ID	Duplex structure	Position	Score	MFE
1	miRNA 3' auUUCGUCGUGUCAUUAUAACc 5' || :: : :| |||||||| Target 5' ggAAATGTTTTA-TAATATTGg 3'	1668 - 1688	147.00	-8.30
2	miRNA 3' auUUCGUCGUGUCAUUAUAAcc 5' | || |||| ||:|||| Target 5' ttATGCTGCAC--TAGTATTcc 3'	869 - 888	128.00	-8.17
3	miRNA 3' auUUC--GU-CGUGUCAUUAUAAcc 5' ||| || | ||||||||| | Target 5' ttAAGGTCATGAACAGTAATAATtt 3'	1354 - 1378	122.00	-9.46

Mutant ID	Mutant Position	Mutant Source
COSN31527117	11	COSMIC
COSN30112904	12	COSMIC
COSN1270054	28	COSMIC
COSN30146198	31	COSMIC
COSN30131503	55	COSMIC
COSN31506035	60	COSMIC
COSN26554482	86	COSMIC
COSN16129758	91	COSMIC
COSN31495769	98	COSMIC
COSN1270052	119	COSMIC
COSN30149192	127	COSMIC
COSN30497356	188	COSMIC
COSN31536213	308	COSMIC
COSN31609131	364	COSMIC
COSN17447657	422	COSMIC
COSN16032350	485	COSMIC
COSN27230588	498	COSMIC
COSN31482008	550	COSMIC
COSN31518597	570	COSMIC
COSN1922121	604	COSMIC
COSN30173585	793	COSMIC
COSN31517016	862	COSMIC
COSN31544305	1047	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs768204169	3	dbSNP
rs746508915	11	dbSNP
rs542987082	12	dbSNP
rs1194358903	16	dbSNP
rs758362547	19	dbSNP
rs143624984	20	dbSNP
rs373592898	22	dbSNP
rs140402906	23	dbSNP
rs776024182	27	dbSNP
rs1157330402	28	dbSNP
rs756970450	28	dbSNP
rs1462372048	29	dbSNP
rs753016492	29	dbSNP
rs1216036834	33	dbSNP
rs767834871	39	dbSNP
rs1413667128	42	dbSNP
rs759753708	44	dbSNP
rs1369608788	45	dbSNP
rs751690453	46	dbSNP
rs1280902449	49	dbSNP
rs766309027	49	dbSNP
rs763541242	51	dbSNP
rs1291814330	53	dbSNP
rs1373834858	54	dbSNP
rs534762091	57	dbSNP
rs930053721	59	dbSNP
rs527471238	61	dbSNP
rs895357813	67	dbSNP
rs565727111	69	dbSNP
rs919913772	83	dbSNP
rs374255337	85	dbSNP
rs1469777475	88	dbSNP
rs942927187	91	dbSNP
rs749510947	94	dbSNP
rs1416324879	95	dbSNP
rs543535910	97	dbSNP
rs1277568923	98	dbSNP
rs987025264	103	dbSNP
rs1330264160	104	dbSNP
rs778050503	108	dbSNP
rs535648814	111	dbSNP
rs1277556699	115	dbSNP
rs1000601531	122	dbSNP
rs17040912	124	dbSNP
rs17040910	129	dbSNP
rs997349564	140	dbSNP
rs879347394	144	dbSNP
rs901766180	150	dbSNP
rs1038989037	154	dbSNP
rs1011271834	159	dbSNP
rs943178505	161	dbSNP
rs530908643	166	dbSNP
rs909074989	175	dbSNP
rs1048480396	179	dbSNP
rs1034247843	180	dbSNP
rs1476646052	185	dbSNP
rs1169156519	187	dbSNP
rs931401729	192	dbSNP
rs1419517024	197	dbSNP
rs1202087649	201	dbSNP
rs1480989439	203	dbSNP
rs1326426570	205	dbSNP
rs918549534	213	dbSNP
rs1377093079	214	dbSNP
rs1415205833	218	dbSNP
rs1311996824	221	dbSNP
rs745431868	222	dbSNP
rs972735337	226	dbSNP
rs970785989	227	dbSNP
rs866703887	235	dbSNP
rs1198307421	238	dbSNP
rs907001363	245	dbSNP
rs182466300	246	dbSNP
rs146742467	247	dbSNP
rs1213083402	250	dbSNP
rs528628971	253	dbSNP
