>IGFBP4|NM_001552|3'UTR
   1 GGCCTGCCAGCAGGCCAGGGACTCAGCGTCCCCTGCTACTCCTGTGCTCTGGAGGCTGCAGAGCTGACCCAGAGTGGAGT
  81 CTGAGTCTGAGTCCTGTCTCTGCCTGCGGCCCAGAAGTTTCCCTCAAATGCGCGTGTGCACGTGTGCGTGTGCGTGCGTG
 161 TGTGTGTGTTTGTGAGCATGGGTGTGCCCTTGGGGTAAGCCAGAGCCTGGGGTGTTCTCTTTGGTGTTACACAGCCCAAG
 241 AGGACTGAGACTGGCACTTAGCCCAAGAGGTCTGAGCCCTGGTGTGTTTCCAGATCGATCCTGGATTCACTCACTCACTC
 321 ATTCCTTCACTCATCCAGCCACCTAAAAACATTTACTGACCATGTACTACGTGCCAGCTCTAGTTTTCAGCCTTGGGAGG
 401 TTTTATTCTGACTTCCTCTGATTTTGGCATGTGGAGACACTCCTATAAGGAGAGTTCAAGCCTGTGGGAGTAGAAAAATC
 481 TCATTCCCAGAGTCAGAGGAGAAGAGACATGTACCTTGACCATCGTCCTTCCTCTCAAGCTAGCCAGAGGGTGGGAGCCT
 561 AAGGAAGCGTGGGGTAGCAGATGGAGTAATGGTCACGAGGTCCAGACCCACTCCCAAAGCTCAGACTTGCCAGGCTCCCT
 641 TTCTCTTCTTCCCCAGGTCCTTCCTTTAGGTCTGGTTGTTGCACCATCTGCTTGGTTGGCTGGCAGCTGAGAGCCCTGCT
 721 GTGGGAGAGCGAAGGGGGTCAAAGGAAGACTTGAAGCACAGAGGGCTAGGGAGGTGGGGTACATTTCTCTGAGCAGTCAG
 801 GGTGGGAAGAAAGAATGCAAGAGTGGACTGAATGTGCCTAATGGAGAAGACCCACGTGCTAGGGGATGAGGGGCTTCCTG
 881 GGTCCTGTTCCCTACCCCATTTGTGGTCACAGCCATGAAGTCACCGGGATGAACCTATCCTTCCAGTGGCTCGCTCCCTG
 961 TAGCTCTGCCTCCCTCTCCATATCTCCTTCCCCTACACCTCCCTCCCCACACCTCCCTACTCCCCTGGGCATCTTCTGGC
1041 TTGACTGGATGGAAGGAGACTTAGGAACCTACCAGTTGGCCATGATGTCTTTTCTTCTTTTTCTTTTTTTTAACAAAACA
1121 GAACAAAACCAAAAAATGTCCAGATGAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ucguGUCUGAACGACACUACAa 5' ||| :| || |||||| Target 5' ctacCAG-TTGGCCATGATGTc 3'	1069 - 1089	125.00	-9.80
2	miRNA 3' ucGUGUCUGAACG-ACAC-UACAa 5' |::: :| ||| |||| :||| Target 5' tgCGTGTGCGTGCGTGTGTGTGTg 3'	145 - 168	112.00	-12.40
3	miRNA 3' ucguGUCUGAACGACACUACAa 5' | ||||| || |||| | Target 5' tattCTGACTTCCTCTGATTTt 3'	404 - 425	110.00	-8.10

Mutant ID	Mutant Position	Mutant Source
COSN508729	19	COSMIC
COSN31498162	21	COSMIC
COSN30457295	33	COSMIC
COSN7166410	37	COSMIC
COSN31540802	103	COSMIC
COSN31610294	108	COSMIC
COSN31502307	109	COSMIC
COSN23444102	710	COSMIC
COSN29392761	954	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs757682541	2	dbSNP
rs201969390	3	dbSNP
rs898560874	8	dbSNP
rs750931016	11	dbSNP
rs1341105574	12	dbSNP
rs374955534	16	dbSNP
rs370718342	17	dbSNP
rs1230401206	20	dbSNP
rs1488894047	21	dbSNP
rs201400987	27	dbSNP
rs775290690	28	dbSNP
rs768221515	29	dbSNP
rs778430180	31	dbSNP
rs760656450	39	dbSNP
rs763851883	44	dbSNP
rs1424696989	45	dbSNP
rs1432421496	48	dbSNP
rs1173680385	51	dbSNP
rs546264729	60	dbSNP
rs189305237	63	dbSNP
rs181964522	76	dbSNP
rs1429342302	77	dbSNP
rs1013598040	80	dbSNP
rs1426316704	86	dbSNP
rs1286944733	88	dbSNP
rs556780529	98	dbSNP
rs1028936217	102	dbSNP
rs1023851478	108	dbSNP
rs1170846651	110	dbSNP
rs10305309	119	dbSNP
rs979997327	122	dbSNP
rs569866362	124	dbSNP
