>TXN|NM_003329|3'UTR
   1 TCATGTTTTCTGAAAATATAACCAGCCATTGGCTATTTAAAACTTGTAATTTTTTTAATTTACAAAAATATAAAATATGA
  81 AGACATAAACCCAGTTGCCATCTGCGTGACAATAAAACATTAATGCTAACACTTTTTAAAACCGTCTCATGTCTGAATAG
 161 CTTTCAAAATAAATGTGAAATGGTCATTTAATGTATTTTCCTATATTCTCAATCACTTTTTAGTAACCTTGTAGGCCACT
 241 GATTATTTTAAGATTTTAAAAATTATTATTGCTACCTTAATGTATTGCTACAAAAATCTCTTGTTGGGGGCAATGCAGGT
 321 AATAAAGTAGTATGTTGTTATTTGTAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gaUUUCUACCUGU---UAACCGAUu 5' ||| || || |||||||| Target 5' gaAAATATAACCAGCCATTGGCTAt 3'	12 - 36	156.00	-8.70

Mutant ID	Mutant Position	Mutant Source
COSN30514395	19	COSMIC
COSN27000729	37	COSMIC
COSN31604095	71	COSMIC
COSN22611449	91	COSMIC
COSN21057877	98	COSMIC
COSN23560460	340	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1459773434	2	dbSNP
rs778458580	3	dbSNP
rs1275140041	5	dbSNP
rs1256344169	6	dbSNP
rs1207201880	9	dbSNP
rs1305751196	12	dbSNP
rs756868949	16	dbSNP
rs5843	17	dbSNP
rs777499965	19	dbSNP
rs545547459	21	dbSNP
rs765460082	21	dbSNP
rs1458202760	22	dbSNP
rs1281000916	23	dbSNP
rs1404004031	25	dbSNP
rs756370144	26	dbSNP
rs753123530	27	dbSNP
rs767899360	29	dbSNP
rs1353274717	32	dbSNP
rs1169777284	33	dbSNP
rs1415134933	34	dbSNP
rs138381266	46	dbSNP
rs751659736	47	dbSNP
rs766617054	49	dbSNP
rs191324292	50	dbSNP
rs186490217	56	dbSNP
rs1167823656	57	dbSNP
rs1389954982	57	dbSNP
rs72549245	62	dbSNP
rs1230327258	63	dbSNP
rs1055786611	82	dbSNP
rs1321342139	93	dbSNP
rs377358418	99	dbSNP
rs546065926	100	dbSNP
rs1200578480	105	dbSNP
rs1256433055	115	dbSNP
rs1484027055	116	dbSNP
rs1454405188	118	dbSNP
rs1249184995	123	dbSNP
rs1251844964	124	dbSNP
rs1183718879	127	dbSNP
rs1191282899	128	dbSNP
rs993366406	131	dbSNP
rs1177237807	138	dbSNP
rs938879177	143	dbSNP
rs182614938	144	dbSNP
rs1273685863	148	dbSNP
rs2776	149	dbSNP
rs1281473976	150	dbSNP
rs1337234133	156	dbSNP
rs968335331	157	dbSNP
rs1218647939	167	dbSNP
rs527887855	180	dbSNP
rs752334735	187	dbSNP
rs1021281360	193	dbSNP
rs1235316302	200	dbSNP
rs985769386	203	dbSNP
rs1483185427	210	dbSNP
rs953380820	212	dbSNP
rs1266232797	213	dbSNP
rs1490320752	222	dbSNP
rs1192331039	227	dbSNP
rs1427890831	235	dbSNP
rs1301518404	248	dbSNP
rs1170191572	251	dbSNP
rs931904666	265	dbSNP
rs1431925522	269	dbSNP
rs560456786	271	dbSNP
rs1030268318	275	dbSNP
rs541862581	275	dbSNP
rs764800345	276	dbSNP
rs1293994739	279	dbSNP
rs957942817	283	dbSNP
rs1369682880	286	dbSNP
rs1380251753	287	dbSNP
rs997730533	297	dbSNP
rs1342423054	302	dbSNP
rs1221734412	303	dbSNP
rs897687566	306	dbSNP
rs189539981	309	dbSNP
rs1221699138	310	dbSNP
rs1016077412	311	dbSNP
rs1248893872	311	dbSNP
rs1485187530	313	dbSNP
rs1188314425	316	dbSNP
rs548838639	319	dbSNP
rs4135227	329	dbSNP
rs4135228	332	dbSNP
rs1048391171	348	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.