>C21orf2|NM_004928|3'UTR
   1 CCGCAGGACCTGAACGCCGCTCCAGCCTCCACGGGGACCCCAGCGTCTTCCCCAGCCCCCGGGAGCTGGAGGGTGGCTGC
  81 CATGGCCGCAGCCCCGGCCCCACACAAAAGCCTCCCCGGTTTGCCACATCGGCCGAGGGCAGGAGTGGGTGTTAGGTACT
 161 GGCTAACCGGGGCGGTGGAGATGCCTGTCTACACCAGTCCTGTCCCCAGGACTCCCCTTCTGTGGTCTGGAGGTTCTAGG
 241 CTGGCCTGGGCTCTTAAAGGGAGGATTTTGCAGGCTGTCCTCCCTAATAAAAGATTTTCCCAAGGTTGATCTGGAGGTGA
 321 CGTTTCCCAAGGCATGGTTGTGACAGTCTTCCTGAAAGCAAGGGCCGTTTCTCCACAGAATGAGGAGGTCTTCACGGATG
 401 GCTTTGCCGATTCCAGCCCTTGGTCCTTGGATAGATTTCTGTTGGGCAAGGGAGACTTCGAGAATGCTGGCACCCATAGC
 481 GACATCTGCCCTGAGCTGCTCAGCAGGCAGGCAGCAGCCTCCCGCACCCATGGGAGAGAGTTTTGTTTTCTTGGCCGGGC
 561 TGGGCAGGTGCGCCTTCCTTTCTCTCTCCTGTGAAGAACTGCAGGAGGGCCCTCAGCTGTGAGGTTGTGGATGAACAGGC
 641 CTGTTCGCCCTGGGGTCCGGGCCTGGCACAGGAAGCAGCTAGACTAGGGGAGTCCTTGGAGCATCTGAGAGGGGTTTTCT
 721 TTCCTCTGGGAAGAGTCGCAAGTCTTATGAGGATGCCACAATCTGGGCAGTGACCCGTGGCCCTGGGGACCTTCCTAGTG
 801 CCCCCCAAAACCAAGGAAGCATTCACGTGAGATGGGGAGTCAGCCTTCCAGCTGGTGTGTAGGAAAGCCAGGTCCCTGGG
 881 CCCTTGTCCCATGTGGGGTTGAGATCCAGATCTCCATGAGATATTCCCATCCTCCGCCGAGCGGTGATGCGTGACCGTGT
 961 GTGCAGGCCGCTGTTCTCCCAAGCTCGGGGCCATGCCGTGCCACCGTCACCAGAGCCAGCTGCAGCACTGGGGCAGCCAC
1041 TGTCGCCGGACTTGGGGAAGCCCAGGGTGAAGACAGTCACTCATCCGTGCAAGCTCTCCAGAAGGGATGCAAGCTCTCCA
1121 GAAGGGGTGTGATCTCTGAGCAGTGGGGAGTGGAGTCACCACTCGGGACATAGAGGGTGGACAGTTCAGGCCTGTGTCTG
1201 CCTCCTTGGGACTGTGGAGTGGGTGCCCTCAGTAAAGCGCTTTGTTGGAATGGTAAAAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' uucacccGACCCUAGGCCCGac 5' |||||:||||||| Target 5' gttcgccCTGGGGTCCGGGCct 3'	643 - 664	151.00	-28.10
2	miRNA 3' uuCACCCGACCCUAGGCCCGAc 5' || || || ||||||| Target 5' ttGTTTTCTTGG--CCGGGCTg 3'	543 - 562	148.00	-19.50
3	miRNA 3' uucACCCGACCCUAGGCCCGAc 5' | |||||| |:||||| Target 5' ttcTAGGCTGG--CCTGGGCTc 3'	234 - 253	143.00	-21.50

Mutant ID	Mutant Position	Mutant Source
COSN30138372	3	COSMIC
COSN30520362	5	COSMIC
COSN30542060	16	COSMIC
COSN23015622	80	COSMIC
COSN20807534	1198	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1356176176	2	dbSNP
rs772736437	3	dbSNP
rs1398011270	4	dbSNP
rs978666131	6	dbSNP
rs1240412487	7	dbSNP
rs965666720	9	dbSNP
rs530847500	15	dbSNP
rs369493459	16	dbSNP
rs773942752	18	dbSNP
rs144775318	19	dbSNP
rs746389197	21	dbSNP
rs1172882851	23	dbSNP
rs950971137	25	dbSNP
rs1163744321	27	dbSNP
rs111631573	30	dbSNP
rs1326197578	31	dbSNP
rs377441507	32	dbSNP
rs9306098	33	dbSNP
rs1044495219	34	dbSNP
rs777832348	36	dbSNP
rs1217189291	37	dbSNP
rs368976859	38	dbSNP
rs752683561	39	dbSNP
rs976822584	40	dbSNP
rs1014370523	44	dbSNP
rs376322324	45	dbSNP
rs754854788	47	dbSNP
rs753781658	49	dbSNP
rs777514004	50	dbSNP
rs934660513	60	dbSNP
rs1214778537	61	dbSNP
rs923846932	62	dbSNP
rs528429254	66	dbSNP
rs763468317	68	dbSNP
rs561344830	69	dbSNP