rs1244674901	132	dbSNP
rs1200226719	133	dbSNP
rs770488097	134	dbSNP
rs55998075	135	dbSNP
rs1202488811	137	dbSNP
rs1482511140	139	dbSNP
rs1360841459	140	dbSNP
rs1247408673	141	dbSNP
rs987945225	141	dbSNP
rs923033125	142	dbSNP
rs1342645095	143	dbSNP
rs1274120160	148	dbSNP
rs984441957	149	dbSNP
rs1286514016	150	dbSNP
rs567146830	150	dbSNP
rs1409337182	151	dbSNP
rs1250151148	152	dbSNP
rs1460030489	153	dbSNP
rs10305310	154	dbSNP
rs1401958261	154	dbSNP
rs558251721	155	dbSNP
rs143529403	158	dbSNP
rs1479282961	158	dbSNP
rs573219539	158	dbSNP
rs772975466	158	dbSNP
rs774983284	158	dbSNP
rs190886856	159	dbSNP
rs1440417305	161	dbSNP
rs540656217	162	dbSNP
rs371803063	167	dbSNP
rs577291607	167	dbSNP
rs182668918	182	dbSNP
rs1454130232	184	dbSNP
rs778185348	185	dbSNP
rs897695903	187	dbSNP
rs1325559809	189	dbSNP
rs930043213	201	dbSNP
rs574432438	217	dbSNP
rs35733690	220	dbSNP
rs1047141380	223	dbSNP
rs765014776	227	dbSNP
rs1227817222	235	dbSNP
rs1403532061	236	dbSNP
rs1290381849	243	dbSNP
rs544910980	251	dbSNP
rs750047877	252	dbSNP
rs1336872326	257	dbSNP
rs35794480	259	dbSNP
rs757997266	261	dbSNP
rs1335252979	263	dbSNP
rs186321441	267	dbSNP
rs545585055	270	dbSNP
rs1159108220	277	dbSNP
rs10305311	281	dbSNP
rs779647270	287	dbSNP
rs1001165794	297	dbSNP
rs1052549000	300	dbSNP
rs1321727134	301	dbSNP
rs749661906	304	dbSNP
rs1203093069	311	dbSNP
rs1187956884	313	dbSNP
rs865895373	315	dbSNP
rs1462508371	330	dbSNP
rs748675619	331	dbSNP
rs1032918134	340	dbSNP
rs1208044916	346	dbSNP
rs956863726	347	dbSNP
rs901657483	354	dbSNP
rs1286424606	360	dbSNP
rs1010152662	364	dbSNP
rs1226730769	366	dbSNP
rs1030014461	371	dbSNP
rs954475517	372	dbSNP
rs1363485761	373	dbSNP
rs756633291	378	dbSNP
rs1320396019	380	dbSNP
rs1436466614	389	dbSNP
rs1391539936	393	dbSNP
rs771151455	405	dbSNP
rs1403135732	408	dbSNP
rs910240244	409	dbSNP
rs11555390	416	dbSNP
rs1446168472	437	dbSNP
rs1006551288	439	dbSNP
rs546622920	446	dbSNP
rs1468919189	455	dbSNP
rs191228437	462	dbSNP
rs929112411	464	dbSNP
rs1219416477	472	dbSNP
rs1057003850	481	dbSNP
rs962045473	483	dbSNP
rs917976168	489	dbSNP
rs971822610	495	dbSNP
rs1803792	505	dbSNP
rs1297308855	512	dbSNP
rs1439411270	525	dbSNP
rs1296944039	526	dbSNP
rs1373336680	532	dbSNP
rs79890570	535	dbSNP
rs9520	544	dbSNP
rs1292321439	546	dbSNP
rs1045089058	550	dbSNP
rs1290654338	554	dbSNP
rs1433608857	564	dbSNP
rs1344051329	566	dbSNP
rs1348807547	569	dbSNP
rs528821435	570	dbSNP
rs749691285	572	dbSNP
rs1001284380	575	dbSNP
rs10498	584	dbSNP
rs370771399	597	dbSNP
rs1009663513	622	dbSNP
rs1030487634	628	dbSNP
rs954443072	629	dbSNP
rs1189415343	631	dbSNP
rs1250659500	632	dbSNP
rs1007303082	645	dbSNP
rs1480946583	647	dbSNP
