ID	Duplex structure	Position	Score	MFE
1	miRNA 3' uucaauaugguUUA--UACGGUCc 5' |:| ||||||| Target 5' agtggggggacAGTCCATGCCAGg 3'	1061 - 1084	141.00	-15.30
2	miRNA 3' uucAAUAUGGUUUAUACGGUCc 5' ||: : ::: |:|||||| Target 5' accTTGGGGTGGTTGTGCCAGc 3'	109 - 130	135.00	-10.37
3	miRNA 3' uucaAUAU-GGUUU-AUACGGUCc 5' || | |||: | ||||| Target 5' cctcTAGAGGCAAGCCAGGCCAGg 3'	393 - 416	114.00	-15.60

Mutant ID	Mutant Position	Mutant Source
COSN8584505	17	COSMIC
COSN13340933	18	COSMIC
COSN30509827	22	COSMIC
COSN30503540	24	COSMIC
COSN30105491	25	COSMIC
COSN26568887	39	COSMIC
COSN31527099	85	COSMIC
COSN30230227	440	COSMIC
COSN31547235	732	COSMIC
COSN1136308	768	COSMIC
COSN30542935	853	COSMIC
COSN30542500	854	COSMIC
COSN31550348	928	COSMIC
COSN10090631	1039	COSMIC
COSN31589209	1114	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1246824997	3	dbSNP
rs920697017	3	dbSNP
rs754909793	9	dbSNP
rs758885245	10	dbSNP
rs751527501	12	dbSNP
rs757388869	23	dbSNP
rs1178139062	24	dbSNP
rs1410858288	25	dbSNP
rs781511855	26	dbSNP
rs908355221	27	dbSNP
rs764748473	30	dbSNP
rs1406864541	31	dbSNP
rs768537493	33	dbSNP
rs778915788	38	dbSNP
rs778618525	41	dbSNP
rs570504731	46	dbSNP
rs1340082964	48	dbSNP
rs1447098840	50	dbSNP
rs1279886943	53	dbSNP
rs1169950970	63	dbSNP
rs1293875492	64	dbSNP
rs1450968231	69	dbSNP
rs539496082	71	dbSNP
rs199638754	77	dbSNP
rs1382964618	81	dbSNP
rs1212694234	95	dbSNP
rs752174476	106	dbSNP
rs976656328	111	dbSNP
rs1297464307	114	dbSNP
rs922304147	122	dbSNP
rs1437095981	124	dbSNP
rs932340156	127	dbSNP
rs1049828296	130	dbSNP
rs1197287346	142	dbSNP
rs893571116	150	dbSNP
rs746234689	160	dbSNP
rs546668385	170	dbSNP
rs1246967659	173	dbSNP
rs1385164991	179	dbSNP
rs35387404	186	dbSNP
rs1042558862	189	dbSNP
rs566661095	192	dbSNP
rs902677223	212	dbSNP
rs369343587	213	dbSNP
rs1277742805	214	dbSNP
rs547060405	218	dbSNP
rs1365318057	223	dbSNP
rs555296733	224	dbSNP
rs895366896	227	dbSNP
rs575446528	234	dbSNP
rs1469588598	242	dbSNP
rs1474732724	243	dbSNP
rs372284211	263	dbSNP
rs1028044310	267	dbSNP
rs1489814498	269	dbSNP
rs758009351	271	dbSNP
rs1361786101	273	dbSNP
rs1432955090	273	dbSNP
rs1282308870	277	dbSNP
rs1223263894	288	dbSNP
rs983927094	296	dbSNP
rs1015468471	310	dbSNP
rs1403574270	312	dbSNP
rs961199169	314	dbSNP
rs1304123267	326	dbSNP
rs1377473288	328	dbSNP
rs1424961499	330	dbSNP
rs537757006	331	dbSNP
rs1156448577	333	dbSNP
rs1297692849	334	dbSNP
rs138330073	350	dbSNP
rs4647596	354	dbSNP
rs763709425	358	dbSNP
rs1290542562	363	dbSNP
rs1479414408	367	dbSNP
rs558123128	370	dbSNP
