ID	Duplex structure	Position	Score	MFE
1	miRNA 3' uuUAGG-GUAGG--GGU-CCUUGGgg 5' |||: :| || ||| ||:||| Target 5' --ATCTATAGCCAACCAGGGGACCac 3'	1 - 24	122.00	-17.40
2	miRNA 3' uuuaggguaggggucCUUGGGg 5' |||||| Target 5' gcaggagaattgcttGAACCCa 3'	291 - 312	120.00	-12.20
3	miRNA 3' uuUAGGGU--AGGGGUCCUUGGGg 5' |||||| |::::|||: || Target 5' taATCCCAGCACTTTGGGAGGCCg 3'	127 - 150	118.00	-21.20

Mutant ID	Mutant Position	Mutant Source
COSN26968226	3	COSMIC
COSN30473227	49	COSMIC
COSN30493179	52	COSMIC
COSN31552207	57	COSMIC
COSN30139856	120	COSMIC
COSN5276506	215	COSMIC
COSN16273139	721	COSMIC
COSN26262958	746	COSMIC
COSN22250134	821	COSMIC
COSN5859839	864	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs769037979	2	dbSNP
rs761947124	4	dbSNP
rs1041278623	6	dbSNP
rs904393626	7	dbSNP
rs752893520	16	dbSNP
rs17879039	18	dbSNP
rs1253519929	20	dbSNP
rs750888847	23	dbSNP
rs1236905552	24	dbSNP
rs761145191	27	dbSNP
rs766761833	31	dbSNP
rs754197188	34	dbSNP
rs1162066027	41	dbSNP
rs1224773044	43	dbSNP
rs542009468	48	dbSNP
rs777354391	49	dbSNP
rs888846940	50	dbSNP
rs1330317956	61	dbSNP
rs1006069078	63	dbSNP
rs1305820944	72	dbSNP
rs1391649981	73	dbSNP
rs1398356378	82	dbSNP
rs1300923398	93	dbSNP
rs1014162764	98	dbSNP
rs1025009779	100	dbSNP
rs1178530405	106	dbSNP
rs1037507431	107	dbSNP
rs897749416	108	dbSNP
rs993455331	115	dbSNP
rs1351298555	120	dbSNP
rs1362177975	121	dbSNP
rs1181356360	135	dbSNP
rs1419964824	137	dbSNP
rs1252950057	141	dbSNP
rs1002739256	150	dbSNP
rs1035606230	151	dbSNP
rs960344692	153	dbSNP
rs1215305503	156	dbSNP
rs1283295834	160	dbSNP
rs1012901295	162	dbSNP
rs1264243513	163	dbSNP
rs1206173802	172	dbSNP
rs1023490502	173	dbSNP
rs1347877802	175	dbSNP
rs1278507675	188	dbSNP
rs1239297743	195	dbSNP
rs1337101118	200	dbSNP
rs1490682142	202	dbSNP
rs963761320	204	dbSNP
rs968804051	213	dbSNP
rs1383321915	216	dbSNP
rs1199711025	218	dbSNP
rs751474682	221	dbSNP
rs1455640191	222	dbSNP
rs185693154	223	dbSNP
rs1026418373	230	dbSNP
rs1158013372	230	dbSNP
rs924820543	231	dbSNP
rs10883798	232	dbSNP
rs1364929563	237	dbSNP
rs1365718746	238	dbSNP
rs987669004	249	dbSNP
rs1419596107	251	dbSNP
rs1157343330	252	dbSNP
rs977000457	257	dbSNP
rs797018563	264	dbSNP
rs17881031	265	dbSNP
rs564095616	267	dbSNP
rs1050063566	268	dbSNP
rs910299238	274	dbSNP
rs934376199	277	dbSNP
rs941723393	280	dbSNP
rs748058096	281	dbSNP
rs1316970124	294	dbSNP
rs917076039	296	dbSNP
rs1325720958	299	dbSNP
rs1318931207	301	dbSNP
rs1382802968	305	dbSNP
rs897698585	306	dbSNP
rs1409355966	309	dbSNP
rs1161866552	313	dbSNP
rs1424332713	314	dbSNP
rs949982791	319	dbSNP
rs1165798197	324	dbSNP
rs1384925217	331	dbSNP
rs1044334169	337	dbSNP
rs1242002413	342	dbSNP
rs531237403	344	dbSNP
rs189373200	345	dbSNP
rs1266234621	346	dbSNP
rs1239361825	351	dbSNP
rs1359636984	360	dbSNP
rs1306912611	369	dbSNP
rs11191456	375	dbSNP
rs1338535660	377	dbSNP
rs1222576513	378	dbSNP
rs1002219978	380	dbSNP
rs1264551737	383	dbSNP
rs1487287767	386	dbSNP
rs1197969730	387	dbSNP
rs1251729636	391	dbSNP
rs1334687012	392	dbSNP
rs1366353743	392	dbSNP
