ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gaccUAACUUCUC---UUUUGGGUu 5' |||||: :| |||||| Target 5' catcATTGAGCGGTTCTTAACCCAt 3'	43 - 67	122.00	-10.90
2	miRNA 3' gaccuaacuucucUUUUGGGUu 5' ||||:||: Target 5' cgatcagtctgtaAAAATCCGg 3'	664 - 685	113.00	-6.90
3	miRNA 3' gacCUAACUUC--UC-------UUUUGGGUu 5' | || ||| || ||||::| Target 5' ccaGCTTTAAGCCAGTGTTTTCTAAACTTAt 3'	459 - 489	109.00	-5.90

Mutant ID	Mutant Position	Mutant Source
COSN8871274	48	COSMIC
COSN26343350	764	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1283334356	10	dbSNP
rs561295414	15	dbSNP
rs766712348	19	dbSNP
rs1203524018	20	dbSNP
rs758804818	24	dbSNP
rs753366106	27	dbSNP
rs1188880140	31	dbSNP
rs1466497197	32	dbSNP
rs1488112934	34	dbSNP
rs1259724150	41	dbSNP
rs763874086	47	dbSNP
rs1486237248	48	dbSNP
rs1264731073	49	dbSNP
rs1424352434	53	dbSNP
rs1193052867	54	dbSNP
rs1430055267	55	dbSNP
rs1480079134	63	dbSNP
rs1174102802	78	dbSNP
rs1413948968	82	dbSNP
rs1317347204	115	dbSNP
rs1343112700	117	dbSNP
rs1438165817	133	dbSNP
rs1175863027	142	dbSNP
rs543125111	153	dbSNP
rs1344250157	202	dbSNP
rs1223471271	208	dbSNP
rs1281877735	216	dbSNP
rs1353440892	219	dbSNP
rs1224723121	236	dbSNP
rs1283996821	247	dbSNP
rs1445551718	361	dbSNP
rs1426049165	392	dbSNP
rs1269705711	424	dbSNP
rs1490196318	426	dbSNP
rs113536491	448	dbSNP
rs1197223035	451	dbSNP
rs1194580108	454	dbSNP
rs1470454380	487	dbSNP
rs62423425	489	dbSNP
rs62423424	533	dbSNP
rs1212645203	536	dbSNP
rs575846351	566	dbSNP
rs62423423	586	dbSNP
rs1221160809	588	dbSNP
rs1309279420	590	dbSNP
rs1338112765	597	dbSNP
rs1443542631	598	dbSNP
rs1319317673	602	dbSNP
rs1278472998	627	dbSNP
rs1248486854	638	dbSNP
rs1213590421	641	dbSNP
rs1292719250	648	dbSNP
rs1359393175	650	dbSNP
rs1220405591	652	dbSNP
rs563867866	659	dbSNP
rs1180927755	664	dbSNP
rs1230992018	667	dbSNP
rs1473627329	668	dbSNP
rs1448461144	677	dbSNP
rs1384266576	680	dbSNP
rs1358570528	683	dbSNP
rs1334527295	684	dbSNP
rs1396516530	685	dbSNP
rs1468307820	686	dbSNP
rs1328728682	690	dbSNP
rs1425806467	700	dbSNP
rs1161928042	705	dbSNP
rs1382396105	706	dbSNP
rs1244040584	708	dbSNP
rs1253165121	713	dbSNP
rs1171693326	718	dbSNP
rs1428182317	720	dbSNP
rs1195178232	732	dbSNP
rs1270856464	737	dbSNP
rs1462571400	739	dbSNP
rs1184040645	740	dbSNP
rs1417608172	759	dbSNP
rs9483323	764	dbSNP
rs1442405904	766	dbSNP
rs1373184105	769	dbSNP
rs1474767969	773	dbSNP
rs1165632818	778	dbSNP
rs1473293335	779	dbSNP
rs1395023018	783	dbSNP
rs1471240792	784	dbSNP
rs1337868466	785	dbSNP
rs1243086033	795	dbSNP
rs1202278459	797	dbSNP
rs1327224442	799	dbSNP
rs1458739173	802	dbSNP
rs1258193494	804	dbSNP
rs1203184027	809	dbSNP
rs1250695041	815	dbSNP
rs1204152152	816	dbSNP
rs1262282269	821	dbSNP

- Cell host & microbe, 2011

Primary effusion lymphoma (PEL) is caused by Kaposi's sarcoma-associated herpesvirus (KSHV) and frequently also harbors Epstein-Barr virus (EBV). The expression of KSHV- and EBV-encoded microRNAs (miRNAs) in PELs suggests a role for these miRNAs in latency and lymphomagenesis. Using PAR-CLIP, a technology which allows the direct and transcriptome-wide identification of miRNA targets, we delineate the target sites for all viral and cellular miRNAs expressed in PEL cell lines. The resulting data set revealed that KSHV miRNAs directly target more than 2000 cellular mRNAs, including many involved in pathways relevant to KSHV pathogenesis. Moreover, 58% of these mRNAs are also targeted by EBV miRNAs, via distinct binding sites. In addition to a known viral analog of cellular miR-155, we show that KSHV encodes a viral miRNA that mimics cellular miR-142-3p function. In summary, this study identifies an extensive list of KSHV miRNA targets, which are likely to influence viral replication and pathogenesis.