rs751262803	372	dbSNP
rs1489612280	375	dbSNP
rs1240611980	379	dbSNP
rs1215270410	382	dbSNP
rs756458323	385	dbSNP
rs1317606817	386	dbSNP
rs1286347935	397	dbSNP
rs1218392348	399	dbSNP
rs1222293049	406	dbSNP
rs879334406	415	dbSNP
rs914874596	428	dbSNP
rs946516419	429	dbSNP
rs374488587	441	dbSNP
rs1042113016	443	dbSNP
rs577707409	446	dbSNP
rs187984335	455	dbSNP
rs1444722617	458	dbSNP
rs1160727860	464	dbSNP
rs190872929	466	dbSNP
rs1468213157	468	dbSNP
rs763037630	469	dbSNP
rs1403344802	471	dbSNP
rs1243197463	476	dbSNP
rs1417055045	477	dbSNP
rs1486312762	481	dbSNP
rs1250041043	490	dbSNP
rs1201826554	492	dbSNP
rs1488382438	495	dbSNP
rs1264334682	498	dbSNP
rs902231199	501	dbSNP
rs1192120680	502	dbSNP
rs1306134733	503	dbSNP
rs1397226045	514	dbSNP
rs1295304674	515	dbSNP
rs1454874273	520	dbSNP
rs148363068	533	dbSNP
rs1322020614	542	dbSNP
rs1378607994	546	dbSNP
rs1402515619	555	dbSNP
rs768788181	565	dbSNP
rs1337325582	566	dbSNP
rs1345686101	573	dbSNP
rs1322711699	587	dbSNP
rs1169467116	613	dbSNP
rs1429386521	614	dbSNP
rs895417861	628	dbSNP
rs560272297	631	dbSNP
rs1181931040	636	dbSNP
rs1323685146	644	dbSNP
rs1027683238	652	dbSNP
rs1243759083	660	dbSNP
rs1202778627	662	dbSNP
rs533565138	662	dbSNP
rs1441201640	663	dbSNP
rs1251156914	664	dbSNP
rs1005007577	665	dbSNP
rs4647597	669	dbSNP
rs1299391611	670	dbSNP
rs539992725	676	dbSNP
rs1243247355	688	dbSNP
rs1348009273	689	dbSNP
rs1381407862	692	dbSNP
rs1315130354	713	dbSNP
rs1397772002	714	dbSNP
rs1371059991	719	dbSNP
rs573796023	724	dbSNP
rs138582021	733	dbSNP
rs1321676483	740	dbSNP
rs143815887	748	dbSNP
rs1029479801	749	dbSNP
rs1161914804	749	dbSNP
rs1424261747	757	dbSNP
rs1386005646	770	dbSNP
rs531177167	771	dbSNP
rs1189682366	777	dbSNP
rs544576285	784	dbSNP
rs1255297971	785	dbSNP
rs779009395	786	dbSNP
rs1178232151	787	dbSNP
rs954011535	788	dbSNP
rs1289961324	790	dbSNP
rs1219880439	797	dbSNP
rs1358266960	800	dbSNP
rs985769081	801	dbSNP
rs748206492	806	dbSNP
rs1178327774	816	dbSNP
rs1265566498	816	dbSNP
rs1246309764	822	dbSNP
rs1306224317	823	dbSNP
rs1333432877	823	dbSNP
rs1231362385	832	dbSNP
rs914946603	837	dbSNP
rs1352180439	848	dbSNP
rs1301053910	854	dbSNP
rs767407036	860	dbSNP
rs968116188	873	dbSNP
rs1413119203	898	dbSNP
rs1451749603	899	dbSNP
rs564468673	900	dbSNP
rs977692984	901	dbSNP
rs533142276	905	dbSNP
rs1460866582	908	dbSNP
rs1045412997	911	dbSNP
rs1162635553	914	dbSNP
rs1473854541	920	dbSNP
rs1396489204	923	dbSNP
rs923704448	928	dbSNP
rs4647598	929	dbSNP
rs1056580259	939	dbSNP
rs773551253	964	dbSNP
