>NKD2|NM_033120|3'UTR
   1 CGCCACTGCCAAGCACACCTCGCTCCCAGCACACCACGGCCCGCGACCTCAGGGCAGGGAGCAGAGCAGCTGCCGGCTGT
  81 GTGCCCATGGGGAGCCCAGCCCCCACCCCCCACCTCCGACAGCAAACAGCAACTGACTGCAGGTGCTGGCATGATGGAGG
 161 TGGTGCACCTTGGACACGTGGACAAGGCCCAGGCGCCCTCTGCTCTTCTGCCCTCGATGCCACATGGCGGTGAACACATC
 241 TGAAGCCACTATGTTTCCTGGCTCTAAGGCTCGTCTGTGTAACCCATAAAACCTGCTTTGATTCCAAAATGAGGCCCTGG
 321 AGTGCGCAAGGAGTGCCCGGATGCTTGGGGTGGGTGTTCCTCCCGGGGCTTCAAGGGGTGACTGCTGTAGGCTGTCCCAG
 401 TGCGAGGCCGGGAGCGAATGGAAAAGCTGAGGCTTTGCC

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' accuaacaaagaaaACGGCAc 5' |||:|| Target 5' cttcaaggggtgacTGCTGTa 3'	369 - 389	104.00	-6.60
2	miRNA 3' accuaacaaagaaaACGGCac 5' ||||| Target 5' gggagcagagcagcTGCCGgc 3'	57 - 77	100.00	-10.85
3	miRNA 3' accuaacaaAGAAAACGGCAc 5' |||| |||| | Target 5' gccctctgcTCTTCTGCCCTc 3'	195 - 215	96.00	-5.42

Mutant ID	Mutant Position	Mutant Source
COSM5498899	3	COSMIC
COSM5515033	23	COSMIC
COSM7234593	38	COSMIC
COSM4159344	39	COSMIC
COSM9226148	63	COSMIC
COSM9009063	74	COSMIC
COSM1619293	100	COSMIC
COSM2990141	112	COSMIC
COSM9110508	112	COSMIC
COSM2990140	115	COSMIC
COSM9004929	143	COSMIC
COSM4003250	179	COSMIC
COSM8843653	188	COSMIC
COSM6203179	196	COSMIC
COSM8537838	196	COSMIC
COSM9440683	198	COSMIC
COSM7674631	201	COSMIC
COSM2990152	229	COSMIC
COSM8899525	230	COSMIC
COSN26435282	281	COSMIC
COSN24582721	411	COSMIC
COSN9248880	421	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs565925360	1	dbSNP
rs536787443	2	dbSNP
rs143147967	3	dbSNP
rs1310501514	5	dbSNP
rs973352004	7	dbSNP
rs1235571679	10	dbSNP
rs1210849384	11	dbSNP
rs1488320118	14	dbSNP
rs1287614813	15	dbSNP
rs1263957201	17	dbSNP
rs573800761	19	dbSNP
rs768461323	20	dbSNP
rs776551587	21	dbSNP
rs747904708	22	dbSNP
rs887884762	23	dbSNP
rs777124338	24	dbSNP
rs1434376511	25	dbSNP
rs774739096	26	dbSNP
rs1422405691	28	dbSNP
rs147500743	31	dbSNP
rs1168892164	34	dbSNP
rs1356635943	35	dbSNP
rs1451727738	35	dbSNP
rs386684356	37	dbSNP
rs117476328	38	dbSNP
rs3889678	39	dbSNP
rs1293432973	40	dbSNP
rs1366162970	42	dbSNP
rs373815595	43	dbSNP
rs187224672	44	dbSNP
rs762186974	45	dbSNP
rs1217037591	46	dbSNP
rs762574142	47	dbSNP
rs1485273853	49	dbSNP
rs1265626673	50	dbSNP
rs1307850275	56	dbSNP
rs1220619616	59	dbSNP
rs1263580018	60	dbSNP
rs977223411	61	dbSNP
rs912356870	63	dbSNP
rs1199433898	65	dbSNP
rs943881853	68	dbSNP
rs1223365953	73	dbSNP
rs532719389	75	dbSNP
rs139370266	76	dbSNP
rs1342223546	79	dbSNP
rs1195379592	86	dbSNP
rs1419847920	88	dbSNP
rs1276241862	89	dbSNP
rs891632450	92	dbSNP
rs1410848845	95	dbSNP
rs998470055	99	dbSNP
rs1010797406	100	dbSNP
rs3840988	100	dbSNP
rs1348601382	101	dbSNP
rs779669812	102	dbSNP
rs1164576824	105	dbSNP
rs755214207	105	dbSNP
rs1466486444	106	dbSNP
rs931982936	107	dbSNP
rs1065335	108	dbSNP
rs527272705	109	dbSNP
rs1274055448	110	dbSNP
rs1309476174	111	dbSNP
rs754448179	112	dbSNP
rs879076311	113	dbSNP
rs542731833	114	dbSNP
rs114167981	115	dbSNP
rs200932190	116	dbSNP
rs531798393	118	dbSNP
rs549915325	119	dbSNP
rs777682187	120	dbSNP
rs1285292585	123	dbSNP
rs1487009378	124	dbSNP
rs1218210564	127	dbSNP
rs372411692	131	dbSNP
rs1368983081	137	dbSNP
rs1472274843	146	dbSNP
rs1034590974	153	dbSNP
rs1181583134	155	dbSNP
rs1402961713	156	dbSNP
rs1412081903	159	dbSNP
rs1461972043	161	dbSNP