rs1486097764	254	dbSNP
rs1210642192	255	dbSNP
rs1316292009	259	dbSNP
rs1032488176	262	dbSNP
rs781754336	266	dbSNP
rs1449238808	268	dbSNP
rs966436667	269	dbSNP
rs1373202403	272	dbSNP
rs1038762831	273	dbSNP
rs1225095406	278	dbSNP
rs942687587	283	dbSNP
rs911230985	284	dbSNP
rs1434893203	290	dbSNP
rs1172791076	296	dbSNP
rs1373389524	307	dbSNP
rs559603816	307	dbSNP
rs997131871	308	dbSNP
rs1383911285	316	dbSNP
rs1325972444	320	dbSNP
rs1428757566	329	dbSNP
rs542768241	333	dbSNP
rs1233752626	334	dbSNP
rs1348880991	334	dbSNP
rs557010510	335	dbSNP
rs1051246953	341	dbSNP
rs1039350292	342	dbSNP
rs1364102032	343	dbSNP
rs1007488224	350	dbSNP
rs1445730089	351	dbSNP
rs924102282	352	dbSNP
rs368323320	353	dbSNP
rs554177845	353	dbSNP
rs967520790	355	dbSNP
rs1375772792	370	dbSNP
rs1343912785	372	dbSNP
rs914300351	375	dbSNP
rs757887097	377	dbSNP
rs1158892181	387	dbSNP
rs1384188349	389	dbSNP
rs1455519849	391	dbSNP
rs887583410	393	dbSNP
rs990325750	397	dbSNP
rs1440516290	398	dbSNP
rs958360772	398	dbSNP
rs1301497135	406	dbSNP
rs1337941597	407	dbSNP
rs1240239644	410	dbSNP
rs751922855	411	dbSNP
rs1002784125	425	dbSNP
rs1431106414	428	dbSNP
rs1216093318	429	dbSNP
rs1263160911	432	dbSNP
rs1468524696	434	dbSNP
rs546830568	436	dbSNP
rs1025463392	443	dbSNP
rs1246101717	445	dbSNP
rs994030179	445	dbSNP
rs1471605360	448	dbSNP
rs1205560753	450	dbSNP
rs931349577	459	dbSNP
rs778230681	461	dbSNP
rs1231277137	463	dbSNP
rs529469315	465	dbSNP
rs1309522195	468	dbSNP
rs1037155471	469	dbSNP
rs949398056	474	dbSNP
rs1334338552	477	dbSNP
rs1235733385	479	dbSNP
rs1007387327	486	dbSNP
rs1334726779	488	dbSNP
rs1214035514	493	dbSNP
rs1263102705	496	dbSNP
rs1342096803	501	dbSNP
rs1180413920	508	dbSNP
rs917955896	509	dbSNP
rs1196009550	510	dbSNP
rs1051078316	511	dbSNP
rs544125875	511	dbSNP
rs889757509	511	dbSNP
rs934228152	511	dbSNP
rs991452910	513	dbSNP
rs11549873	515	dbSNP
rs1374861948	519	dbSNP
rs758478970	522	dbSNP
rs543741360	525	dbSNP
rs1042634153	540	dbSNP
rs1297804294	550	dbSNP
rs925416152	556	dbSNP
rs979579050	561	dbSNP
rs1313818845	562	dbSNP
rs966884985	569	dbSNP
rs1453989509	571	dbSNP
rs958734545	572	dbSNP
rs1310036288	577	dbSNP
rs577562367	579	dbSNP
rs752974257	580	dbSNP
rs1250380384	584	dbSNP
rs997303257	585	dbSNP
rs189676274	587	dbSNP
rs1257885481	588	dbSNP
rs1374414159	589	dbSNP
rs1485343052	597	dbSNP
rs1017288319	603	dbSNP
rs1264006985	609	dbSNP
rs1429171435	610	dbSNP
rs1007846962	613	dbSNP
rs1169782365	615	dbSNP
rs971290143	626	dbSNP
rs1436758524	629	dbSNP
rs1174658476	630	dbSNP
rs1375214549	631	dbSNP
rs34297281	631	dbSNP
rs1427406701	635	dbSNP
rs1291117820	636	dbSNP
rs1363504268	644	dbSNP
rs564889818	648	dbSNP
rs187178327	660	dbSNP
rs887700400	662	dbSNP
rs1027605946	663	dbSNP