rs1235468109	71	dbSNP
rs888678813	72	dbSNP
rs149386620	85	dbSNP
rs994310278	87	dbSNP
rs1469775617	88	dbSNP
rs1216227306	95	dbSNP
rs896006307	96	dbSNP
rs1475812043	100	dbSNP
rs1056865687	103	dbSNP
rs921792952	107	dbSNP
rs1477673545	111	dbSNP
rs974453462	117	dbSNP
rs1323543562	118	dbSNP
rs1397246955	118	dbSNP
rs575555871	118	dbSNP
rs1348767878	122	dbSNP
rs911651292	124	dbSNP
rs1430874331	127	dbSNP
rs1359456130	130	dbSNP
rs1217727222	131	dbSNP
rs115529052	135	dbSNP
rs950440122	146	dbSNP
rs1027896877	147	dbSNP
rs913137201	149	dbSNP
rs1447616985	151	dbSNP
rs995126306	155	dbSNP
rs1240519728	168	dbSNP
rs1488090949	169	dbSNP
rs1189007307	173	dbSNP
rs545183540	174	dbSNP
rs923110058	175	dbSNP
rs1163151761	177	dbSNP
rs1302561642	178	dbSNP
rs1400732751	183	dbSNP
rs756662341	185	dbSNP
rs974582417	187	dbSNP
rs1358160158	191	dbSNP
rs1361385310	192	dbSNP
rs753202185	197	dbSNP
rs1329961328	200	dbSNP
rs1023167787	207	dbSNP
rs1014444075	209	dbSNP
rs1313164357	210	dbSNP
rs964474372	217	dbSNP
rs895860715	218	dbSNP
rs1056689	220	dbSNP
rs1465590302	225	dbSNP
rs577858726	233	dbSNP
rs1056687	236	dbSNP
rs1351332043	251	dbSNP
rs1225475801	263	dbSNP
rs1172929913	264	dbSNP
rs1353145261	273	dbSNP
rs998860290	277	dbSNP
rs552792461	278	dbSNP
rs1413432352	284	dbSNP
rs534722715	286	dbSNP
rs1025880256	288	dbSNP
rs372930994	294	dbSNP
rs1157405983	297	dbSNP
rs1377922886	306	dbSNP
rs946666467	307	dbSNP
rs181149547	321	dbSNP
rs768002305	322	dbSNP
rs1038822367	334	dbSNP
rs944543095	340	dbSNP
rs1394012983	341	dbSNP
rs1035851733	342	dbSNP
rs573366125	346	dbSNP
rs911609247	351	dbSNP
rs983639203	365	dbSNP
rs928982772	366	dbSNP
rs543710749	367	dbSNP
rs374967367	371	dbSNP
rs1282675654	375	dbSNP
rs73907170	377	dbSNP
rs1023241528	384	dbSNP
rs992963135	386	dbSNP
rs73907169	388	dbSNP
rs1180247601	389	dbSNP
rs1439977566	389	dbSNP
rs1229219584	394	dbSNP
rs569949897	395	dbSNP
rs999369920	396	dbSNP
rs1307562636	406	dbSNP
rs904511047	408	dbSNP
rs1021554365	409	dbSNP
rs774845265	418	dbSNP
rs766675596	422	dbSNP
rs1396910553	426	dbSNP
rs551740814	430	dbSNP
rs1411487094	431	dbSNP
rs911270496	441	dbSNP
rs1441651478	442	dbSNP
rs1333444327	450	dbSNP
rs996823766	452	dbSNP
rs533156525	459	dbSNP
rs139131768	464	dbSNP
rs1271033488	476	dbSNP
rs546739223	477	dbSNP
rs773374302	478	dbSNP
rs890323245	481	dbSNP
rs1469311133	483	dbSNP
rs960274685	493	dbSNP
rs1254323437	495	dbSNP
rs1047453932	497	dbSNP
rs1373327000	499	dbSNP
rs1035966782	502	dbSNP
rs1176558222	503	dbSNP
rs528601860	504	dbSNP
rs929075520	508	dbSNP
rs1438936170	510	dbSNP
rs920369924	519	dbSNP
rs1476244640	523	dbSNP
rs973041664	524	dbSNP
rs1399372461	527	dbSNP
rs1461890848	528	dbSNP
rs561098091	529	dbSNP
rs1021769233	531	dbSNP
rs1179956654	537	dbSNP
