ID	Duplex structure	Position	Score	MFE
1	miRNA 3' uuuaauccaucaccGUCACCUu 5' ||||||| Target 5' tgccctggggcacaCAGTGGAc 3'	184 - 205	140.00	-15.00
2	miRNA 3' uuUAAUC---CAUCACCGUCACCUu 5' | |:| | :|||||:| ||| Target 5' ggAGTGGGGCGGGGTGGCGGGGGAg 3'	351 - 375	116.00	-21.10
3	miRNA 3' uuUAAU-CCAUCACCGUCAccuu 5' || | |||| |||||| Target 5' agATCAGGGTA-AGGCAGTcagg 3'	598 - 619	103.00	-13.50

Mutant ID	Mutant Position	Mutant Source
COSN30523048	11	COSMIC
COSN30151864	14	COSMIC
COSN26563611	23	COSMIC
COSN30513196	43	COSMIC
COSN31552055	66	COSMIC
COSN7269298	133	COSMIC
COSN31605949	134	COSMIC
COSN9441033	186	COSMIC
COSN31575539	224	COSMIC
COSN22130537	278	COSMIC
COSN16485525	540	COSMIC
COSN29360022	635	COSMIC
COSN23216636	1260	COSMIC
COSN22363068	1545	COSMIC
COSN1707068	1607	COSMIC
COSN20923364	1675	COSMIC
COSN25525767	1736	COSMIC
COSN49958	2047	COSMIC
COSN9651625	2332	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs781497327	3	dbSNP
rs574134904	5	dbSNP
rs769990140	7	dbSNP
rs774386992	8	dbSNP
rs752367615	16	dbSNP
rs374643844	17	dbSNP
rs539898670	21	dbSNP
rs746416214	21	dbSNP
rs907775197	22	dbSNP
rs771995634	23	dbSNP
rs772909486	25	dbSNP
rs1432200519	29	dbSNP
rs760392264	32	dbSNP
rs766029964	36	dbSNP
rs1388937519	37	dbSNP
rs758853124	37	dbSNP
rs116767947	42	dbSNP
rs1473248389	44	dbSNP
rs759118405	45	dbSNP
rs764625263	47	dbSNP
rs1203910904	48	dbSNP
rs753299394	49	dbSNP
rs1180081701	51	dbSNP
rs868855113	52	dbSNP
rs1337789225	54	dbSNP
rs544747473	67	dbSNP
rs557032749	72	dbSNP
rs901654462	80	dbSNP
rs998681209	81	dbSNP
rs1287452030	85	dbSNP
rs1339688173	86	dbSNP
rs575706611	86	dbSNP
rs542815490	91	dbSNP
rs745927550	92	dbSNP
rs1000152283	98	dbSNP
rs1033245357	99	dbSNP
rs907773699	100	dbSNP
rs540629320	114	dbSNP
rs1226211609	116	dbSNP
rs1294795770	116	dbSNP
rs1010457429	118	dbSNP
rs973241865	121	dbSNP
rs1204298657	124	dbSNP
rs1244894748	131	dbSNP
rs1024911318	132	dbSNP
rs560314246	133	dbSNP
rs573241189	134	dbSNP
rs1157166764	144	dbSNP
rs1475886409	148	dbSNP
rs1412725082	151	dbSNP
rs760790452	152	dbSNP
rs1471116892	160	dbSNP
rs758034732	164	dbSNP
rs1451914908	172	dbSNP
rs980266924	173	dbSNP
rs1423225787	174	dbSNP
rs1233410316	175	dbSNP
rs865828638	177	dbSNP
rs16958753	179	dbSNP
rs562193676	181	dbSNP
rs904664571	185	dbSNP
rs907509965	187	dbSNP
rs1373562140	190	dbSNP
rs1433290936	192	dbSNP
rs940622490	193	dbSNP
rs996339215	194	dbSNP
rs532561716	199	dbSNP
rs756359605	199	dbSNP
rs1432524871	201	dbSNP
rs1161421901	202	dbSNP
rs1040254136	203	dbSNP
