ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gugaaugaaGAAACGUCUACUc 5' |||| ::||||| Target 5' ggtagatagCTTT-TGGATGAt 3'	889 - 909	120.00	-5.40
2	miRNA 3' gugaAUGAAGAAACGUCUACUc 5' || ||| || |||| Target 5' attaTAACACTTACCATATGAt 3'	819 - 840	118.00	-7.61
3	miRNA 3' guGAAUGA-AGAAAC--GUCUACuc 5' ||| :| |||| | || ||| Target 5' acCTTCTTATCTTGGGCCACATGtc 3'	528 - 552	110.00	-6.09

Mutant ID	Mutant Position	Mutant Source
COSN30185316	21	COSMIC
COSN22278003	42	COSMIC
COSN30454458	58	COSMIC
COSN5743329	77	COSMIC
COSN30186964	91	COSMIC
COSN31602094	107	COSMIC
COSN31491914	152	COSMIC
COSN30536962	221	COSMIC
COSN6465986	275	COSMIC
COSN4751719	405	COSMIC
COSN5375509	716	COSMIC
COSN20094937	741	COSMIC
COSN17822890	772	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs369993141	7	dbSNP
rs754040008	10	dbSNP
rs1041921525	20	dbSNP
rs201647517	24	dbSNP
rs377219130	27	dbSNP
rs750545446	39	dbSNP
rs1376634355	43	dbSNP
rs1005113451	51	dbSNP
rs1297277480	52	dbSNP
rs1417532738	56	dbSNP
rs952338890	61	dbSNP
rs947279347	62	dbSNP
rs1346683564	63	dbSNP
rs1252995530	71	dbSNP
rs1177844506	75	dbSNP
rs1488198433	78	dbSNP
rs1271128600	92	dbSNP
rs1281739835	93	dbSNP
rs1215506712	101	dbSNP
rs1335438111	103	dbSNP
rs772970035	105	dbSNP
rs576227712	110	dbSNP
rs1012039308	113	dbSNP
rs1479664551	119	dbSNP
rs894895252	120	dbSNP
rs1318352134	123	dbSNP
rs1307268484	130	dbSNP
rs595662	136	dbSNP
rs1197244690	137	dbSNP
rs1003217938	144	dbSNP
rs1428936482	149	dbSNP
rs1169233265	158	dbSNP
rs902148559	166	dbSNP
rs1042721254	171	dbSNP
rs1459177583	171	dbSNP
rs1364457805	177	dbSNP
rs1301862943	196	dbSNP
rs1342694174	196	dbSNP
rs1404854321	196	dbSNP
rs1324423255	205	dbSNP
rs1443711168	212	dbSNP
rs952985062	213	dbSNP
rs1247304324	217	dbSNP
rs76255519	220	dbSNP
rs1358840817	227	dbSNP
rs113086890	228	dbSNP
rs1443991724	234	dbSNP
rs553853037	239	dbSNP
rs1486041270	243	dbSNP
rs1185704987	245	dbSNP
rs184637262	256	dbSNP
rs1425154807	259	dbSNP
rs1004787985	262	dbSNP
rs1384026967	271	dbSNP
rs676753	275	dbSNP
rs1347449763	279	dbSNP
rs1454823515	280	dbSNP
rs558881607	294	dbSNP
rs1251187739	296	dbSNP
rs922026108	313	dbSNP
rs1027161547	330	dbSNP
rs976107424	336	dbSNP
rs1468852333	343	dbSNP
rs1013127257	349	dbSNP
rs966457556	359	dbSNP
rs1243890890	372	dbSNP
rs1203089332	377	dbSNP
rs1486733788	378	dbSNP
rs1260898790	387	dbSNP
rs1232120785	391	dbSNP
rs1258716574	396	dbSNP
rs1484126248	396	dbSNP
rs907853706	407	dbSNP
rs1242159057	414	dbSNP
rs1442456796	416	dbSNP
rs1179967559	418	dbSNP
rs1408124222	421	dbSNP
rs1345344900	422	dbSNP
rs1420177924	428	dbSNP
rs1304961772	439	dbSNP
rs894451007	447	dbSNP
