ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gacGCCUUUCUCUUCGUGCACc 5' || || |:||||:||| Target 5' ttcCGTCCAG-GGAGCATGTGg 3'	92 - 112	138.00	-20.20
2	miRNA 3' gaCGCCUUUCUCUUCGUGCACc 5' |:||::|| || |||| || Target 5' gaGTGGGGAG-GATGCAC-TGc 3'	16 - 35	115.00	-16.90
3	miRNA 3' gacgccUUUCUCU--UCG-UGCAcc 5' ||||||| ||: |||| Target 5' attgaaAAAGAGAACAGTGACGTag 3'	490 - 514	102.00	-13.50

Mutant ID	Mutant Position	Mutant Source
COSN26997513	21	COSMIC
COSN21667214	25	COSMIC
COSN30124448	46	COSMIC
COSN31573646	61	COSMIC
COSN31500210	63	COSMIC
COSN26635492	69	COSMIC
COSN30469933	94	COSMIC
COSN30502697	102	COSMIC
COSN31545637	103	COSMIC
COSN31539350	113	COSMIC
COSN31581818	118	COSMIC
COSN9275694	131	COSMIC
COSN14850014	141	COSMIC
COSN30141232	144	COSMIC
rs2281789	439	GWAS

Mutant ID	Mutant Position	Mutant Source
rs1431959360	1	dbSNP
rs751506826	4	dbSNP
rs779793096	8	dbSNP
rs758231333	9	dbSNP
rs750172263	11	dbSNP
rs765475640	18	dbSNP
rs373388512	21	dbSNP
rs368926094	23	dbSNP
rs764221933	28	dbSNP
rs760604186	29	dbSNP
rs776077272	37	dbSNP
rs767417499	38	dbSNP
rs772407732	40	dbSNP
rs749508433	42	dbSNP
rs774822672	43	dbSNP
rs200435366	47	dbSNP
rs534529462	52	dbSNP
rs565834339	53	dbSNP
rs1456839558	54	dbSNP
rs1177406000	55	dbSNP
rs1361345406	65	dbSNP
rs1189826412	66	dbSNP
rs1446470050	70	dbSNP
rs368841685	71	dbSNP
rs376440859	72	dbSNP
rs1286119814	78	dbSNP
rs1012084594	81	dbSNP
rs960496726	84	dbSNP
rs150720171	85	dbSNP
rs1280146641	90	dbSNP
rs1310324576	94	dbSNP
rs776833707	95	dbSNP
rs999377652	96	dbSNP
rs549849093	98	dbSNP
rs902548577	100	dbSNP
rs1217486634	101	dbSNP
rs1184608672	104	dbSNP
rs532932132	110	dbSNP
rs1046334832	112	dbSNP
rs540282935	114	dbSNP
rs1427394447	120	dbSNP
rs1413216037	129	dbSNP
rs2281790	141	dbSNP
rs142040646	142	dbSNP
rs984329690	144	dbSNP
rs1305785918	149	dbSNP
rs889873367	163	dbSNP
rs1405211289	164	dbSNP
rs1345480494	165	dbSNP
rs528698359	166	dbSNP
rs918644301	172	dbSNP
rs1412203883	174	dbSNP
rs1428026278	187	dbSNP
rs934182547	188	dbSNP
rs972797581	190	dbSNP
rs965393357	194	dbSNP
rs1200724785	199	dbSNP
rs1020029557	204	dbSNP
rs922735718	220	dbSNP
rs183598613	231	dbSNP
rs1222618686	239	dbSNP
rs1186372207	244	dbSNP
rs1248506094	263	dbSNP
rs1486403835	264	dbSNP
rs745878113	266	dbSNP
rs1391391346	268	dbSNP
rs1037305379	273	dbSNP
rs1167033349	275	dbSNP
rs559483954	282	dbSNP
rs1405567671	283	dbSNP
rs1021798004	292	dbSNP
rs1325157970	293	dbSNP
rs907574482	304	dbSNP
rs757719231	314	dbSNP
rs546442131	316	dbSNP
rs984471424	323	dbSNP
rs1347602316	332	dbSNP
rs1435201537	333	dbSNP
rs1320655235	335	dbSNP
rs542795019	336	dbSNP
rs1367187526	342	dbSNP
rs1226133430	343	dbSNP
rs1296538842	346	dbSNP
rs1322847661	351	dbSNP
rs951763606	359	dbSNP
rs73530687	360	dbSNP
rs990948936	361	dbSNP
rs999214100	366	dbSNP
rs960548557	371	dbSNP
rs1248732662	372	dbSNP
rs1466598495	373	dbSNP
rs1389903354	377	dbSNP
rs1034800335	382	dbSNP
rs1046480894	393	dbSNP
rs1381386685	395	dbSNP
rs948007915	397	dbSNP
rs1159206106	398	dbSNP
rs1390235011	399	dbSNP
rs1432783194	400	dbSNP
rs148609544	406	dbSNP
rs1048235452	409	dbSNP
rs966589390	410	dbSNP
rs1282230130	419	dbSNP
rs1022755992	421	dbSNP
rs764431344	424	dbSNP
rs1404699160	431	dbSNP
rs1268826097	436	dbSNP
rs368276605	437	dbSNP
rs931160301	438	dbSNP
rs2281789	439	dbSNP
rs1248009371	449	dbSNP
rs753534314	473	dbSNP
rs2281788	486	dbSNP
rs912570838	487	dbSNP
rs985826044	499	dbSNP
rs998653358	504	dbSNP
rs901364644	510	dbSNP
rs557974238	511	dbSNP
rs569974052	517	dbSNP
rs956231977	519	dbSNP
rs11284956	535	dbSNP
rs1416109569	535	dbSNP
rs769538300	535	dbSNP
rs940295355	538	dbSNP
rs910139825	545	dbSNP
rs1049088753	567	dbSNP
rs183865858	568	dbSNP
rs78229426	571	dbSNP
rs75946912	573	dbSNP
rs1339704311	587	dbSNP
rs555636641	590	dbSNP
rs1414364236	594	dbSNP
rs1289288864	611	dbSNP
rs757734614	632	dbSNP
rs1226588657	636	dbSNP
rs1260223053	637	dbSNP
rs1202728005	638	dbSNP
rs1276920107	639	dbSNP
rs1442249127	640	dbSNP
rs535641733	659	dbSNP
rs1182446990	662	dbSNP
rs1253602201	665	dbSNP
rs1461070142	669	dbSNP
rs930341129	682	dbSNP
rs1243817112	688	dbSNP
rs916210788	690	dbSNP
rs1180750100	697	dbSNP
rs1205712774	699	dbSNP
rs1316161277	701	dbSNP
rs550117565	702	dbSNP

- Cell, 2010

RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.

- 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.