rs1424574629	209	dbSNP
rs1171885724	211	dbSNP
rs751094543	217	dbSNP
rs1464140390	218	dbSNP
rs1248313355	221	dbSNP
rs1217528559	222	dbSNP
rs374298689	225	dbSNP
rs931827754	226	dbSNP
rs1277305722	229	dbSNP
rs1220261534	236	dbSNP
rs1049842148	249	dbSNP
rs1264870338	250	dbSNP
rs1295853788	252	dbSNP
rs1327035470	256	dbSNP
rs1207842449	257	dbSNP
rs1284752049	258	dbSNP
rs373089255	258	dbSNP
rs1290801974	261	dbSNP
rs1447783777	262	dbSNP
rs889852964	263	dbSNP
rs11548445	264	dbSNP
rs1491119265	264	dbSNP
rs1390595807	265	dbSNP
rs1482079449	265	dbSNP
rs1491571092	265	dbSNP
rs768997456	266	dbSNP
rs973294045	272	dbSNP
rs530575855	273	dbSNP
rs1027915254	276	dbSNP
rs891773756	278	dbSNP
rs1200262696	293	dbSNP
rs969235733	293	dbSNP
rs16958754	303	dbSNP
rs1226762259	314	dbSNP
rs1378788089	315	dbSNP
rs567559483	316	dbSNP
rs190048746	320	dbSNP
rs1284826669	321	dbSNP
rs546936117	322	dbSNP
rs1024527133	328	dbSNP
rs1368819310	330	dbSNP
rs907399950	331	dbSNP
rs1001700872	338	dbSNP
rs1158865996	340	dbSNP
rs927400289	342	dbSNP
rs1354843782	347	dbSNP
rs1172343048	354	dbSNP
rs938720444	355	dbSNP
rs1034128863	361	dbSNP
rs571119971	362	dbSNP
rs984514983	363	dbSNP
rs1204987561	364	dbSNP
rs529489461	369	dbSNP
rs946318037	370	dbSNP
rs1043282598	371	dbSNP
rs1284693224	377	dbSNP
rs1014599586	378	dbSNP
rs1348531467	381	dbSNP
rs148649560	384	dbSNP
rs976437269	385	dbSNP
rs556732670	387	dbSNP
rs923208684	388	dbSNP
rs931829526	390	dbSNP
rs753910724	398	dbSNP
rs1299638530	399	dbSNP
rs1456243278	404	dbSNP
rs890199732	406	dbSNP
rs1165144961	412	dbSNP
rs1462693170	413	dbSNP
rs985915886	417	dbSNP
rs1207857342	418	dbSNP
rs1190009054	428	dbSNP
rs1488338291	431	dbSNP
rs1247665237	433	dbSNP
rs749749289	434	dbSNP
rs79793182	435	dbSNP
rs1229132570	439	dbSNP
rs113745190	445	dbSNP
rs1271207051	446	dbSNP
rs1232486914	449	dbSNP
rs1366557349	451	dbSNP
rs554776574	459	dbSNP
rs1442627260	460	dbSNP
rs140117270	473	dbSNP
rs1157728081	477	dbSNP
rs1453797181	482	dbSNP
rs891800636	483	dbSNP
rs540499226	484	dbSNP
rs969668668	485	dbSNP
rs980623523	489	dbSNP
rs569484364	492	dbSNP
rs565588216	500	dbSNP
rs960115326	505	dbSNP
rs1046443228	506	dbSNP
rs1471331978	507	dbSNP
rs907434016	509	dbSNP
rs913246664	518	dbSNP
rs769177036	519	dbSNP
rs1311589502	520	dbSNP
rs1303864273	527	dbSNP
rs1236266296	530	dbSNP
rs1034534252	533	dbSNP
rs887905759	539	dbSNP
rs1362800646	541	dbSNP
rs1382443820	544	dbSNP
rs946035174	544	dbSNP
rs1304417300	549	dbSNP
rs979446779	553	dbSNP
rs779375705	555	dbSNP