rs1197988263	393	dbSNP
rs1202069576	393	dbSNP
rs1270536597	393	dbSNP
rs1341181950	393	dbSNP
rs1427833820	393	dbSNP
rs1476707627	393	dbSNP
rs1490380850	393	dbSNP
rs370301616	393	dbSNP
rs386372295	393	dbSNP
rs1439420520	394	dbSNP
rs1177330167	395	dbSNP
rs1387560302	401	dbSNP
rs1445387543	404	dbSNP
rs1038079837	406	dbSNP
rs1348410283	407	dbSNP
rs1197467028	408	dbSNP
rs1259585118	409	dbSNP
rs1321259178	409	dbSNP
rs1346254266	409	dbSNP
rs1463746493	410	dbSNP
rs1491041372	411	dbSNP
rs10679836	412	dbSNP
rs1400773897	412	dbSNP
rs111383152	413	dbSNP
rs1329308547	417	dbSNP
rs202234330	421	dbSNP
rs1228444024	423	dbSNP
rs375956115	427	dbSNP
rs369772168	432	dbSNP
rs1480466850	435	dbSNP
rs1484547027	452	dbSNP
rs1057426595	453	dbSNP
rs1251472198	469	dbSNP
rs1175110219	473	dbSNP
rs1469360235	477	dbSNP
rs1233110143	481	dbSNP
rs41310292	486	dbSNP
rs1459836950	487	dbSNP
rs1197142924	489	dbSNP
rs755782532	493	dbSNP
rs1022932994	501	dbSNP
rs993972360	505	dbSNP
rs180954710	509	dbSNP
rs1411741246	511	dbSNP
rs534291133	519	dbSNP
rs1430320109	525	dbSNP
rs552424615	526	dbSNP
rs1381107975	527	dbSNP
rs1423175254	535	dbSNP
rs1464958527	538	dbSNP
rs1470625688	544	dbSNP
rs1329018097	549	dbSNP
rs1360373380	551	dbSNP
rs1031703091	555	dbSNP
rs1156239556	565	dbSNP
rs1408260834	570	dbSNP
rs1009140186	577	dbSNP
rs1448710427	580	dbSNP
rs1017815201	582	dbSNP
rs1442520067	584	dbSNP
rs1355127244	589	dbSNP
rs965296369	595	dbSNP
rs978463086	596	dbSNP
rs558466019	598	dbSNP
rs1376363650	602	dbSNP
rs956228709	604	dbSNP
rs976921037	611	dbSNP
rs1316440228	614	dbSNP
rs1285197547	619	dbSNP
rs1030338288	620	dbSNP
rs1242640912	622	dbSNP
rs954285603	633	dbSNP
rs986205008	634	dbSNP
rs1314858464	639	dbSNP
rs1316910598	639	dbSNP
rs1217242160	640	dbSNP
rs1381885216	649	dbSNP
rs577065711	651	dbSNP
rs988552631	653	dbSNP
rs910259065	656	dbSNP
rs1429331597	662	dbSNP
rs375571471	667	dbSNP
rs1429355403	668	dbSNP
rs1324650277	684	dbSNP
rs941671160	685	dbSNP
rs1422433254	687	dbSNP
rs569371381	688	dbSNP
rs1163912477	697	dbSNP
rs917127989	698	dbSNP
rs1236160403	701	dbSNP
rs973180706	702	dbSNP
rs1486926886	703	dbSNP
rs949867589	704	dbSNP
rs1185913745	705	dbSNP
rs1485568208	708	dbSNP
rs1262799306	715	dbSNP
rs1476945987	716	dbSNP
rs918991274	729	dbSNP
rs1291319218	730	dbSNP
rs1247118457	732	dbSNP
rs1219478241	734	dbSNP
rs929142161	736	dbSNP
rs531706040	740	dbSNP
rs1175278346	741	dbSNP
rs895730546	745	dbSNP
rs1357357688	746	dbSNP
rs1299435575	755	dbSNP
rs1454949071	757	dbSNP
rs948703634	774	dbSNP
rs1044695385	782	dbSNP
rs1459232905	785	dbSNP
rs1339491060	786	dbSNP
rs17884001	789	dbSNP
rs1140107	790	dbSNP
rs1000134191	791	dbSNP
rs1140108	798	dbSNP
rs1031732528	804	dbSNP
rs891850579	815	dbSNP
rs1037732764	816	dbSNP
rs1223564550	819	dbSNP
rs899147211	837	dbSNP
rs993629769	852	dbSNP
rs540811697	856	dbSNP
rs1280685534	867	dbSNP
rs1284738122	875	dbSNP
rs1047799054	877	dbSNP
rs890498703	878	dbSNP
rs556611661	882	dbSNP
rs1394055906	887	dbSNP
rs1218999633	895	dbSNP
rs1017698665	908	dbSNP
rs574742253	916	dbSNP
rs568318005	919	dbSNP
