>ABCB5|NM_001163941|3'UTR
   1 TGCTGTTGAGGTAGCACATATTTTGATGTTCGTGTAATGCAAAGAAGGAGTACTTAATAATTACTTGGCAAGCTTTGATC
  81 TCTTTTATTGCATATATCAATACCTAGAATCATGCTACTCAAGTACATACATGTTCTATTCACACACCATCTGACCTTCA
 161 GATTTTTAAAAGGAAGCAAAAATTTGCTTATTTCATGTAAGTGAAATAATGCTTATATCCTTCACTTTATAAAACTATTC
 241 TAGCACATTTGCTTGTAAAGCAGTTTTCTACAAGGTGAATTTATTTCCCATCAACTTCTGCTATAAAATCGGAAATATGT
 321 TTCCAGGGGGAATATTATCCAATTAACCATGTTGAAGGTTTTAGCAAAGGCAGTGTAAGATAGAGTGGGGCCTGTAGCAT
 401 TGCAGGGAGAGTGTCTTTCACTTGGAATTTTGTTTTGCAGCACATATTACAGTAGTTTTGCTAGTCCCTTTTCTCCAGAC
 481 CGTAGGGATTTCTCTCAATAAGTATTCACTATTTCTCTAAATTTTATTCTATTTTTTTGTTGAGCAGGGAATAGAAAGGA
 561 TTACGATGTAAAATTTCTGGGAGGATTAGGTAGCTATCTCCTACTTCACCAGTAAGTGAAGTGCCTCACATGAGCCATCC
 641 CAAAGATTCATTATTCCAAACCTTGGGTTTGGCAGTATAAGTCACAGGCCTACCTGTTTATGAAAACTTACTTACTTAAA
 721 ATAAGAGCTACTTTTGGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGAACTTTGGGAGGCCGAGGAGGGCGGATCAC
 801 TTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAACACAAAAATTAGCCAATCT
 881 TGGTGGCGGGCACCTGGAATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCATTTGAACCTAGGAGGCAGAGGTTGCA
 961 GTGAGCCGAGATCTCACCACTGCACTCCAGCCTGCGCAACAGAGCGAGACTCCATCTCAAAAAATAATAAATAAGAGCTA
1041 ATTTTATTGTGGGTGAAAATTTTTAAACGTCTTTCTCTATAATAAAATAATTTCCTTAAATTTTATATATACTTTATCAT
1121 ATATAATGTGTGAATGATTTTAAAGTTCTGTGTAAATAACAATATTGGTAAAATGAGTTACATTTTCAACTTACTTAAAT
1201 ATGTAATGTCACCTGGTGATTTTATCTTTATTCTTCAGTGTATTTTCTTCCATTTACACATTTAGCTAGCCTCCCTAAAG
1281 TGTACTCTACCAATAATTGAAATCTTGTTAAACAAAATTAAAACCATTTATATATTATGCTGCTTTCTTTAAAATGCAAA
1361 ATAAAAATAAGATTGGGGACTTGAGAATCA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' guAUGGA-UAUCUAU-----GUUCGAAc 5' |||:| ||| || ||||||| Target 5' agTACTTAATAATTACTTGGCAAGCTTt 3'	49 - 76	156.00	-8.69
2	miRNA 3' guAUGGAUAUCUAUGUUCGAac 5' |||||| | || || ||| Target 5' aaTACCTAGA-AT-CATGCTac 3'	99 - 118	114.00	-9.00
3	miRNA 3' guAUGGAUAU---CUAUGUU-CGAAc 5' | | |:|| || |:|| |||| Target 5' atTTCATGTAAGTGAAATAATGCTTa 3'	190 - 215	112.00	-6.40

Mutant ID	Mutant Position	Mutant Source
COSN30156114	9	COSMIC
COSN30463735	11	COSMIC
COSN30155225	32	COSMIC
COSN30449623	32	COSMIC
COSN31539347	33	COSMIC
COSN30184027	48	COSMIC
COSN30123675	75	COSMIC
COSN30192734	81	COSMIC
COSN30121820	83	COSMIC
COSN30452986	84	COSMIC
COSN31604962	112	COSMIC
COSN31610269	125	COSMIC
COSN1347188	202	COSMIC
COSN20561473	366	COSMIC
COSN6875345	404	COSMIC
COSN29329843	448	COSMIC
COSN31962745	482	COSMIC
COSN21484259	483	COSMIC
COSN8789648	681	COSMIC
COSN4868571	741	COSMIC
COSN17243559	752	COSMIC
COSN7974124	757	COSMIC
COSN6875346	841	COSMIC
COSN17078572	1095	COSMIC
COSN20372106	1176	COSMIC
COSN9315615	1197	COSMIC
COSN26305364	1260	COSMIC
COSN9939392	1314	COSMIC
COSN29258585	1321	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs779617009	2	dbSNP
rs748969374	3	dbSNP
rs754596539	4	dbSNP
rs1269753671	6	dbSNP
rs1047034992	9	dbSNP
rs1461691358	12	dbSNP
rs1480702661	13	dbSNP