rs1465977188	556	dbSNP
rs1396252655	562	dbSNP
rs932174455	563	dbSNP
rs1307549633	564	dbSNP
rs1050623539	565	dbSNP
rs912041153	566	dbSNP
rs944453367	572	dbSNP
rs1036101554	574	dbSNP
rs1276457497	575	dbSNP
rs1200007963	576	dbSNP
rs1283425128	576	dbSNP
rs1281009712	578	dbSNP
rs1014666616	584	dbSNP
rs577123765	588	dbSNP
rs1049485964	590	dbSNP
rs975753118	592	dbSNP
rs544597285	594	dbSNP
rs779599493	595	dbSNP
rs953311546	600	dbSNP
rs1428384194	602	dbSNP
rs746182720	604	dbSNP
rs1195321927	615	dbSNP
rs1251818286	617	dbSNP
rs1440095651	619	dbSNP
rs960497010	621	dbSNP
rs112064500	622	dbSNP
rs1186899651	623	dbSNP
rs1014319848	624	dbSNP
rs182699507	626	dbSNP
rs562841033	637	dbSNP
rs1444859219	638	dbSNP
rs530260252	639	dbSNP
rs967821707	647	dbSNP
rs1196200110	654	dbSNP
rs978776080	655	dbSNP
rs925911194	657	dbSNP
rs148340997	664	dbSNP
rs1461001830	671	dbSNP
rs1355466250	675	dbSNP
rs1294611402	678	dbSNP
rs1298284781	679	dbSNP
rs1408522508	680	dbSNP
rs925121750	681	dbSNP
rs1398508743	682	dbSNP
rs1394272026	684	dbSNP
rs1389048919	685	dbSNP
rs1162823929	690	dbSNP
rs1335830575	690	dbSNP
rs936475234	693	dbSNP
rs1471552080	694	dbSNP
rs990229100	694	dbSNP
rs986761062	696	dbSNP
rs879706300	704	dbSNP
rs12258	705	dbSNP
rs772099788	707	dbSNP
rs1212616984	709	dbSNP
rs946063161	714	dbSNP
rs772224184	716	dbSNP
rs1226079583	719	dbSNP
rs907173984	730	dbSNP
rs937579215	738	dbSNP
rs1329657183	740	dbSNP
rs1226739701	743	dbSNP
rs1441915134	746	dbSNP
rs1397011382	747	dbSNP
rs1252014447	755	dbSNP
rs1056023239	756	dbSNP
rs887977980	757	dbSNP
rs1408849015	765	dbSNP
rs1159006853	768	dbSNP
rs1048725990	776	dbSNP
rs904831815	787	dbSNP
rs561034241	788	dbSNP
rs1185837111	789	dbSNP
rs1445874655	797	dbSNP
rs1036543335	798	dbSNP
rs145223739	799	dbSNP
rs1179009051	800	dbSNP
rs997648882	802	dbSNP
rs1030019792	815	dbSNP
rs1225963447	822	dbSNP
rs1343580069	823	dbSNP
rs1303094901	824	dbSNP
rs1235540507	826	dbSNP
rs953012150	832	dbSNP
rs1007440711	835	dbSNP
rs1373676073	841	dbSNP
rs1009352652	843	dbSNP
rs1020360031	846	dbSNP
rs1170512396	847	dbSNP
rs371480240	850	dbSNP
rs967495569	850	dbSNP
rs1320434766	857	dbSNP
rs1402369674	860	dbSNP
rs1400026139	868	dbSNP
rs1032214469	869	dbSNP
rs957905916	879	dbSNP
rs187328936	884	dbSNP
rs571519085	886	dbSNP
rs913336016	888	dbSNP
rs967507101	892	dbSNP
rs981894016	893	dbSNP
rs1033028361	904	dbSNP
rs775651848	907	dbSNP
rs1242193110	909	dbSNP
rs1175543488	910	dbSNP
rs1406755489	912	dbSNP
rs1454339123	913	dbSNP
rs953491136	913	dbSNP