rs1217488363	920	dbSNP
rs559483876	926	dbSNP
rs1029790726	954	dbSNP
rs796946519	958	dbSNP
rs748879649	960	dbSNP
rs1468276867	964	dbSNP
rs535749222	966	dbSNP
rs1428730383	971	dbSNP
rs1201877733	977	dbSNP
rs1435189593	988	dbSNP
rs1269789626	990	dbSNP
rs139614098	999	dbSNP
rs1017187443	1016	dbSNP
rs1458512114	1024	dbSNP
rs1260529906	1025	dbSNP
rs1046778	1028	dbSNP
rs955896169	1033	dbSNP
rs988436645	1034	dbSNP
rs1234804826	1041	dbSNP
rs973041717	1046	dbSNP
rs1420778839	1048	dbSNP
rs1159142035	1049	dbSNP
rs1391706111	1052	dbSNP
rs919023735	1062	dbSNP
rs929006386	1064	dbSNP
rs917010519	1065	dbSNP
rs545863602	1066	dbSNP
rs1405423269	1071	dbSNP
rs917122192	1074	dbSNP
rs776303877	1076	dbSNP
rs1173174628	1077	dbSNP
rs1377822343	1082	dbSNP
rs563999499	1085	dbSNP
rs979952977	1087	dbSNP
rs1044343360	1108	dbSNP
rs1304650450	1119	dbSNP
rs927102473	1120	dbSNP
rs1240491866	1123	dbSNP
rs1350092293	1131	dbSNP
rs1461217309	1145	dbSNP
rs1257483163	1147	dbSNP
rs941318784	1148	dbSNP
rs1436266356	1149	dbSNP
rs974387724	1150	dbSNP
rs145412261	1152	dbSNP
rs773810340	1154	dbSNP
rs1375930704	1156	dbSNP
rs925846786	1159	dbSNP
rs1047685906	1163	dbSNP
rs929309693	1163	dbSNP
rs1383387594	1167	dbSNP
rs890554033	1170	dbSNP
rs1397838322	1173	dbSNP
rs541948236	1177	dbSNP
rs1288508766	1180	dbSNP
rs1351607859	1183	dbSNP
rs1224813332	1195	dbSNP

- Genes & development, 2013

When adapting to environmental stress, cells attenuate and reprogram their translational output. In part, these altered translation profiles are established through changes in the interactions between RNA-binding proteins and mRNAs. The Argonaute 2 (Ago2)/microRNA (miRNA) machinery has been shown to participate in stress-induced translational up-regulation of a particular mRNA, CAT-1; however, a detailed, transcriptome-wide understanding of the involvement of Ago2 in the process has been lacking. Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by cross-linking immunoprecipitation (CLIP) followed by high-throughput sequencing (CLIP-seq). Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3' untranslated region (UTR) and coding sequence (CDS) sites exhibiting stronger interaction. Interestingly, target sites that were destined for release from Ago2 upon stress were depleted in miRNA complementarity signatures, suggesting an alternative mode of interaction. To compare the changes in Ago2-binding patterns across transcripts with changes in their translational states, we measured mRNA profiles on ribosome/polysome gradients by RNA sequencing (RNA-seq). Increased Ago2 occupancy correlated with stronger repression of translation for those mRNAs, as evidenced by a shift toward lighter gradient fractions upon stress, while release of Ago2 was associated with the limited number of transcripts that remained translated. Taken together, these data point to a role for Ago2 and the mammalian miRNAs in mediating the translational component of the stress response.

- 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.