ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ugGGAGA---CU-UUCCUUCGu 5' :|||| || | |||||| Target 5' caTCTCTCAGGACACGGAAGCa 3'	83 - 104	124.00	-15.90
2	miRNA 3' ugggAGAC-UUUCCUUcgu 5' |:|| ||||||| Target 5' gggaTTTGAAAAGGAAagg 3'	433 - 451	118.00	-7.20
3	miRNA 3' ugGGAGA---CUU-UCCUUCGu 5' |:||| || ||||| | Target 5' agCTTCTCCCCAACAGGAAACt 3'	409 - 430	116.00	-6.60

Mutant ID	Mutant Position	Mutant Source
297147	21	ClinVar
1200883	106	ClinVar
297146	138	ClinVar
297145	284	ClinVar
297144	293	ClinVar
297143	309	ClinVar
297142	369	ClinVar
297141	386	ClinVar
297140	399	ClinVar
297139	439	ClinVar
297138	452	ClinVar
297137	539	ClinVar
297136	599	ClinVar
297135	680	ClinVar
297134	681	ClinVar
297133	724	ClinVar
COSN30190822	6	COSMIC
COSN19735355	14	COSMIC
COSN30616847	16	COSMIC
COSN30483276	18	COSMIC
COSN2530893	28	COSMIC
COSN30154347	54	COSMIC
COSN30154337	58	COSMIC
COSN30509607	64	COSMIC
COSN26599274	197	COSMIC
COSN31513900	299	COSMIC
COSN31544438	357	COSMIC
COSN25221884	555	COSMIC
COSN32008113	605	COSMIC
COSN5371074	648	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs771314633	4	dbSNP
rs1452443769	5	dbSNP
rs1188754782	14	dbSNP
rs1249827285	15	dbSNP
rs749697240	16	dbSNP
rs777955605	18	dbSNP
rs781560790	20	dbSNP
rs149812692	21	dbSNP
rs758807329	22	dbSNP
rs1313051365	24	dbSNP
rs1245862756	25	dbSNP
rs1300619730	27	dbSNP
rs1448765809	32	dbSNP
rs750871661	33	dbSNP
rs751669673	34	dbSNP
rs1205683945	35	dbSNP
rs765250908	47	dbSNP
rs1208006443	55	dbSNP
rs1268779294	58	dbSNP
rs1276902575	59	dbSNP
rs933078773	69	dbSNP
rs1364704912	71	dbSNP
rs924396529	77	dbSNP
rs1022517973	81	dbSNP
rs1439035416	88	dbSNP
rs1220436664	97	dbSNP
rs538986203	98	dbSNP
rs112037794	106	dbSNP
rs760241532	107	dbSNP
rs1204796554	108	dbSNP
rs959497468	110	dbSNP
rs1428584051	111	dbSNP
rs1387927529	114	dbSNP
rs1034895128	116	dbSNP
rs1478202329	117	dbSNP
rs1245920565	119	dbSNP
rs1196616499	122	dbSNP
rs190556254	125	dbSNP
rs1351104166	126	dbSNP
rs1282568422	137	dbSNP
rs41265857	138	dbSNP
rs1271077097	139	dbSNP
rs886402993	147	dbSNP
rs1047728933	148	dbSNP
rs981517291	160	dbSNP
rs995303205	169	dbSNP
rs538069830	193	dbSNP
rs1346099912	199	dbSNP
rs1274652735	202	dbSNP
rs772114341	204	dbSNP
rs35504526	207	dbSNP
rs1039551397	210	dbSNP
rs567446820	213	dbSNP
rs1309235677	218	dbSNP
rs1408670624	220	dbSNP
rs943536356	221	dbSNP
rs912098353	226	dbSNP
rs1025756048	228	dbSNP
rs1052014226	237	dbSNP
rs1414716178	242	dbSNP
rs995493162	244	dbSNP
rs934900115	245	dbSNP
rs1053448	248	dbSNP
rs1170573409	252	dbSNP
rs544493865	260	dbSNP
rs575566299	261	dbSNP
rs1007891148	266	dbSNP
rs1428947029	273	dbSNP
rs1197906508	280	dbSNP
rs968176690	282	dbSNP
rs150690731	284	dbSNP
rs1212446414	288	dbSNP
rs1443191058	289	dbSNP
rs1052024512	291	dbSNP
rs16866009	293	dbSNP
rs180881898	297	dbSNP
rs1192535032	301	dbSNP
rs370883906	308	dbSNP
rs372462149	309	dbSNP
rs1289466316	320	dbSNP
rs1228328357	325	dbSNP
rs1286606510	331	dbSNP
rs1041477747	334	dbSNP
rs778815402	335	dbSNP
rs1034821441	337	dbSNP
rs1003382031	342	dbSNP
rs1304105817	346	dbSNP
rs950649114	349	dbSNP
rs1026250916	368	dbSNP
rs879511403	369	dbSNP
rs1329624042	382	dbSNP
rs144131403	386	dbSNP
rs1412439810	387	dbSNP
rs1458605425	387	dbSNP
rs1039109057	391	dbSNP
rs1158280425	396	dbSNP
rs1221649828	397	dbSNP
rs1008095662	398	dbSNP
rs1057515511	399	dbSNP
rs890588915	399	dbSNP
rs937599919	408	dbSNP
rs189698373	418	dbSNP
rs1429393583	421	dbSNP
rs1237102040	425	dbSNP
rs532734575	426	dbSNP
rs1466480263	432	dbSNP
rs1269198765	434	dbSNP
rs1324391190	436	dbSNP
rs184249741	439	dbSNP
rs1315487563	441	dbSNP
rs981606818	446	dbSNP
rs142185532	452	dbSNP
rs1312373353	462	dbSNP
rs1405836726	464	dbSNP
rs1436871132	466	dbSNP
rs934868758	479	dbSNP
rs748331867	489	dbSNP
rs1319617578	492	dbSNP
rs765324724	497	dbSNP
rs1351541237	499	dbSNP
rs1165463409	501	dbSNP
rs1424409705	506	dbSNP
rs1413176664	515	dbSNP
rs1471271189	522	dbSNP
rs758419455	529	dbSNP
rs1181940401	538	dbSNP
rs550239801	539	dbSNP
rs1167478575	548	dbSNP
rs1214600395	552	dbSNP
rs531834594	566	dbSNP
rs1043733434	572	dbSNP
rs561525459	574	dbSNP
rs1188294908	575	dbSNP
rs1485136737	580	dbSNP
rs542816112	599	dbSNP
rs962700279	607	dbSNP
rs1320548817	608	dbSNP
rs1288984333	609	dbSNP
rs1230037058	616	dbSNP
rs1365432361	618	dbSNP
rs1296497267	624	dbSNP
rs914933026	625	dbSNP
rs1243862713	629	dbSNP
rs1380296057	637	dbSNP
rs1189484027	640	dbSNP
rs1461010733	644	dbSNP
rs12145	650	dbSNP
rs1018698842	659	dbSNP
rs1053482	661	dbSNP
rs1457377559	665	dbSNP
rs1006925839	667	dbSNP
rs1161726404	672	dbSNP
rs536402126	680	dbSNP
rs78319035	681	dbSNP
rs1188231936	682	dbSNP
rs981930420	685	dbSNP
rs1213850380	688	dbSNP
rs573873811	700	dbSNP
rs1267427869	707	dbSNP
rs1206673241	713	dbSNP
rs1342324573	717	dbSNP
rs1273387259	720	dbSNP
rs1057515549	724	dbSNP
rs950577466	724	dbSNP
rs1026216397	729	dbSNP
rs1313702790	731	dbSNP
rs1301750102	739	dbSNP
rs1470091199	743	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.