rs986404651	914	dbSNP
rs146886282	917	dbSNP
rs1212268344	919	dbSNP
rs75216754	929	dbSNP
rs550591178	941	dbSNP
rs1056096313	943	dbSNP
rs1295876604	947	dbSNP
rs568843038	949	dbSNP
rs551505028	953	dbSNP
rs1271971073	955	dbSNP
rs909443606	961	dbSNP
rs942202990	965	dbSNP
rs1036542782	966	dbSNP
rs919386786	967	dbSNP
rs930431084	969	dbSNP
rs1328206311	972	dbSNP
rs984917299	973	dbSNP
rs897966944	974	dbSNP
rs191424403	975	dbSNP
rs1419853557	981	dbSNP
rs1187925837	986	dbSNP
rs937653802	988	dbSNP
rs1324923163	990	dbSNP
rs1189197348	991	dbSNP
rs371691474	994	dbSNP
rs1272926938	995	dbSNP
rs571633098	998	dbSNP
rs1308274008	1003	dbSNP
rs76730569	1003	dbSNP
rs1226850707	1006	dbSNP
rs888817082	1009	dbSNP
rs9931847	1010	dbSNP
rs1415322997	1012	dbSNP
rs1357336838	1016	dbSNP
rs1032244212	1018	dbSNP
rs1186816615	1020	dbSNP
rs577516670	1021	dbSNP
rs1172002136	1032	dbSNP
rs903656528	1032	dbSNP
rs1416505896	1034	dbSNP
rs529380077	1035	dbSNP
rs544273353	1036	dbSNP
rs1429868051	1040	dbSNP
rs970932195	1045	dbSNP
rs59177504	1051	dbSNP
rs1177154442	1052	dbSNP
rs1156666174	1054	dbSNP
rs889162747	1054	dbSNP
rs1234963558	1055	dbSNP
rs1219572815	1056	dbSNP
rs1334526341	1062	dbSNP
rs981582811	1065	dbSNP
rs928700345	1066	dbSNP
rs958716835	1070	dbSNP
rs991473537	1071	dbSNP
rs760725845	1072	dbSNP
rs1373716829	1073	dbSNP
rs1289607295	1075	dbSNP
rs942318508	1077	dbSNP
rs1387444083	1081	dbSNP
rs35628469	1082	dbSNP
rs1403138494	1085	dbSNP
rs919442433	1085	dbSNP
rs933478714	1086	dbSNP
rs1325968174	1087	dbSNP
rs1462511201	1088	dbSNP
rs1361589151	1090	dbSNP
rs1346673757	1094	dbSNP
rs1051562701	1095	dbSNP
rs138277158	1096	dbSNP
rs542307409	1097	dbSNP
rs984577708	1098	dbSNP
rs1053398322	1102	dbSNP
rs184472996	1105	dbSNP
rs1463547844	1110	dbSNP
rs1216980979	1114	dbSNP
rs1293812814	1118	dbSNP
rs1260234832	1119	dbSNP
rs528245428	1119	dbSNP
rs867055378	1121	dbSNP
rs867281541	1122	dbSNP
rs937712950	1123	dbSNP
rs1317515295	1124	dbSNP
rs367830721	1129	dbSNP
rs991794378	1129	dbSNP
rs1231870608	1130	dbSNP
rs1021282224	1138	dbSNP
rs868279597	1139	dbSNP
rs945312529	1140	dbSNP
rs1382064998	1141	dbSNP
rs1003767446	1145	dbSNP
rs1035804239	1150	dbSNP
rs958787771	1153	dbSNP
rs3852690	1155	dbSNP
rs1016277207	1156	dbSNP
rs1396074214	1158	dbSNP
rs1195670658	1159	dbSNP
rs963675750	1163	dbSNP
rs201158777	1164	dbSNP
rs972378849	1165	dbSNP
rs919500538	1166	dbSNP
rs1179841287	1175	dbSNP
rs1404842232	1176	dbSNP
rs554354819	1178	dbSNP
rs567754470	1179	dbSNP
rs1280794819	1190	dbSNP