rs1387790421	664	dbSNP
rs1185286843	666	dbSNP
rs993326170	668	dbSNP
rs1461732213	669	dbSNP
rs1242264972	670	dbSNP
rs375073216	671	dbSNP
rs781764784	672	dbSNP
rs557774314	678	dbSNP
rs1486127746	680	dbSNP
rs1006965101	681	dbSNP
rs949511532	688	dbSNP
rs183150942	689	dbSNP
rs998114433	689	dbSNP
rs1394902895	693	dbSNP
rs1413090140	694	dbSNP
rs1161682585	698	dbSNP
rs140008056	700	dbSNP
rs777846318	702	dbSNP
rs1319383133	709	dbSNP
rs375639263	709	dbSNP
rs555190686	710	dbSNP
rs1317268973	712	dbSNP
rs576026987	714	dbSNP
rs202125130	715	dbSNP
rs1247287462	719	dbSNP
rs1366424620	720	dbSNP
rs535608651	726	dbSNP
rs1382738007	728	dbSNP
rs866188261	733	dbSNP
rs946967284	733	dbSNP
rs771348955	735	dbSNP
rs1311259014	736	dbSNP
rs893967372	738	dbSNP
rs1055740430	739	dbSNP
rs749968736	739	dbSNP
rs1214592442	746	dbSNP
rs1252643987	757	dbSNP
rs569897354	758	dbSNP
rs1397742740	762	dbSNP
rs1179331386	768	dbSNP
rs1409084398	768	dbSNP
rs937089237	769	dbSNP
rs1461186882	770	dbSNP
rs555020441	770	dbSNP
rs1157560050	771	dbSNP
rs1385857847	772	dbSNP
rs927058493	775	dbSNP
rs1325940771	776	dbSNP
rs1348958891	779	dbSNP
rs1433775902	780	dbSNP
rs1368110022	784	dbSNP
rs979694278	787	dbSNP
rs1357888645	790	dbSNP
rs1164969794	801	dbSNP
rs1444762559	803	dbSNP
rs1336804608	804	dbSNP
rs981200474	807	dbSNP
rs1289165181	808	dbSNP
rs1185398886	809	dbSNP
rs1450086872	809	dbSNP
rs945534658	814	dbSNP
rs949676026	817	dbSNP
rs1250973095	823	dbSNP
rs756789683	824	dbSNP
rs1482915662	825	dbSNP
rs1491172507	825	dbSNP
rs1180421281	833	dbSNP
rs1420685465	834	dbSNP
rs918257730	836	dbSNP
rs1482209365	837	dbSNP
rs1293991563	842	dbSNP
rs747781541	845	dbSNP
rs1223277145	847	dbSNP
rs914084611	851	dbSNP
rs1354932964	859	dbSNP
rs765433393	866	dbSNP
rs965823051	868	dbSNP
rs1264200551	873	dbSNP
rs1357303533	876	dbSNP
rs759605226	877	dbSNP
rs1016763033	879	dbSNP
rs1283740727	899	dbSNP
rs1354311540	901	dbSNP
rs1216588706	905	dbSNP
rs985806093	906	dbSNP
rs556473243	913	dbSNP
rs548047475	916	dbSNP
rs1408800214	919	dbSNP
rs1027553595	921	dbSNP
rs146584585	924	dbSNP
rs897633363	934	dbSNP
rs1304639523	935	dbSNP
rs1236436130	939	dbSNP
rs1424721718	941	dbSNP
rs867703514	947	dbSNP
rs1389465665	958	dbSNP
rs1161319532	961	dbSNP
rs1455293733	963	dbSNP
rs1020947289	964	dbSNP
rs763682905	964	dbSNP
rs902489939	964	dbSNP
rs1364109102	966	dbSNP
rs753962438	966	dbSNP
rs1180859567	967	dbSNP
rs1338587448	971	dbSNP
rs1471510409	971	dbSNP
rs778546408	973	dbSNP
rs1200503217	974	dbSNP
rs1490188165	976	dbSNP
rs1014047762	977	dbSNP
rs896578929	983	dbSNP
rs1282989472	984	dbSNP
rs1207362443	987	dbSNP
rs1349017271	987	dbSNP
rs1801741	989	dbSNP
rs938024855	990	dbSNP
rs1801742	993	dbSNP
rs1449186066	996	dbSNP
rs551713444	997	dbSNP