rs1482182415	648	dbSNP
rs1184288268	649	dbSNP
rs1266455614	651	dbSNP
rs1309653432	660	dbSNP
rs1299744673	661	dbSNP
rs1219161305	662	dbSNP
rs1017680285	667	dbSNP
rs963042788	669	dbSNP
rs973478298	676	dbSNP
rs771234436	683	dbSNP
rs774565638	685	dbSNP
rs772147926	687	dbSNP
rs572704793	698	dbSNP
rs1356070824	701	dbSNP
rs149581824	715	dbSNP
rs950703151	717	dbSNP
rs11555389	723	dbSNP
rs992645657	725	dbSNP
rs568782201	727	dbSNP
rs746019785	731	dbSNP
rs949442426	732	dbSNP
rs1045141553	736	dbSNP
rs1364038149	739	dbSNP
rs1209928917	744	dbSNP
rs775616833	746	dbSNP
rs926705621	746	dbSNP
rs1284154346	754	dbSNP
rs1224762979	769	dbSNP
rs11555391	773	dbSNP
rs1348103248	784	dbSNP
rs888983339	795	dbSNP
rs1391612022	796	dbSNP
rs1370049167	797	dbSNP
rs1300844951	810	dbSNP
rs1006126513	819	dbSNP
rs1212858626	821	dbSNP
rs1406674661	827	dbSNP
rs1178523358	843	dbSNP
rs1016620407	845	dbSNP
rs1411332603	852	dbSNP
rs1294885055	855	dbSNP
rs897762686	856	dbSNP
rs936662421	857	dbSNP
rs15207	867	dbSNP
rs1181599321	871	dbSNP
rs1483796522	872	dbSNP
rs772205540	892	dbSNP
rs1207395277	893	dbSNP
rs1035328254	895	dbSNP
rs1266925539	896	dbSNP
rs1289522713	904	dbSNP
rs1490121524	905	dbSNP
rs1318320760	916	dbSNP
rs1310174059	917	dbSNP
rs1395185304	926	dbSNP
rs1223036148	927	dbSNP
rs1383272293	929	dbSNP
rs892706999	930	dbSNP
rs1009799058	932	dbSNP
rs1387888711	935	dbSNP
rs1051875982	938	dbSNP
rs1289500523	941	dbSNP
rs775625602	944	dbSNP
rs775866103	949	dbSNP
rs1007689353	950	dbSNP
rs991238864	953	dbSNP
rs947481863	954	dbSNP
rs1041862046	956	dbSNP
rs1387470379	957	dbSNP
rs903390163	960	dbSNP
rs969989339	967	dbSNP
rs979688422	973	dbSNP
rs6413494	975	dbSNP
rs183012255	976	dbSNP
rs935608654	979	dbSNP
rs9890	988	dbSNP
rs898925381	991	dbSNP
rs760575687	993	dbSNP
rs1043572	997	dbSNP
rs923266973	1006	dbSNP
rs1026427503	1007	dbSNP
rs764059586	1011	dbSNP
rs933386879	1013	dbSNP
rs992779700	1017	dbSNP
rs1050530624	1019	dbSNP
rs10305312	1030	dbSNP
rs969842399	1040	dbSNP
rs1383938223	1045	dbSNP
rs548703318	1064	dbSNP
rs1352007350	1066	dbSNP
rs1428840906	1067	dbSNP
rs1037555701	1069	dbSNP
rs979951187	1073	dbSNP
rs1425524105	1076	dbSNP
rs1288514548	1088	dbSNP
rs897702843	1089	dbSNP
rs144293341	1093	dbSNP
rs1362683189	1094	dbSNP
rs776393942	1095	dbSNP
rs565640495	1101	dbSNP
rs1035316835	1104	dbSNP
rs3211536	1104	dbSNP
rs1195966694	1112	dbSNP
rs1429702699	1116	dbSNP
rs1264645698	1120	dbSNP
rs895519168	1120	dbSNP
rs566982349	1121	dbSNP
rs1293542558	1124	dbSNP
rs1202711396	1125	dbSNP
rs1341214701	1129	dbSNP
rs534032043	1131	dbSNP
rs761119836	1131	dbSNP
rs1229514660	1142	dbSNP
rs1300655064	1143	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.