rs910692394	1191	dbSNP
rs943125309	1192	dbSNP
rs1053434749	1193	dbSNP
rs1347153806	1194	dbSNP
rs759419372	1196	dbSNP
rs765137485	1197	dbSNP
rs752525305	1198	dbSNP
rs1018976106	1199	dbSNP
rs762800055	1200	dbSNP
rs1376432099	1202	dbSNP
rs550284180	1202	dbSNP
rs901817759	1203	dbSNP
rs1373285560	1212	dbSNP
rs1460628335	1217	dbSNP
rs1372768449	1222	dbSNP
rs371397787	1223	dbSNP
rs568484289	1224	dbSNP
rs1309662982	1225	dbSNP
rs1255492152	1226	dbSNP
rs1042329281	1228	dbSNP
rs1485335522	1230	dbSNP
rs1257958343	1232	dbSNP
rs1202019616	1234	dbSNP
rs1337232839	1237	dbSNP
rs1250376777	1239	dbSNP
rs906428062	1242	dbSNP
rs1290969850	1245	dbSNP
rs1414705052	1246	dbSNP
rs1003431480	1248	dbSNP
rs1033529424	1252	dbSNP
rs1490680465	1254	dbSNP
rs894944250	1255	dbSNP
rs1202435510	1262	dbSNP
rs1013016860	1271	dbSNP
rs1480942467	1275	dbSNP
rs1016351153	1276	dbSNP
rs529657324	1277	dbSNP
rs143300744	1281	dbSNP
rs756726346	1282	dbSNP
rs1435797148	1285	dbSNP
rs991845260	1285	dbSNP
rs972456847	1286	dbSNP
rs1196008316	1289	dbSNP
rs1026597417	1293	dbSNP
rs1270699384	1296	dbSNP
rs955142005	1298	dbSNP
rs987659538	1303	dbSNP
rs910728348	1307	dbSNP
rs1426278525	1318	dbSNP
rs1335485265	1319	dbSNP
rs1426579251	1322	dbSNP
rs1168471698	1341	dbSNP
rs1392602098	1342	dbSNP
rs1325506452	1344	dbSNP
rs113671952	1349	dbSNP
rs534123317	1350	dbSNP
rs1300258807	1353	dbSNP
rs914955902	1356	dbSNP
rs945089068	1357	dbSNP
rs1212712896	1360	dbSNP
rs1468481961	1363	dbSNP
rs559148995	1367	dbSNP
rs1334786189	1371	dbSNP
rs927625874	1373	dbSNP
rs555519773	1374	dbSNP
rs1055016443	1376	dbSNP
rs1280469979	1377	dbSNP
rs1242709970	1379	dbSNP
rs1361189899	1381	dbSNP
rs895016540	1382	dbSNP
rs1351677181	1390	dbSNP
rs1005388713	1398	dbSNP
rs1307994290	1401	dbSNP
rs188998142	1402	dbSNP
rs1037814612	1403	dbSNP
rs193115835	1404	dbSNP
rs1040467419	1410	dbSNP
rs901866684	1415	dbSNP
rs1243937944	1416	dbSNP
rs1454487775	1420	dbSNP
rs1247942670	1422	dbSNP
rs1446719959	1423	dbSNP
rs1235297042	1424	dbSNP
rs1268474050	1424	dbSNP
rs1327131391	1424	dbSNP
rs1370059931	1424	dbSNP
rs1430051987	1424	dbSNP
rs765941939	1424	dbSNP
rs988848062	1424	dbSNP
rs77601707	1426	dbSNP
rs538560336	1427	dbSNP
rs1048007328	1434	dbSNP
rs1373375149	1438	dbSNP
rs1166214165	1439	dbSNP
rs993567834	1439	dbSNP
rs1434916377	1440	dbSNP
rs556592520	1441	dbSNP
rs1196453636	1442	dbSNP
rs1242207512	1442	dbSNP
rs1026753066	1443	dbSNP
rs574842724	1450	dbSNP
rs1212112373	1452	dbSNP
rs542244259	1457	dbSNP
rs1271094991	1460	dbSNP
