP
rs1452427528	871	dbSNP
rs1175454876	876	dbSNP
rs763769124	879	dbSNP
rs1007723128	880	dbSNP
rs953554039	883	dbSNP
rs1317871650	884	dbSNP
rs1181523772	885	dbSNP
rs1436482186	887	dbSNP
rs1258495683	891	dbSNP
rs1321727775	895	dbSNP
rs897909119	897	dbSNP
rs1232675028	899	dbSNP
rs1277148872	901	dbSNP
rs566740941	903	dbSNP
rs1000299354	906	dbSNP
rs942045433	913	dbSNP
rs76735572	916	dbSNP
rs758185816	917	dbSNP
rs1221538883	918	dbSNP
rs1352743609	924	dbSNP
rs1252084124	926	dbSNP
rs931880541	928	dbSNP
rs1195384133	931	dbSNP
rs539720134	932	dbSNP
rs144964434	939	dbSNP
rs1280121379	941	dbSNP
rs754133829	946	dbSNP
rs1056336327	952	dbSNP
rs923134567	955	dbSNP
rs1458960420	957	dbSNP
rs1238031139	958	dbSNP
rs1160207563	962	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.