rs778511230	14	dbSNP
rs1371112405	15	dbSNP
rs938208503	19	dbSNP
rs748103889	20	dbSNP
rs1490738831	21	dbSNP
rs376697135	22	dbSNP
rs773083608	30	dbSNP
rs746830015	32	dbSNP
rs1042404193	33	dbSNP
rs1365732539	34	dbSNP
rs1399918542	39	dbSNP
rs1276795199	40	dbSNP
rs772885348	42	dbSNP
rs770728639	48	dbSNP
rs775632145	49	dbSNP
rs763176128	51	dbSNP
rs1202911341	52	dbSNP
rs1225051209	53	dbSNP
rs1324186142	57	dbSNP
rs903945017	60	dbSNP
rs1220021058	74	dbSNP
rs1303068838	79	dbSNP
rs1212577688	85	dbSNP
rs1190977913	91	dbSNP
rs1361099017	94	dbSNP
rs1270960933	101	dbSNP
rs562123497	104	dbSNP
rs1016187289	114	dbSNP
rs1480571958	117	dbSNP
rs1403939569	119	dbSNP
rs529226655	123	dbSNP
rs1336198681	125	dbSNP
rs1470551339	130	dbSNP
rs762499792	137	dbSNP
rs963324342	141	dbSNP
rs763731854	144	dbSNP
rs1017651318	146	dbSNP
rs964196245	150	dbSNP
rs544535719	151	dbSNP
rs995997016	162	dbSNP
rs1186694147	169	dbSNP
rs562623909	172	dbSNP
rs1450973871	174	dbSNP
rs185005502	178	dbSNP
rs530367631	186	dbSNP
rs1182463874	197	dbSNP
rs1461426796	198	dbSNP
rs955350744	211	dbSNP
rs1202406601	212	dbSNP
rs1029268334	213	dbSNP
rs954464812	217	dbSNP
rs1230836764	227	dbSNP
rs987641580	232	dbSNP
rs982440852	236	dbSNP
rs967018476	237	dbSNP
rs751144657	241	dbSNP
rs1296932267	242	dbSNP
rs1442143315	245	dbSNP
rs1355435916	256	dbSNP
rs908168400	262	dbSNP
rs753662823	265	dbSNP
rs962376624	268	dbSNP
rs756915608	273	dbSNP
rs1162614675	275	dbSNP
rs1407012557	278	dbSNP
rs569093487	280	dbSNP
rs767166741	285	dbSNP
rs750261001	293	dbSNP
rs1055949643	299	dbSNP
rs757133433	301	dbSNP
rs1276469460	305	dbSNP
rs926414339	311	dbSNP
rs917424469	312	dbSNP
rs950134056	325	dbSNP
rs1047596404	326	dbSNP
rs1228303126	329	dbSNP
rs189467333	330	dbSNP
rs368812636	339	dbSNP
rs1056664767	343	dbSNP
rs1323526506	345	dbSNP
rs1341420416	347	dbSNP
rs1243616614	359	dbSNP
rs373030334	363	dbSNP
rs918156972	364	dbSNP
rs945689280	365	dbSNP
rs540563616	366	dbSNP
rs1403491789	370	dbSNP
rs903830430	376	dbSNP
rs1365392310	379	dbSNP
rs1000835299	380	dbSNP
rs560447474	382	dbSNP
rs900612857	390	dbSNP
rs1038408616	392	dbSNP
rs1446045442	396	dbSNP
rs1418371826	401	dbSNP
rs997075779	403	dbSNP
rs1412616359	407	dbSNP
rs780085757	421	dbSNP
rs1489788057	433	dbSNP
rs1193331101	441	dbSNP
rs1267942601	445	dbSNP
rs1029535612	448	dbSNP
rs996116500	452	dbSNP
rs1258975645	453	dbSNP
rs1238401042	454	dbSNP
rs180978142	456	dbSNP
rs1290725135	462	dbSNP
rs1222281059	473	dbSNP
rs1345223260	479	dbSNP
rs566294742	482	dbSNP
rs531960949	483	dbSNP
rs1163447235	488	dbSNP
rs1386257640	499	dbSNP
rs1015530609	504	dbSNP
rs1427024826	506	dbSNP
rs1452392422	518	dbSNP
rs1388795578	519	dbSNP
rs962349814	520	dbSNP
rs1008609970	528	dbSNP
rs1020449408	532	dbSNP
rs973759579	532	dbSNP
rs1033836158	534	dbSNP
rs745454938	540	dbSNP
rs184930142	543	dbSNP
rs959187997	545	dbSNP
rs978382466	546	dbSNP
rs992735101	550	dbSNP
rs1486224152	552	dbSNP
rs1338716495	558	dbSNP