rs984140093	459	dbSNP
rs1337574647	473	dbSNP
rs192472835	476	dbSNP
rs1027866443	480	dbSNP
rs1012425013	482	dbSNP
rs1380824068	486	dbSNP
rs903261183	486	dbSNP
rs775047417	487	dbSNP
rs1041839450	493	dbSNP
rs947173342	494	dbSNP
rs959495196	497	dbSNP
rs775663284	498	dbSNP
rs569843170	504	dbSNP
rs1434319602	514	dbSNP
rs1232900654	521	dbSNP
rs1003275101	526	dbSNP
rs1480042599	529	dbSNP
rs902206091	552	dbSNP
rs1406446194	563	dbSNP
rs931899352	572	dbSNP
rs1177600597	574	dbSNP
rs1042047247	575	dbSNP
rs1468411969	582	dbSNP
rs879228158	595	dbSNP
rs1331155567	601	dbSNP
rs1355149967	607	dbSNP
rs923212910	616	dbSNP
rs1347314794	619	dbSNP
rs549934931	622	dbSNP
rs749414065	628	dbSNP
rs893724658	633	dbSNP
rs148058487	634	dbSNP
rs1273271775	640	dbSNP
rs76272036	641	dbSNP
rs1201811915	649	dbSNP
rs984567723	651	dbSNP
rs779944569	654	dbSNP
rs1040461748	656	dbSNP
rs944798009	662	dbSNP
rs907902406	674	dbSNP
rs991644487	681	dbSNP
rs983471075	687	dbSNP
rs958927568	699	dbSNP
rs930601029	701	dbSNP
rs1409673822	702	dbSNP
rs1168381011	703	dbSNP
rs1262131688	703	dbSNP
rs920855515	713	dbSNP
rs576477554	718	dbSNP
rs1035940966	719	dbSNP
rs1302502184	726	dbSNP
rs756369678	732	dbSNP
rs991041804	734	dbSNP
rs112396146	745	dbSNP
rs56291538	745	dbSNP
rs1432650147	755	dbSNP
rs1484477422	757	dbSNP
rs1270614167	771	dbSNP
rs1360834457	775	dbSNP
rs774525430	777	dbSNP
rs1293298719	778	dbSNP
rs959547386	799	dbSNP
rs1359561447	800	dbSNP
rs1282099913	801	dbSNP
rs1291700373	814	dbSNP
rs1003277055	815	dbSNP
rs1450177254	815	dbSNP
rs768753366	816	dbSNP
rs1243094326	822	dbSNP
rs1210892650	826	dbSNP
rs1475194970	829	dbSNP
rs1185020596	833	dbSNP
rs1387119783	839	dbSNP
rs1340855884	842	dbSNP
rs903191335	844	dbSNP
rs1363626396	853	dbSNP
rs1402447465	853	dbSNP
rs1270072860	858	dbSNP
rs1020748610	861	dbSNP
rs547041174	865	dbSNP
rs1011678920	867	dbSNP
rs1316756065	868	dbSNP
rs1382802610	870	dbSNP
rs892947468	877	dbSNP
rs1312361213	889	dbSNP
rs1035172253	896	dbSNP
rs1207460964	898	dbSNP
rs1225915444	898	dbSNP
rs982301974	904	dbSNP
rs1446814358	913	dbSNP
rs1296728052	914	dbSNP
rs1206984588	916	dbSNP
rs1424304684	919	dbSNP
rs1245210591	920	dbSNP
rs1414628285	929	dbSNP
rs901758900	931	dbSNP
rs1040327820	937	dbSNP
rs527271908	937	dbSNP
rs1315024723	942	dbSNP
rs1471109552	948	dbSNP
rs1383919400	950	dbSNP
rs746008301	950	dbSNP
rs1395903760	954	dbSNP
rs1166271572	958	dbSNP
rs1476337967	960	dbSNP
rs752211106	960	dbSNP
rs1373631128	969	dbSNP
rs1451512090	969	dbSNP
rs940318010	976	dbSNP
rs1337040077	980	dbSNP
rs148236608	986	dbSNP
rs1280649064	992	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.