ID	Duplex structure	Position	Score	MFE
1	miRNA 3' uaUUUGCUGUGGAGGAACUCUu 5' |||:|| | |||||| Target 5' tgAAATGA-A-----TTGAGAa 3'	289 - 304	121.00	-8.90
2	miRNA 3' uaUUUGCUGUGGAGGAACUcuu 5' || ||:: :||:|||| Target 5' gtAATCGGTTGTTCTTTGAacg 3'	343 - 364	108.00	-9.42
3	miRNA 3' uauuugcuguggaggaACUCUu 5' ||||| Target 5' catctgtgtttttaagTGAGAt 3'	205 - 226	100.00	-6.60

Mutant ID	Mutant Position	Mutant Source
COSN31507316	1	COSMIC
COSN31505198	12	COSMIC
COSN30466128	19	COSMIC
COSN30116568	20	COSMIC
COSN30178472	23	COSMIC
COSN30469065	32	COSMIC
COSN30580183	57	COSMIC
COSN23266065	78	COSMIC
COSN31511467	78	COSMIC
COSN31506033	119	COSMIC
COSN31584211	131	COSMIC
COSN9622367	179	COSMIC
COSN7038358	217	COSMIC
COSN20801480	228	COSMIC
COSN1669791	273	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs747027019	1	dbSNP
rs778020558	2	dbSNP
rs1178858077	3	dbSNP
rs758655095	4	dbSNP
rs1425667246	6	dbSNP
rs374658626	7	dbSNP
rs758118772	8	dbSNP
rs1365290859	10	dbSNP
rs1362867333	19	dbSNP
rs566506798	20	dbSNP
rs754299507	29	dbSNP
rs750303660	30	dbSNP
rs1400199662	32	dbSNP
rs1185989652	35	dbSNP
rs34498210	35	dbSNP
rs1282283922	36	dbSNP
rs1364869699	41	dbSNP
rs1474586198	43	dbSNP
rs766845457	47	dbSNP
rs756631995	49	dbSNP
rs771940768	58	dbSNP
rs1290641257	60	dbSNP
rs369367209	62	dbSNP
rs1340343468	63	dbSNP
rs1217619328	64	dbSNP
rs1401050528	71	dbSNP
rs1246408315	72	dbSNP
rs995890784	74	dbSNP
rs78609920	75	dbSNP
rs746065614	76	dbSNP
rs1426002647	92	dbSNP
rs539556193	102	dbSNP
rs9785	107	dbSNP
rs1382518216	108	dbSNP
rs1382973860	112	dbSNP
rs1158201866	121	dbSNP
rs1347693118	122	dbSNP
rs1055839322	130	dbSNP
rs550786085	131	dbSNP
rs1458014078	133	dbSNP
rs1053383490	134	dbSNP
rs935037066	143	dbSNP
rs907386628	144	dbSNP
rs10739	152	dbSNP
rs372960771	162	dbSNP
rs532769431	163	dbSNP
rs1236768383	169	dbSNP
rs949562529	178	dbSNP
rs867874000	179	dbSNP
rs990866651	185	dbSNP
rs1177304736	189	dbSNP
rs952763083	190	dbSNP
rs1440859798	194	dbSNP
rs920045204	196	dbSNP
rs1162965776	202	dbSNP
rs972709186	206	dbSNP
rs984419012	207	dbSNP
rs931676754	211	dbSNP
rs1165093379	219	dbSNP
rs921674142	221	dbSNP
rs562053527	224	dbSNP
rs1332812723	226	dbSNP
rs1269653815	230	dbSNP
rs1447243738	232	dbSNP
rs1282167330	235	dbSNP
rs8920	249	dbSNP
rs1378910382	250	dbSNP
rs1285300631	252	dbSNP
rs1196761943	255	dbSNP
rs1450895163	266	dbSNP
rs1324743765	269	dbSNP
rs1320026747	273	dbSNP
rs528758213	277	dbSNP
rs954667253	283	dbSNP
rs1031228871	294	dbSNP
rs1028776421	306	dbSNP
rs189280500	308	dbSNP
rs1422401515	311	dbSNP
rs1463742171	314	dbSNP
rs545843285	327	dbSNP
rs977965281	330	dbSNP
rs893540261	333	dbSNP
rs1022208101	334	dbSNP
rs778206989	341	dbSNP
rs1448552167	342	dbSNP
rs1277343426	348	dbSNP
rs999571003	349	dbSNP
rs902197552	350	dbSNP
rs1034418088	353	dbSNP
rs1280117821	357	dbSNP
rs1340201300	358	dbSNP
rs575715331	363	dbSNP
rs1277193005	366	dbSNP
rs751169727	379	dbSNP
rs949667001	382	dbSNP
rs895432068	387	dbSNP
rs1055296338	388	dbSNP
rs1464968333	389	dbSNP
rs888028757	397	dbSNP
rs1249433208	407	dbSNP
rs1211514162	410	dbSNP
rs1423678259	412	dbSNP
rs1477445461	416	dbSNP
rs767529021	418	dbSNP
rs1049375958	419	dbSNP
rs931491652	422	dbSNP
rs1291104190	423	dbSNP
rs919994351	427	dbSNP
rs1337967514	433	dbSNP
rs931624522	435	dbSNP
rs1300355371	445	dbSNP

- Genes & development, 2011

MicroRNAs are important regulators in many cellular processes, including stem cell self-renewal. Recent studies demonstrated their function as pluripotency factors with the capacity for somatic cell reprogramming. However, their role in human embryonic stem (ES) cells (hESCs) remains poorly understood, partially due to the lack of genome-wide strategies to identify their targets. Here, we performed comprehensive microRNA profiling in hESCs and in purified neural and mesenchymal derivatives. Using a combination of AGO cross-linking and microRNA perturbation experiments, together with computational prediction, we identified the targets of the miR-302/367 cluster, the most abundant microRNAs in hESCs. Functional studies identified novel roles of miR-302/367 in maintaining pluripotency and regulating hESC differentiation. We show that in addition to its role in TGF-beta signaling, miR-302/367 promotes bone morphogenetic protein (BMP) signaling by targeting BMP inhibitors TOB2, DAZAP2, and SLAIN1. This study broadens our understanding of microRNA function in hESCs and is a valuable resource for future studies in this area.

- 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.