rs959502920	1464	dbSNP
rs185173796	1476	dbSNP
rs964871821	1479	dbSNP
rs989592781	1482	dbSNP
rs1312022334	1486	dbSNP
rs8054382	1489	dbSNP
rs762776965	1497	dbSNP
rs188951811	1499	dbSNP
rs1409070481	1501	dbSNP
rs755594508	1508	dbSNP
rs74197901	1509	dbSNP
rs1055086904	1512	dbSNP
rs916484464	1517	dbSNP
rs1484402155	1524	dbSNP
rs532228180	1526	dbSNP
rs1204072656	1527	dbSNP
rs1260040025	1531	dbSNP
rs544462314	1532	dbSNP
rs985367952	1533	dbSNP
rs1322779205	1536	dbSNP
rs1228835794	1538	dbSNP
rs1381055162	1539	dbSNP
rs1296305604	1542	dbSNP
rs1440990877	1543	dbSNP
rs1400645252	1545	dbSNP
rs1204031147	1547	dbSNP
rs748528593	1551	dbSNP
rs896963955	1552	dbSNP
rs772473561	1556	dbSNP
rs1166031572	1557	dbSNP
rs943831927	1565	dbSNP
rs993992039	1566	dbSNP
rs1047799601	1567	dbSNP
rs890496767	1568	dbSNP
rs1440528287	1569	dbSNP
rs1008834461	1577	dbSNP
rs1240205048	1581	dbSNP
rs1212089600	1582	dbSNP
rs923340599	1584	dbSNP
rs1222211457	1585	dbSNP
rs1241757892	1591	dbSNP
rs1475753636	1600	dbSNP
rs1304575016	1602	dbSNP
rs929370893	1603	dbSNP
rs1195972015	1604	dbSNP
rs1017839947	1612	dbSNP
rs1393074590	1613	dbSNP
rs1293671471	1615	dbSNP
rs1480425207	1619	dbSNP
rs964943039	1628	dbSNP
rs1006896804	1629	dbSNP
rs1159046813	1634	dbSNP
rs1055364794	1636	dbSNP
rs562453880	1638	dbSNP
rs373049190	1643	dbSNP
rs966867394	1646	dbSNP
rs1280758180	1656	dbSNP
rs1025065964	1660	dbSNP
rs1484949442	1670	dbSNP
rs978281793	1671	dbSNP
rs1258854264	1673	dbSNP
rs927735555	1674	dbSNP
rs1223975684	1675	dbSNP
rs777873276	1678	dbSNP
rs1348352172	1679	dbSNP
rs866495635	1683	dbSNP
rs1387956500	1684	dbSNP
rs1359289848	1687	dbSNP
rs747213754	1692	dbSNP
rs1283876884	1693	dbSNP
rs957716888	1698	dbSNP
rs1172209405	1703	dbSNP
rs76901399	1710	dbSNP
rs1218917263	1711	dbSNP
rs1266788805	1712	dbSNP
rs985803160	1720	dbSNP
rs770936410	1721	dbSNP
rs1261149220	1724	dbSNP
rs973978345	1728	dbSNP
rs1488613434	1730	dbSNP
rs918449625	1735	dbSNP
rs547828774	1745	dbSNP
rs1208520346	1749	dbSNP
rs1344062034	1752	dbSNP
rs72795273	1765	dbSNP
rs890526387	1768	dbSNP
rs539837568	1769	dbSNP
rs1294318303	1771	dbSNP
rs1219752215	1774	dbSNP
rs1342990479	1775	dbSNP
rs944762302	1778	dbSNP
rs1414512396	1780	dbSNP
rs1039027688	1782	dbSNP
rs1403365872	1783	dbSNP
rs527418725	1789	dbSNP
rs1011580954	1790	dbSNP
rs1372572211	1792	dbSNP
rs1171520375	1795	dbSNP
rs1478092190	1802	dbSNP
rs1022539948	1806	dbSNP
rs1441564942	1807	dbSNP
rs918383777	1813	dbSNP
rs1408300760	1819	dbSNP
rs1256845928	1832	dbSNP
