>TMEM81|NM_203376|3'UTR
   1 CAGCTTCAAGAACTTAACAGCCTTGCTCCTGAAGAACTGGCTGCCCAGGAAGCCAAGCTAGCTTTTTAGGGGAGTGTTCC
  81 AGCTGCTGGTAGTGGATCAGCTTAGAGGGAACACTCCCACAGCCAAAAGAATGAGTGGGAGAAATGGAGGGGACAATCTC
 161 CTGGGAGCTATGCGCAGTAACCTAACTTCCTTATGTCCCATGGATCTCTTCCTGATCTTCCCTGCCCATTGGGTACCCAG
 241 GAAACTGCAAGCATTGCCTGTGTTCCTGGGAAGAGTTCTAAGAAGCTTGCATTCATTTTCTACCCTTTATGACTTGGATG
 321 CCTCCCCACCTCCATTTCCCCTCTTCTGAGCTGTGTATTCATGTAGAGGGATGTATTCAGCCTTTTTAGTGAACATTTTT
 401 TTTCAATAAAAGTAATTCACAGTAAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gaCCCUCAU-------ACCCCCGUCCCu 5' ||||||: || ||:|| | Target 5' agGGGAGTGTTCCAGCTGCTGGTAGTGg 3'	68 - 95	107.00	-20.21
2	miRNA 3' gaCCCUC-AUACCCCCGUCCCu 5' ||||| || || :||| Target 5' gtGGGAGAAAT---GGAGGGGa 3'	135 - 153	104.00	-19.70
3	miRNA 3' gaCCCUC-AUACCCCCGUCccu 5' ||||| |||| |||| Target 5' ctGGGAGCTATGC--GCAGtaa 3'	161 - 180	98.00	-16.92

Mutant ID	Mutant Position	Mutant Source
COSN511200	1	COSMIC
COSN30139601	14	COSMIC
COSN30614841	14	COSMIC
COSN30469337	28	COSMIC
COSN26999131	43	COSMIC
COSN30462616	44	COSMIC
COSN30160387	45	COSMIC
COSN26999130	63	COSMIC
COSN31525460	71	COSMIC
COSN7983674	89	COSMIC
COSN30135303	129	COSMIC
COSN31599647	146	COSMIC
COSN30527518	166	COSMIC
COSN32065138	238	COSMIC
COSN7199137	347	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs199727080	10	dbSNP
rs1433013101	20	dbSNP
rs151238335	21	dbSNP
rs1362663405	26	dbSNP
rs773391999	28	dbSNP
rs772089533	29	dbSNP
rs1329505795	35	dbSNP
rs762933245	39	dbSNP
rs1173897147	46	dbSNP
rs940279710	52	dbSNP
rs1467109013	54	dbSNP
rs1291782969	56	dbSNP
rs887346624	72	dbSNP
rs1036000623	80	dbSNP
rs1370070023	81	dbSNP
rs772678796	83	dbSNP
rs906189587	97	dbSNP
rs1326570314	101	dbSNP
rs931433577	110	dbSNP
rs199577492	115	dbSNP
rs185457648	126	dbSNP
rs1386607196	130	dbSNP
rs1217635811	143	dbSNP
rs947956938	147	dbSNP
rs372994426	151	dbSNP
rs991504131	152	dbSNP
rs938700681	159	dbSNP
rs1401463978	162	dbSNP
rs1264255045	165	dbSNP
rs1488454735	169	dbSNP
rs539551661	170	dbSNP
rs557171706	173	dbSNP
rs989677492	174	dbSNP
rs1193288968	183	dbSNP
rs1424422297	189	dbSNP
rs1254173330	193	dbSNP
rs1162571477	194	dbSNP
rs1349179085	199	dbSNP
rs1458373798	200	dbSNP
rs538069347	208	dbSNP
rs977378554	211	dbSNP
rs966684632	216	dbSNP
rs192900771	220	dbSNP
rs1398991122	222	dbSNP
rs1021290173	223	dbSNP
rs1278513532	225	dbSNP
rs772588576	228	dbSNP
rs748595389	229	dbSNP
rs1245716406	234	dbSNP
rs924720586	252	dbSNP
rs1226073254	260	dbSNP
rs142284266	261	dbSNP
rs1214479642	263	dbSNP
rs958078643	267	dbSNP
rs977487849	268	dbSNP
rs1294386843	281	dbSNP
rs1487551577	286	dbSNP
rs535379914	288	dbSNP
rs1216124652	290	dbSNP
rs536113807	292	dbSNP
rs1019357403	300	dbSNP
rs996574884	304	dbSNP
rs900905203	314	dbSNP
rs1424263394	324	dbSNP
rs1346952184	329	dbSNP
rs1304038114	331	dbSNP
rs546199250	346	dbSNP
rs1378243055	347	dbSNP
rs1418926211	351	dbSNP
rs1298609367	353	dbSNP
rs1362023294	365	dbSNP
rs1362981918	372	dbSNP
rs1019320479	375	dbSNP
rs1379339705	387	dbSNP
rs12028064	389	dbSNP
rs1317826805	395	dbSNP
rs45462698	396	dbSNP
rs1431576526	397	dbSNP
rs1347124608	401	dbSNP
rs1027841493	404	dbSNP
rs1448888042	405	dbSNP
rs757819514	405	dbSNP
rs1208294817	408	dbSNP
rs1236961002	414	dbSNP
rs1483655865	418	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.