rs377233575	1005	dbSNP
rs1448567837	1006	dbSNP
rs1055286514	1009	dbSNP
rs1237896714	1014	dbSNP
rs938149132	1015	dbSNP
rs761765508	1016	dbSNP
rs1226924062	1022	dbSNP
rs1396704816	1024	dbSNP
rs1466389801	1028	dbSNP
rs1326173901	1033	dbSNP
rs774096217	1034	dbSNP
rs1400000946	1035	dbSNP
rs542198069	1036	dbSNP
rs906716352	1036	dbSNP
rs1284796169	1037	dbSNP
rs768503526	1037	dbSNP
rs1387986177	1042	dbSNP
rs1405179638	1042	dbSNP
rs1329942596	1052	dbSNP
rs761171945	1053	dbSNP
rs1321033504	1055	dbSNP
rs1433227128	1055	dbSNP
rs949788271	1060	dbSNP
rs1312005493	1066	dbSNP
rs1180387525	1070	dbSNP
rs918246521	1073	dbSNP
rs1233010036	1081	dbSNP
rs1273381485	1085	dbSNP
rs1353473222	1088	dbSNP
rs914030706	1092	dbSNP
rs1268276468	1093	dbSNP
rs199586110	1096	dbSNP
rs976284772	1101	dbSNP
rs1464025531	1105	dbSNP
rs944903292	1106	dbSNP
rs546438916	1107	dbSNP
rs910298416	1112	dbSNP
rs1455439975	1113	dbSNP
rs1206238868	1120	dbSNP
rs1254520784	1126	dbSNP
rs528481804	1135	dbSNP
rs566137965	1138	dbSNP
rs374360027	1150	dbSNP
rs972847648	1150	dbSNP
rs941268055	1154	dbSNP
rs1245016779	1158	dbSNP
rs909764332	1159	dbSNP
rs1455735991	1161	dbSNP
rs1327948522	1162	dbSNP
rs951680218	1163	dbSNP
rs1195380683	1170	dbSNP
rs1391736855	1175	dbSNP
rs1386360954	1176	dbSNP
rs549083065	1176	dbSNP
rs1322061521	1184	dbSNP
rs985415290	1186	dbSNP
rs971952385	1187	dbSNP
rs1240447938	1189	dbSNP
rs961958959	1190	dbSNP
rs953843242	1191	dbSNP
rs868291477	1194	dbSNP
rs1261629762	1199	dbSNP
rs574818858	1200	dbSNP
rs1274435955	1205	dbSNP
rs1488643063	1206	dbSNP
rs1207460330	1209	dbSNP
rs1208861243	1209	dbSNP
rs1182578606	1211	dbSNP
rs1411175263	1220	dbSNP
rs529430868	1221	dbSNP
rs958828676	1222	dbSNP
rs35557901	1225	dbSNP
rs1033752379	1230	dbSNP
rs1369122398	1234	dbSNP
rs1457646472	1236	dbSNP
rs150004928	1237	dbSNP
rs903838457	1242	dbSNP
rs1410854243	1245	dbSNP
rs1043708595	1246	dbSNP
rs1009738783	1252	dbSNP
rs1417160240	1253	dbSNP
rs1294659268	1256	dbSNP
rs1243669165	1261	dbSNP
rs1321776153	1261	dbSNP
rs771265798	1262	dbSNP
rs1272758768	1264	dbSNP
rs1228944784	1265	dbSNP
rs892710490	1267	dbSNP
rs1020935755	1269	dbSNP
rs1205623078	1275	dbSNP
rs554838053	1283	dbSNP
rs1011354050	1284	dbSNP
rs1482070809	1288	dbSNP
rs534947466	1292	dbSNP
rs1257012116	1294	dbSNP
rs550051562	1295	dbSNP
rs1375017277	1297	dbSNP
rs1430572898	1299	dbSNP
rs910738794	1304	dbSNP
rs1050155605	1314	dbSNP
rs1002458374	1316	dbSNP
rs1303908017	1321	dbSNP
rs1432829050	1323	dbSNP
rs906664023	1326	dbSNP
rs1046633784	1329	dbSNP
rs1366918966	1343	dbSNP
rs1014008673	1349	dbSNP
rs1273717320	1358	dbSNP
rs1339776848	1358	dbSNP
rs879786952	1358	dbSNP
rs930398984	1360	dbSNP
rs755985344	1361	dbSNP
rs533634759	1364	dbSNP
rs368938417	1373	dbSNP