rs918054407	560	dbSNP
rs189691870	565	dbSNP
rs182002068	566	dbSNP
rs917390567	568	dbSNP
rs1292970588	569	dbSNP
rs567298629	580	dbSNP
rs1258709056	585	dbSNP
rs1365236628	591	dbSNP
rs186188564	595	dbSNP
rs1205304882	598	dbSNP
rs1468112484	603	dbSNP
rs1405242496	610	dbSNP
rs936661714	611	dbSNP
rs1467364234	612	dbSNP
rs778009086	621	dbSNP
rs557672541	630	dbSNP
rs1459539018	633	dbSNP
rs1249905047	637	dbSNP
rs900580574	639	dbSNP
rs933379320	640	dbSNP
rs569429801	651	dbSNP
rs1460974480	655	dbSNP
rs771209139	657	dbSNP
rs757997869	665	dbSNP
rs1004065532	667	dbSNP
rs776822774	668	dbSNP
rs1337800233	672	dbSNP
rs540111885	675	dbSNP
rs1226155108	676	dbSNP
rs558400817	678	dbSNP
rs1244345085	687	dbSNP
rs899848788	689	dbSNP
rs1449825494	691	dbSNP
rs995164649	694	dbSNP
rs931853519	696	dbSNP
rs1050776942	699	dbSNP
rs532249075	699	dbSNP
rs1033392503	700	dbSNP
rs535584317	702	dbSNP
rs1020142361	706	dbSNP
rs902921055	708	dbSNP
rs1363529155	709	dbSNP
rs1238147002	712	dbSNP
rs1454515414	713	dbSNP
rs959301381	720	dbSNP
rs1436581859	723	dbSNP
rs746285478	729	dbSNP
rs1404176220	740	dbSNP
rs141089246	741	dbSNP
rs770180176	742	dbSNP
rs1025158758	748	dbSNP
rs776035685	753	dbSNP
rs190602322	755	dbSNP
rs779488519	757	dbSNP
rs1383492039	758	dbSNP
rs936962332	764	dbSNP
rs1032610668	766	dbSNP
rs1328169201	768	dbSNP
rs13228201	775	dbSNP
rs574013272	776	dbSNP
rs1372223506	778	dbSNP
rs1301471161	782	dbSNP
rs1334895001	785	dbSNP
rs1424298100	786	dbSNP
rs991715501	789	dbSNP
rs921920034	791	dbSNP
rs544257075	792	dbSNP
rs1414539185	794	dbSNP
rs1165086303	795	dbSNP
rs1468718262	802	dbSNP
rs1363721753	804	dbSNP
rs1484230493	805	dbSNP
rs933328158	806	dbSNP
rs1051831727	814	dbSNP
rs562870795	817	dbSNP
rs939824531	818	dbSNP
rs1289901152	823	dbSNP
rs773871763	836	dbSNP
rs983337318	839	dbSNP
rs1287615751	842	dbSNP
rs577530197	846	dbSNP
rs1352055971	848	dbSNP
rs767236030	849	dbSNP
rs1034023495	851	dbSNP
rs941399689	854	dbSNP
rs1250264716	870	dbSNP
rs894782052	878	dbSNP
rs1325852180	883	dbSNP
rs1420123164	884	dbSNP
rs143451572	888	dbSNP
rs760572414	889	dbSNP
rs1024713428	890	dbSNP
rs12112555	898	dbSNP
rs376711277	911	dbSNP
rs911783809	918	dbSNP
rs1246924631	942	dbSNP
rs1200601392	944	dbSNP
rs1444758520	945	dbSNP
rs944661477	950	dbSNP
rs753765075	955	dbSNP
rs1408329186	958	dbSNP
rs1218419405	959	dbSNP
rs958205773	961	dbSNP
rs974992011	964	dbSNP
rs1467534329	968	dbSNP
rs922193648	969	dbSNP
rs1054135294	976	dbSNP
rs527478047	978	dbSNP
rs1459235905	981	dbSNP
rs1404522123	984	dbSNP
rs954713167	986	dbSNP
rs987907340	988	dbSNP
rs188321562	989	dbSNP
rs940796078	994	dbSNP
rs191015629	996	dbSNP
rs531368173	997	dbSNP
rs919725261	1001	dbSNP
rs777954042	1003	dbSNP
rs1012985184	1005	dbSNP
rs1055027894	1006	dbSNP
rs1283378886	1007	dbSNP
rs1313372472	1008	dbSNP
rs1241159395	1015	dbSNP
rs140253766	1016	dbSNP
rs571189181	1021	dbSNP
rs972033871	1029	dbSNP
rs1004483697	1032	dbSNP
rs1341744459	1033	dbSNP