rs1011327315	539	dbSNP
rs369516551	541	dbSNP
rs891427444	541	dbSNP
rs542989343	543	dbSNP
rs1052717893	548	dbSNP
rs1217111508	550	dbSNP
rs916157772	553	dbSNP
rs1277957022	555	dbSNP
rs769714219	556	dbSNP
rs1235652985	557	dbSNP
rs993120284	558	dbSNP
rs1038966593	560	dbSNP
rs1323161346	562	dbSNP
rs960218167	571	dbSNP
rs530851137	572	dbSNP
rs563632372	580	dbSNP
rs1191147727	582	dbSNP
rs1218310754	584	dbSNP
rs1378282239	584	dbSNP
rs1475441363	585	dbSNP
rs1166958328	589	dbSNP
rs1312163956	589	dbSNP
rs1457419875	593	dbSNP
rs1159220971	602	dbSNP
rs1385119331	604	dbSNP
rs977633395	605	dbSNP
rs1366946326	608	dbSNP
rs545343167	609	dbSNP
rs1438800230	613	dbSNP
rs1021670029	619	dbSNP
rs115857899	621	dbSNP
rs553545644	623	dbSNP
rs60469495	625	dbSNP
rs1260800272	626	dbSNP
rs1017471235	627	dbSNP
rs1262070945	635	dbSNP
rs573655806	637	dbSNP
rs1253910241	639	dbSNP
rs534691618	643	dbSNP
rs980399050	646	dbSNP
rs555204989	647	dbSNP
rs1376319982	652	dbSNP
rs1047990563	654	dbSNP
rs1191274942	655	dbSNP
rs774221821	658	dbSNP
rs898875889	659	dbSNP
rs537034772	662	dbSNP
rs1216319870	664	dbSNP
rs1378436118	673	dbSNP
rs1237352405	674	dbSNP
rs1284793302	678	dbSNP
rs573994334	680	dbSNP
rs1354914293	684	dbSNP
rs1348158666	689	dbSNP
rs1012198284	690	dbSNP
rs759959014	691	dbSNP
rs1031411862	693	dbSNP
rs1037489627	695	dbSNP
rs1239971921	696	dbSNP
rs73907168	696	dbSNP
rs915604575	698	dbSNP
rs1312132141	699	dbSNP
rs1301986347	707	dbSNP
rs1435126948	707	dbSNP
rs901537589	709	dbSNP
rs1017901412	712	dbSNP
rs1462852096	712	dbSNP
rs1300376052	719	dbSNP
rs1221080684	722	dbSNP
rs1338694934	723	dbSNP
rs558035641	725	dbSNP
rs938906018	730	dbSNP
rs1220572698	733	dbSNP
rs1298787645	736	dbSNP
rs924909322	737	dbSNP
rs1400876654	738	dbSNP
rs116737357	739	dbSNP
rs1259851283	743	dbSNP
rs745710040	746	dbSNP
rs887727255	757	dbSNP
rs968924686	758	dbSNP
rs138214126	759	dbSNP
rs975510784	765	dbSNP
rs1424763161	774	dbSNP
rs963996813	776	dbSNP
rs1176141287	777	dbSNP
rs150368688	780	dbSNP
rs753477607	783	dbSNP
rs1327218386	784	dbSNP
rs550953519	790	dbSNP
rs1192425656	791	dbSNP
rs1488423279	794	dbSNP
rs1438023882	798	dbSNP
rs535319791	807	dbSNP
rs1199094984	810	dbSNP
rs1483205550	811	dbSNP
rs954764615	817	dbSNP
rs1026234123	818	dbSNP
rs1235486838	820	dbSNP
rs1316103747	822	dbSNP
rs1277671605	824	dbSNP
rs1279856214	826	dbSNP
rs1315901099	827	dbSNP
rs1217913664	828	dbSNP
rs938640612	834	dbSNP
rs993729085	839	dbSNP
rs1219495326	845	dbSNP
rs140378076	849	dbSNP
rs1219420908	854	dbSNP
rs899037207	857	dbSNP
rs948990402	863	dbSNP
rs778538755	866	dbSNP
rs1012698921	867	dbSNP
rs1261451237	868	dbSNP
rs1477720380	875	dbSNP
rs894241325	878	dbSNP
rs1166232122	880	dbSNP
rs1057175542	883	dbSNP
rs770644907	886	dbSNP
