ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ucgUACAUGGGUGUCAc 5' :| | :||||||| Target 5' gagGTTTCTCCACAGTc 3'	29 - 45	146.00	-10.70
2	miRNA 3' ucGUACAUGGGUGUCac 5' ||| | :|:|||| Target 5' gcCAT-TTTCTACAGct 3'	670 - 685	114.00	-8.20
3	miRNA 3' ucgUACAUGGGUGUCAc 5' | | | ||||| | Target 5' tagACGGAGCCACACTa 3'	193 - 209	114.00	-6.72

Mutant ID	Mutant Position	Mutant Source
COSN30451919	8	COSMIC
COSN30483849	21	COSMIC
COSN30477433	28	COSMIC
COSN30156707	49	COSMIC
COSN30142639	63	COSMIC
COSN19411583	66	COSMIC
COSN30143783	105	COSMIC
COSN31593174	162	COSMIC
COSN9324487	162	COSMIC
COSN22329319	192	COSMIC
COSN20114540	545	COSMIC
COSN32058069	609	COSMIC
rs1046875	380	GWAS
rs1046896	487	GWAS

Mutant ID	Mutant Position	Mutant Source
rs1399256846	1	dbSNP
rs774622828	3	dbSNP
rs201702321	4	dbSNP
rs1458616913	7	dbSNP
rs150881814	8	dbSNP
rs773658584	10	dbSNP
rs1484312104	14	dbSNP
rs762806453	18	dbSNP
rs996557769	19	dbSNP
rs758937034	22	dbSNP
rs1172566939	27	dbSNP
rs775451448	28	dbSNP
rs766961869	32	dbSNP
rs890808948	33	dbSNP
rs1173934460	41	dbSNP
rs1360803257	43	dbSNP
rs1448172662	45	dbSNP
rs754291026	47	dbSNP
rs762622947	49	dbSNP
rs981340698	51	dbSNP
rs1233964875	59	dbSNP
rs1205523494	66	dbSNP
rs1299306473	70	dbSNP
rs1218676245	76	dbSNP
rs1362931018	79	dbSNP
rs2243446	80	dbSNP
rs560293370	81	dbSNP
rs990811972	82	dbSNP
rs1365011706	85	dbSNP
rs1201300992	91	dbSNP
rs956231553	99	dbSNP
rs916583249	101	dbSNP
rs1174782183	102	dbSNP
rs1409982721	103	dbSNP
rs1261095294	105	dbSNP
rs1421008733	111	dbSNP
rs990760842	119	dbSNP
rs1448466998	123	dbSNP
rs1021812470	125	dbSNP
rs941465616	127	dbSNP
rs1459946748	135	dbSNP
rs370972441	136	dbSNP
rs76587147	141	dbSNP
rs1249771309	145	dbSNP
rs980200937	161	dbSNP
rs1308216904	166	dbSNP
rs146163729	167	dbSNP
rs1364705045	172	dbSNP
rs1316199384	184	dbSNP
rs1172722689	185	dbSNP
rs1377638574	191	dbSNP
rs1393105745	194	dbSNP
rs992069694	195	dbSNP
rs528835266	198	dbSNP
rs1428727391	199	dbSNP
rs1385424128	201	dbSNP
rs1165241141	208	dbSNP
rs1442492080	211	dbSNP
rs1051350167	218	dbSNP
rs891350096	221	dbSNP
rs1038131349	226	dbSNP
rs942925671	228	dbSNP
rs570401293	231	dbSNP
rs1172840823	233	dbSNP
rs1234726012	234	dbSNP
rs919760796	240	dbSNP
rs1039818733	243	dbSNP
rs1292690198	254	dbSNP
rs58962659	261	dbSNP
rs72046641	261	dbSNP
rs1322002954	262	dbSNP
rs1320364318	269	dbSNP
rs892787544	270	dbSNP
rs1312414599	272	dbSNP
rs890780831	277	dbSNP
rs1376101896	278	dbSNP
rs537853921	279	dbSNP
rs1008350154	285	dbSNP
rs771337712	286	dbSNP
rs1304646666	297	dbSNP
rs1011772238	298	dbSNP
rs1214834540	299	dbSNP
rs1020007866	304	dbSNP
rs112990290	306	dbSNP
rs549670852	306	dbSNP
rs1440834124	307	dbSNP
rs1002625815	308	dbSNP
rs556745340	309	dbSNP
rs1035477893	310	dbSNP
rs958654421	316	dbSNP
rs535519039	323	dbSNP
rs1234212537	324	dbSNP
rs563003827	328	dbSNP
rs11551832	329	dbSNP
rs1487614120	331	dbSNP
rs974582210	338	dbSNP
rs1042869128	339	dbSNP
rs960065641	345	dbSNP
rs1268865577	346	dbSNP
rs1465282635	349	dbSNP
rs572258264	351	dbSNP
rs930137048	352	dbSNP
rs1384770196	355	dbSNP
rs775986588	356	dbSNP
rs987001210	362	dbSNP
rs912735484	365	dbSNP
rs1386377460	366	dbSNP
rs907878098	372	dbSNP
rs748900999	378	dbSNP
rs942958189	379	dbSNP
rs1046875	380	dbSNP
rs571818746	386	dbSNP
rs1266853357	389	dbSNP
rs576216402	396	dbSNP
rs1206100961	397	dbSNP
rs947032271	399	dbSNP
rs932513860	402	dbSNP
rs1266626457	404	dbSNP
rs1208699034	408	dbSNP
rs1041864532	420	dbSNP
rs193216896	422	dbSNP
rs140176973	426	dbSNP