rs1377689155	163	dbSNP
rs746143253	166	dbSNP
rs1164762103	169	dbSNP
rs1360506129	170	dbSNP
rs1417907286	172	dbSNP
rs200189281	173	dbSNP
rs1345948803	174	dbSNP
rs963153881	177	dbSNP
rs761285847	178	dbSNP
rs61744596	179	dbSNP
rs1021286292	181	dbSNP
rs967021567	182	dbSNP
rs1246504453	184	dbSNP
rs1257702455	185	dbSNP
rs767401283	191	dbSNP
rs1351457729	193	dbSNP
rs370727382	195	dbSNP
rs547757661	196	dbSNP
rs1364361751	197	dbSNP
rs975675459	199	dbSNP
rs566092734	202	dbSNP
rs150049668	203	dbSNP
rs1403457016	207	dbSNP
rs916865348	209	dbSNP
rs114282654	213	dbSNP
rs777033952	216	dbSNP
rs868433230	217	dbSNP
rs940678495	218	dbSNP
rs1160304116	221	dbSNP
rs762275096	222	dbSNP
rs1442283699	223	dbSNP
rs988579709	224	dbSNP
rs570122092	225	dbSNP
rs1174189426	227	dbSNP
rs538038930	229	dbSNP
rs1036417103	230	dbSNP
rs1422446882	234	dbSNP
rs1330452666	235	dbSNP
rs1374496902	237	dbSNP
rs933838343	238	dbSNP
rs1480514077	240	dbSNP
rs1444300428	241	dbSNP
rs1280134894	243	dbSNP
rs1050957274	244	dbSNP
rs750770030	247	dbSNP
rs764749305	250	dbSNP
rs907302375	252	dbSNP
rs889739941	254	dbSNP
rs1217021650	260	dbSNP
rs1280264095	263	dbSNP
rs1323855396	266	dbSNP
rs1238718615	270	dbSNP
rs556440775	272	dbSNP
rs376402377	273	dbSNP
rs374099714	274	dbSNP
rs1397875624	276	dbSNP
rs898499213	278	dbSNP
rs894726250	284	dbSNP
rs1298204244	287	dbSNP
rs1160728301	294	dbSNP
rs1401951903	295	dbSNP
rs1012204579	300	dbSNP
rs1021841358	307	dbSNP
rs902828009	316	dbSNP
rs1157671121	319	dbSNP
rs553756764	326	dbSNP
rs755101678	327	dbSNP
rs1185698827	336	dbSNP
rs965531901	339	dbSNP
rs753721076	340	dbSNP
rs896636654	346	dbSNP
rs1028613769	349	dbSNP
rs1282374575	354	dbSNP
rs1204817693	357	dbSNP
rs572025422	365	dbSNP
rs542219025	366	dbSNP
rs1231853752	369	dbSNP
rs969660820	370	dbSNP
rs1311074394	387	dbSNP
rs1354145015	392	dbSNP
rs1432243192	393	dbSNP
rs1324217876	401	dbSNP
rs144397616	404	dbSNP
rs940646459	405	dbSNP
rs10474865	410	dbSNP
rs777711703	411	dbSNP
rs543105454	415	dbSNP
rs1456543626	416	dbSNP
rs192098829	417	dbSNP
rs913010152	419	dbSNP
rs1452336051	423	dbSNP
rs112130637	438	dbSNP
rs1255141275	439	dbSNP
rs1212160503	447	dbSNP
rs1055887318	449	dbSNP
rs367812894	450	dbSNP
rs933807299	457	dbSNP
rs1239021931	466	dbSNP
rs1454062392	467	dbSNP
rs1171210965	468	dbSNP
rs1336870359	470	dbSNP
rs1269151629	471	dbSNP
rs1436573625	471	dbSNP
rs894602492	473	dbSNP
rs377307131	476	dbSNP
rs1043266414	477	dbSNP
rs903468954	478	dbSNP
rs1408194325	479	dbSNP
rs183873875	480	dbSNP
rs1019273699	481	dbSNP
rs1397077978	483	dbSNP
rs1192033431	485	dbSNP
rs1468303424	485	dbSNP
rs898464083	489	dbSNP
rs771038653	490	dbSNP
rs930024040	494	dbSNP
rs148808822	499	dbSNP
rs896611340	505	dbSNP
rs1219252648	513	dbSNP
rs1233172120	514	dbSNP
rs758541879	514	dbSNP
rs1028078545	515	dbSNP
rs60241368	516	dbSNP
rs983970655	517	dbSNP
rs1334785639	519	dbSNP
rs1015499588	521	dbSNP
rs1435385690	522	dbSNP
rs961320359	524	dbSNP
rs745759618	525	dbSNP
rs1454054000	527	dbSNP
rs972058931	532	dbSNP
rs1179257982	534	dbSNP
rs1197072963	535	dbSNP
rs756103929	548	dbSNP
rs143988606	550	dbSNP
rs1212272744	551	dbSNP
rs779662140	552	dbSNP
rs938704627	558	dbSNP
rs776153899	561	dbSNP
rs916016169	563	dbSNP
rs1209701782	565	dbSNP
rs188601576	570	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.