- Genome research, 2016

DNA damage activates TP53-regulated surveillance mechanisms that are crucial in suppressing tumorigenesis. TP53 orchestrates these responses directly by transcriptionally modulating genes, including microRNAs (miRNAs), and by regulating miRNA biogenesis through interacting with the DROSHA complex. However, whether the association between miRNAs and AGO2 is regulated following DNA damage is not yet known. Here, we show that, following DNA damage, TP53 interacts with AGO2 to induce or reduce AGO2's association of a subset of miRNAs, including multiple let-7 family members. Furthermore, we show that specific mutations in TP53 decrease rather than increase the association of let-7 family miRNAs, reducing their activity without preventing TP53 from interacting with AGO2. This is consistent with the oncogenic properties of these mutants. Using AGO2 RIP-seq and PAR-CLIP-seq, we show that the DNA damage-induced increase in binding of let-7 family members to the RISC complex is functional. We unambiguously determine the global miRNA-mRNA interaction networks involved in the DNA damage response, validating them through the identification of miRNA-target chimeras formed by endogenous ligation reactions. We find that the target complementary region of the let-7 seed tends to have highly fixed positions and more variable ones. Additionally, we observe that miRNAs, whose cellular abundance or differential association with AGO2 is regulated by TP53, are involved in an intricate network of regulatory feedback and feedforward circuits. TP53-mediated regulation of AGO2-miRNA interaction represents a new mechanism of miRNA regulation in carcinogenesis.

- 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.