rs557214649	1373	dbSNP
rs1482853732	1376	dbSNP
rs1263942209	1377	dbSNP
rs920220158	1377	dbSNP
rs1337185072	1378	dbSNP
rs1036797628	1382	dbSNP
rs941003115	1390	dbSNP
rs1169929805	1396	dbSNP
rs1475777748	1406	dbSNP
rs1455881976	1407	dbSNP
rs971731670	1408	dbSNP
rs1359105505	1422	dbSNP
rs775195943	1423	dbSNP
rs769401565	1426	dbSNP
rs867064802	1428	dbSNP
rs1300634288	1432	dbSNP
rs917172896	1441	dbSNP
rs993179493	1444	dbSNP
rs1296377638	1446	dbSNP
rs976578707	1446	dbSNP
rs958536343	1447	dbSNP
rs1301637032	1451	dbSNP
rs1311603194	1452	dbSNP
rs770981630	1457	dbSNP
rs1034613126	1458	dbSNP
rs1207920529	1458	dbSNP
rs564627166	1462	dbSNP
rs968108948	1463	dbSNP
rs540992615	1465	dbSNP
rs1246443649	1467	dbSNP
rs1009519812	1470	dbSNP
rs971006172	1473	dbSNP
rs750416243	1476	dbSNP
rs571960497	1477	dbSNP
rs191637952	1483	dbSNP
rs1413582893	1484	dbSNP
rs538868036	1486	dbSNP
rs1226028881	1491	dbSNP
rs1009577423	1492	dbSNP
rs1384863403	1497	dbSNP
rs761758846	1499	dbSNP
rs1217448579	1510	dbSNP
rs57131307	1511	dbSNP
rs889267559	1511	dbSNP
rs1050585816	1523	dbSNP
rs930346444	1531	dbSNP
rs1037151774	1538	dbSNP
rs574519309	1538	dbSNP
rs1222564050	1540	dbSNP
rs920337421	1544	dbSNP
rs1036155974	1549	dbSNP
rs1487691235	1549	dbSNP
rs1253196574	1550	dbSNP
rs1472512508	1553	dbSNP
rs1157861477	1555	dbSNP
rs745348070	1556	dbSNP
rs916932442	1557	dbSNP
rs1165002843	1559	dbSNP
rs992734217	1562	dbSNP
rs1369975942	1566	dbSNP
rs1434063264	1566	dbSNP
rs561749790	1567	dbSNP
rs922551480	1570	dbSNP
rs927111887	1571	dbSNP
rs1446565522	1572	dbSNP
rs1286591119	1573	dbSNP
rs1409127149	1573	dbSNP
rs1454551912	1574	dbSNP
rs187107167	1575	dbSNP
rs1181851068	1577	dbSNP
rs968561875	1577	dbSNP
rs1022317739	1578	dbSNP
rs1491035011	1580	dbSNP
rs370667091	1580	dbSNP
rs554425500	1580	dbSNP
rs576862284	1580	dbSNP
rs796089351	1580	dbSNP
rs1234974646	1587	dbSNP
rs572655675	1588	dbSNP
rs780870073	1594	dbSNP
rs989936759	1606	dbSNP
rs1019383356	1607	dbSNP
rs958180741	1612	dbSNP
rs139378364	1613	dbSNP
rs748549787	1613	dbSNP
rs1202378658	1626	dbSNP
rs889375660	1634	dbSNP
rs1029283182	1647	dbSNP
rs995003836	1649	dbSNP
rs377343722	1651	dbSNP
rs556440475	1658	dbSNP
rs970953783	1659	dbSNP
rs1376629389	1661	dbSNP
rs373339118	1665	dbSNP
rs1203409519	1666	dbSNP
rs1281379131	1678	dbSNP
rs539655992	1685	dbSNP
rs940452263	1699	dbSNP
rs181642842	1700	dbSNP
rs539141406	1707	dbSNP
rs1426613914	1708	dbSNP
rs1190083188	1710	dbSNP
rs1016468673	1711	dbSNP
rs937054856	1717	dbSNP
rs1164622705	1726	dbSNP
rs1414966942	1728	dbSNP
rs1404119459	1730	dbSNP
rs927209749	1731	dbSNP
rs747519229	1734	dbSNP

- mBio, 2013

UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.

- 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.