rs1218660878	1835	dbSNP
rs1319431053	1838	dbSNP
rs902722664	1839	dbSNP
rs112393306	1843	dbSNP
rs1402029105	1844	dbSNP
rs1300755392	1846	dbSNP
rs1364489758	1857	dbSNP
rs552476162	1860	dbSNP
rs1332320804	1866	dbSNP
rs78897721	1876	dbSNP
rs909232807	1880	dbSNP
rs1034798255	1893	dbSNP
rs1304931660	1898	dbSNP
rs538062681	1901	dbSNP
rs990546196	1909	dbSNP
rs1189419928	1910	dbSNP
rs1055338894	1913	dbSNP
rs1237153139	1915	dbSNP
rs1198891449	1930	dbSNP
rs77484954	1934	dbSNP
rs143722027	1937	dbSNP
rs949599928	1944	dbSNP
rs537219898	1952	dbSNP
rs962338552	1954	dbSNP
rs535837951	1957	dbSNP
rs1376666324	1961	dbSNP
rs999713454	1965	dbSNP
rs918492804	1966	dbSNP
rs1032075886	1973	dbSNP
rs554242319	1977	dbSNP
rs1325355004	1978	dbSNP
rs1404675275	1985	dbSNP
rs893500141	1990	dbSNP
rs572549027	1998	dbSNP
rs1006548117	2012	dbSNP
rs1017919133	2014	dbSNP
rs1379472041	2024	dbSNP
rs1490223123	2024	dbSNP
rs1441240146	2027	dbSNP
rs1250559206	2028	dbSNP
rs1223284721	2034	dbSNP
rs769785518	2036	dbSNP
rs947462657	2042	dbSNP
rs1451696607	2045	dbSNP
rs985580146	2047	dbSNP
rs1292592520	2048	dbSNP
rs1203900068	2050	dbSNP
rs1353364812	2052	dbSNP
rs35318292	2054	dbSNP
rs976641631	2055	dbSNP
rs762667387	2058	dbSNP
rs1274508804	2060	dbSNP
rs1437235550	2062	dbSNP
rs1332913701	2064	dbSNP
rs1398140576	2065	dbSNP
rs912369489	2065	dbSNP
rs951232905	2072	dbSNP
rs1159064356	2073	dbSNP
rs1421113151	2077	dbSNP
rs983981318	2081	dbSNP
rs528963850	2083	dbSNP
rs1039058839	2086	dbSNP
rs900542808	2089	dbSNP
rs942076376	2096	dbSNP
rs1384198654	2097	dbSNP
rs181056288	2098	dbSNP
rs916559898	2099	dbSNP
rs183977234	2105	dbSNP
rs1219184781	2106	dbSNP
rs1164451667	2112	dbSNP
rs1278100516	2112	dbSNP
rs777614599	2117	dbSNP
rs1046620972	2121	dbSNP
rs902706398	2122	dbSNP
rs754220181	2123	dbSNP
rs1394278713	2127	dbSNP
rs542879838	2128	dbSNP
rs562439900	2130	dbSNP
rs1390691315	2136	dbSNP
rs935508870	2137	dbSNP
rs763879597	2138	dbSNP
rs1357215443	2139	dbSNP
rs1053976883	2149	dbSNP
rs1329301659	2157	dbSNP
rs902754503	2158	dbSNP
rs1165691942	2168	dbSNP
rs1337378800	2169	dbSNP
rs773909498	2174	dbSNP
rs1484863163	2175	dbSNP
rs1237329507	2176	dbSNP
rs1000159915	2180	dbSNP
rs893562822	2181	dbSNP
rs116148240	2187	dbSNP
rs1017971124	2190	dbSNP
rs1198030050	2191	dbSNP
rs1318729279	2192	dbSNP
rs1278684434	2196	dbSNP
rs900808679	2199	dbSNP
rs1376680747	2208	dbSNP
rs1246840387	2209	dbSNP
rs1267245017	2215	dbSNP
rs1338027248	2234	dbSNP
rs1195798542	2237	dbSNP
rs767260086	2241	dbSNP
rs998131644	2244	dbSNP