rs749611234	1037	dbSNP
rs1376966626	1048	dbSNP
rs1298689505	1051	dbSNP
rs540146590	1052	dbSNP
rs962875280	1053	dbSNP
rs552056477	1066	dbSNP
rs373610561	1069	dbSNP
rs1046526662	1070	dbSNP
rs1267165260	1081	dbSNP
rs1168788696	1090	dbSNP
rs954182673	1094	dbSNP
rs987186050	1097	dbSNP
rs1168876782	1104	dbSNP
rs912580604	1108	dbSNP
rs1382875211	1110	dbSNP
rs902188777	1111	dbSNP
rs1315483651	1113	dbSNP
rs1200335043	1115	dbSNP
rs999196200	1118	dbSNP
rs1482645396	1119	dbSNP
rs1431551854	1124	dbSNP
rs150442227	1131	dbSNP
rs555857965	1132	dbSNP
rs1169812507	1133	dbSNP
rs1357313029	1138	dbSNP
rs1312099322	1139	dbSNP
rs374664463	1140	dbSNP
rs1229332885	1149	dbSNP
rs1381954046	1149	dbSNP
rs1297031344	1151	dbSNP
rs958174395	1163	dbSNP
rs924407820	1175	dbSNP
rs574071962	1176	dbSNP
rs1308205809	1182	dbSNP
rs1431282391	1184	dbSNP
rs1054246651	1185	dbSNP
rs1163480344	1186	dbSNP
rs1423950726	1189	dbSNP
rs138210219	1191	dbSNP
rs1363415855	1197	dbSNP
rs142367245	1208	dbSNP
rs1472129864	1213	dbSNP
rs770129650	1214	dbSNP
rs987488687	1221	dbSNP
rs1207514055	1222	dbSNP
rs907837843	1234	dbSNP
rs1045782367	1236	dbSNP
rs3210441	1241	dbSNP
rs973457267	1242	dbSNP
rs1305458890	1247	dbSNP
rs920696135	1250	dbSNP
rs1308633698	1255	dbSNP
rs1290601425	1256	dbSNP
rs1411216855	1258	dbSNP
rs1231197657	1261	dbSNP
rs1292657120	1263	dbSNP
rs1290061623	1266	dbSNP
rs931142712	1268	dbSNP
rs1156800937	1269	dbSNP
rs1490269881	1270	dbSNP
rs1223688134	1271	dbSNP
rs1271398031	1274	dbSNP
rs1412359226	1278	dbSNP
rs1015853036	1286	dbSNP
rs146328292	1289	dbSNP
rs962991366	1290	dbSNP
rs995660101	1292	dbSNP
rs1489475072	1294	dbSNP
rs1429058859	1295	dbSNP
rs560002430	1301	dbSNP
rs1028517722	1304	dbSNP
rs139006523	1307	dbSNP
rs1330445045	1308	dbSNP
rs1270642435	1311	dbSNP
rs1222067161	1313	dbSNP
rs954244168	1314	dbSNP
rs1300141116	1316	dbSNP
rs1170334880	1320	dbSNP
rs1387015195	1325	dbSNP
rs568156520	1326	dbSNP
rs1456302181	1327	dbSNP
rs1161333683	1328	dbSNP
rs966717	1339	dbSNP
rs1376874026	1341	dbSNP
rs1303508881	1343	dbSNP
rs949287232	1345	dbSNP
rs966738596	1353	dbSNP
rs552626235	1365	dbSNP
rs978101630	1365	dbSNP
rs1351296503	1373	dbSNP
rs1246202836	1374	dbSNP
rs1187993875	1381	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.

- 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.

- Nature methods, 2013

High-throughput sequencing has opened numerous possibilities for the identification of regulatory RNA-binding events. Cross-linking and immunoprecipitation of Argonaute proteins can pinpoint a microRNA (miRNA) target site within tens of bases but leaves the identity of the miRNA unresolved. A flexible computational framework, microMUMMIE, integrates sequence with cross-linking features and reliably identifies the miRNA family involved in each binding event. It considerably outperforms sequence-only approaches and quantifies the prevalence of noncanonical binding modes.