rs1002573464	428	dbSNP
rs570537411	429	dbSNP
rs1383555718	438	dbSNP
rs1490606359	463	dbSNP
rs1035510845	464	dbSNP
rs1046889	465	dbSNP
rs1324531766	474	dbSNP
rs1013261728	485	dbSNP
rs1046896	487	dbSNP
rs1387672003	488	dbSNP
rs1043358978	501	dbSNP
rs1174392758	512	dbSNP
rs963037510	513	dbSNP
rs995486165	517	dbSNP
rs1026057929	518	dbSNP
rs951484881	524	dbSNP
rs143639702	525	dbSNP
rs3087795	530	dbSNP
rs184357380	534	dbSNP
rs912766522	537	dbSNP
rs552639315	541	dbSNP
rs66482220	542	dbSNP
rs1229216896	549	dbSNP
rs57335410	556	dbSNP
rs549876039	557	dbSNP
rs568178549	558	dbSNP
rs1332176143	564	dbSNP
rs1395382715	567	dbSNP
rs947616934	568	dbSNP
rs7208281	570	dbSNP
rs1168548991	576	dbSNP
rs1041420268	577	dbSNP
rs924261249	578	dbSNP
rs1445554935	583	dbSNP
rs1249572944	584	dbSNP
rs1471397488	585	dbSNP
rs746839593	587	dbSNP
rs1183981765	588	dbSNP
rs1412038306	596	dbSNP
rs1474567773	602	dbSNP
rs1162127765	608	dbSNP
rs1046917	609	dbSNP
rs894330026	610	dbSNP
rs7794	614	dbSNP
rs1038032074	616	dbSNP
rs1297955505	617	dbSNP
rs565587577	618	dbSNP
rs1394873563	619	dbSNP
rs1411868588	631	dbSNP
rs947060897	635	dbSNP
rs1336230843	637	dbSNP
rs747430509	642	dbSNP
rs762031695	651	dbSNP
rs1043325759	658	dbSNP
rs906147621	661	dbSNP
rs1231483164	662	dbSNP
rs899116971	666	dbSNP
rs993820088	673	dbSNP
rs539712281	687	dbSNP
rs1364812660	699	dbSNP
rs1183729739	700	dbSNP
rs1471355907	705	dbSNP
rs1245502427	713	dbSNP
rs12296	720	dbSNP
rs1005345111	737	dbSNP
rs77688232	738	dbSNP
rs769835685	744	dbSNP
rs1351317440	751	dbSNP
rs146773542	752	dbSNP
rs1226484134	758	dbSNP
rs1348780076	759	dbSNP
rs1287783488	762	dbSNP
rs1351792203	766	dbSNP
rs964213789	766	dbSNP
rs1252039663	768	dbSNP
rs975640003	768	dbSNP
rs994833006	769	dbSNP
rs914720787	772	dbSNP
rs969019433	775	dbSNP
rs978064207	777	dbSNP
rs1405073964	784	dbSNP
rs1386110768	786	dbSNP
rs1162078758	789	dbSNP
rs1471877074	792	dbSNP
rs1410652736	793	dbSNP
rs1485143561	797	dbSNP
rs924292386	806	dbSNP
rs938325491	814	dbSNP
rs1478826343	816	dbSNP
rs953927776	818	dbSNP
rs1244557525	830	dbSNP
rs1197922490	833	dbSNP
rs1056810997	834	dbSNP
rs1447422725	839	dbSNP

- Nature methods, 2011

Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.

- Neoplasia (New York, N.Y.), 2016

MicroRNA (miRNA) deregulation in prostate cancer (PCa) contributes to PCa initiation and metastatic progression. To comprehensively define the cancer-associated changes in miRNA targeting and function in commonly studied models of PCa, we performed photoactivatable ribonucleoside-enhanced cross-linking immunoprecipitation of the Argonaute protein in a panel of PCa cell lines modeling different stages of PCa progression. Using this comprehensive catalogue of miRNA targets, we analyzed miRNA targeting on known drivers of PCa and examined tissue-specific and stage-specific pathway targeting by miRNAs. We found that androgen receptor is the most frequently targeted PCa oncogene and that miR-148a targets the largest number of known PCa drivers. Globally, tissue-specific and stage-specific changes in miRNA targeting are driven by homeostatic response to active oncogenic pathways. Our findings indicate that, even in advanced PCa, the miRNA pool adapts to regulate continuing alterations in the cancer genome to balance oncogenic molecular changes. These findings are important because they are the first to globally characterize miRNA changes in PCa and demonstrate how the miRNA target spectrum responds to staged tumorigenesis.