rs188652871	2245	dbSNP
rs1274310427	2247	dbSNP
rs1464591283	2258	dbSNP
rs1400409315	2260	dbSNP
rs1459410980	2262	dbSNP
rs73564405	2264	dbSNP
rs951325056	2272	dbSNP
rs749996841	2273	dbSNP
rs1012011642	2278	dbSNP
rs1023386672	2281	dbSNP
rs1231351783	2285	dbSNP
rs563070205	2290	dbSNP
rs1370776525	2291	dbSNP
rs1461039462	2295	dbSNP
rs1260138214	2297	dbSNP
rs973751113	2299	dbSNP
rs765902829	2301	dbSNP
rs1319896647	2303	dbSNP
rs1288851916	2304	dbSNP
rs1168479471	2314	dbSNP
rs963513403	2318	dbSNP
rs531926104	2327	dbSNP
rs1233676091	2328	dbSNP
rs916610826	2331	dbSNP
rs1335789999	2335	dbSNP
rs951346992	2340	dbSNP
rs1166145444	2344	dbSNP
rs1407365496	2345	dbSNP
rs527311211	2346	dbSNP
rs1382332447	2352	dbSNP
rs1453572928	2359	dbSNP
rs1378864008	2362	dbSNP
rs1315109572	2374	dbSNP
rs1440619833	2384	dbSNP
rs1240068119	2389	dbSNP
rs970686083	2390	dbSNP
rs11642705	2392	dbSNP
rs778148877	2399	dbSNP
rs1323274370	2406	dbSNP
rs924206485	2409	dbSNP
rs1238938588	2412	dbSNP
rs912402148	2413	dbSNP
rs935545815	2418	dbSNP
rs115641250	2421	dbSNP
rs1384522768	2425	dbSNP
rs974839345	2428	dbSNP
rs922003152	2433	dbSNP
rs1294569376	2452	dbSNP
rs370769316	2453	dbSNP
rs531927069	2458	dbSNP
rs550436149	2460	dbSNP
rs1201889124	2461	dbSNP
rs1420513604	2462	dbSNP
rs923914047	2471	dbSNP
rs1382350701	2473	dbSNP
rs180779662	2477	dbSNP
rs1427457266	2480	dbSNP
rs1056698080	2487	dbSNP
rs1193232131	2488	dbSNP
rs1426034831	2499	dbSNP
rs527727753	2500	dbSNP
rs1490832447	2504	dbSNP
rs757510040	2509	dbSNP
rs997843933	2518	dbSNP
rs1488509929	2519	dbSNP
rs1479385810	2521	dbSNP
rs1012402131	2529	dbSNP
rs1406638340	2536	dbSNP
rs1044864511	2537	dbSNP
rs781384149	2539	dbSNP
rs887034048	2540	dbSNP
rs114161397	2545	dbSNP
rs1339156433	2546	dbSNP
rs1025308432	2547	dbSNP
rs1400922212	2553	dbSNP
rs1383034004	2555	dbSNP
rs958520554	2555	dbSNP
rs1012311544	2556	dbSNP
rs142809055	2556	dbSNP
rs746001343	2558	dbSNP
rs1178389958	2561	dbSNP
rs1278869631	2561	dbSNP
rs1342951921	2562	dbSNP
rs1421346558	2565	dbSNP
rs951082224	2568	dbSNP
rs115197062	2570	dbSNP
rs923897328	2571	dbSNP
rs116676358	2576	dbSNP
rs1256050019	2579	dbSNP
rs1235854372	2588	dbSNP
rs990109909	2591	dbSNP
rs1278060703	2592	dbSNP
rs915440273	2593	dbSNP
rs1342770858	2599	dbSNP
rs963871309	2606	dbSNP
rs942827481	2607	dbSNP
rs1395650327	2609	dbSNP
rs539460151	2610	dbSNP
rs867829067	2611	dbSNP
rs1039512153	2617	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.

- 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.