rs956221986	889	dbSNP
rs1443481081	890	dbSNP
rs1031360838	892	dbSNP
rs1401388120	896	dbSNP
rs975808365	901	dbSNP
rs376933593	913	dbSNP
rs924821412	920	dbSNP
rs1303402348	922	dbSNP
rs748839544	929	dbSNP
rs1293780621	932	dbSNP
rs116171340	935	dbSNP
rs914767520	936	dbSNP
rs372328814	938	dbSNP
rs964069942	939	dbSNP
rs79299307	940	dbSNP
rs188380965	942	dbSNP
rs987168382	943	dbSNP
rs1189105861	944	dbSNP
rs951421818	950	dbSNP
rs1026646930	951	dbSNP
rs1206070113	956	dbSNP
rs907314583	957	dbSNP
rs993451356	958	dbSNP
rs1334558789	960	dbSNP
rs1044385135	961	dbSNP
rs781779982	962	dbSNP
rs914802147	964	dbSNP
rs990381585	966	dbSNP
rs1242430955	969	dbSNP
rs1016075378	970	dbSNP
rs73907166	976	dbSNP
rs894189053	983	dbSNP
rs1281155219	985	dbSNP
rs368652516	986	dbSNP
rs1056888281	987	dbSNP
rs570156386	989	dbSNP
rs751997749	997	dbSNP
rs1042345580	998	dbSNP
rs947671332	1005	dbSNP
rs893404743	1006	dbSNP
rs1438680048	1011	dbSNP
rs1172848958	1013	dbSNP
rs1404045336	1028	dbSNP
rs1412573503	1030	dbSNP
rs1454450375	1031	dbSNP
rs1039825009	1032	dbSNP
rs1161338769	1033	dbSNP
rs1400954062	1042	dbSNP
rs1449000028	1042	dbSNP
rs1307177420	1044	dbSNP
rs533465673	1045	dbSNP
rs912604490	1047	dbSNP
rs766613870	1048	dbSNP
rs993416019	1057	dbSNP
rs961839021	1066	dbSNP
rs1330082674	1067	dbSNP
rs929948259	1072	dbSNP
rs918623795	1074	dbSNP
rs1034843882	1077	dbSNP
rs73907165	1079	dbSNP
rs907272483	1080	dbSNP
rs1457115966	1081	dbSNP
rs1044887805	1085	dbSNP
rs1476884277	1086	dbSNP
rs750543276	1087	dbSNP
rs963266143	1093	dbSNP
rs1438379034	1099	dbSNP
rs1329289113	1102	dbSNP
rs1399604321	1107	dbSNP
rs1012897782	1111	dbSNP
rs183595358	1112	dbSNP
rs1179314350	1117	dbSNP
rs181944855	1125	dbSNP
rs1051107383	1127	dbSNP
rs1159879943	1127	dbSNP
rs1320505619	1130	dbSNP
rs1217301861	1133	dbSNP
rs1287857051	1134	dbSNP
rs958560523	1139	dbSNP
rs1035847735	1142	dbSNP
rs1338117252	1147	dbSNP
rs1209925006	1148	dbSNP
rs1268933861	1152	dbSNP
rs190790356	1156	dbSNP
rs1002651721	1162	dbSNP
rs924907411	1164	dbSNP
rs185538642	1165	dbSNP
rs1019921347	1167	dbSNP
rs1292144169	1170	dbSNP
rs1422857975	1171	dbSNP
rs1458424374	1173	dbSNP
rs77610661	1175	dbSNP
rs893351123	1176	dbSNP
rs1351399574	1180	dbSNP
rs1056725	1181	dbSNP
rs1388753608	1185	dbSNP
rs986301379	1190	dbSNP
rs951706110	1195	dbSNP
rs1342725853	1196	dbSNP
rs1398563889	1198	dbSNP
rs372506033	1200	dbSNP
rs539717393	1205	dbSNP
rs1266681053	1206	dbSNP
rs1353710882	1207	dbSNP
rs572283576	1217	dbSNP
rs942864421	1220	dbSNP
rs776668740	1221	dbSNP
rs1262303684	1223	dbSNP
rs1051601801	1224	dbSNP
rs1366761161	1225	dbSNP
rs1457496517	1237	dbSNP
rs930046951	1238	dbSNP
rs553818195	1239	dbSNP
rs15145	1247	dbSNP
rs193181783	1251	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.