rs1347933372	971	dbSNP
rs1259628724	973	dbSNP
rs1228993807	975	dbSNP
rs916721415	980	dbSNP
rs948362061	981	dbSNP
rs747298628	986	dbSNP
rs559825035	988	dbSNP
rs1279636815	990	dbSNP
rs1331423379	992	dbSNP
rs372407098	993	dbSNP
rs887998420	998	dbSNP
rs1380678198	1004	dbSNP
rs1004897722	1016	dbSNP
rs1289508554	1017	dbSNP
rs1459327980	1021	dbSNP
rs1427773684	1026	dbSNP
rs1036336904	1031	dbSNP
rs1044768	1037	dbSNP
rs1480978779	1038	dbSNP
rs776301156	1044	dbSNP
rs1200643515	1053	dbSNP
rs1444914147	1064	dbSNP
rs1260495144	1076	dbSNP
rs901948551	1080	dbSNP
rs1465829900	1082	dbSNP
rs997584124	1083	dbSNP
rs1275593105	1088	dbSNP
rs1345460034	1089	dbSNP
rs1276390347	1096	dbSNP
rs1335962981	1107	dbSNP
rs11553937	1108	dbSNP
rs1029527540	1111	dbSNP
rs539415361	1114	dbSNP
rs1298469705	1115	dbSNP
rs1437402673	1117	dbSNP
rs1403933999	1123	dbSNP
rs566601681	1126	dbSNP
rs1415546729	1139	dbSNP
rs760692403	1150	dbSNP
rs1404879895	1152	dbSNP
rs11553936	1157	dbSNP
rs137866238	1157	dbSNP
rs1474247481	1157	dbSNP
rs954005311	1157	dbSNP
rs529375389	1160	dbSNP
rs5858	1162	dbSNP
rs1236995299	1164	dbSNP
rs765121842	1166	dbSNP
rs1442922725	1167	dbSNP
rs1474260942	1168	dbSNP
rs766291795	1180	dbSNP
rs1185803019	1181	dbSNP
rs1193826616	1182	dbSNP
rs1022641447	1183	dbSNP
rs1338458028	1183	dbSNP
rs1419904101	1185	dbSNP
rs1461811860	1189	dbSNP
rs967909361	1190	dbSNP
rs923589521	1193	dbSNP
rs977745165	1193	dbSNP
rs1342753668	1194	dbSNP
rs538093494	1200	dbSNP
rs1327395317	1202	dbSNP
rs35947979	1210	dbSNP
rs775541722	1213	dbSNP
rs960470474	1216	dbSNP
rs1411313643	1217	dbSNP
rs1168843472	1219	dbSNP
rs558064045	1220	dbSNP
rs571603981	1225	dbSNP
rs1358137428	1238	dbSNP
rs665076	1240	dbSNP
rs1412344758	1253	dbSNP
rs1295702619	1261	dbSNP
rs1473107596	1265	dbSNP
rs1239162668	1268	dbSNP
rs868490833	1269	dbSNP
rs991861266	1287	dbSNP
rs533736262	1297	dbSNP
rs1274995005	1299	dbSNP
rs1357528693	1299	dbSNP
rs916791281	1299	dbSNP
rs1228996412	1300	dbSNP
rs948220867	1304	dbSNP
rs1268796328	1310	dbSNP
rs1341845245	1312	dbSNP
rs1196662504	1314	dbSNP
rs553825718	1318	dbSNP
rs1278186523	1323	dbSNP
rs796698779	1325	dbSNP
rs1049197870	1328	dbSNP
rs1351559733	1328	dbSNP
rs1411331115	1330	dbSNP
rs909470217	1334	dbSNP
rs763652242	1335	dbSNP
rs1405464447	1340	dbSNP
rs1484755975	1348	dbSNP
rs4647599	1349	dbSNP
rs576548955	1349	dbSNP
rs901832467	1349	dbSNP
rs542347951	1353	dbSNP
rs1252337472	1355	dbSNP
rs997636435	1364	dbSNP
rs1489780421	1371	dbSNP
rs754480716	1378	dbSNP
rs556269971	1379	dbSNP
rs369482110	1383	dbSNP
rs756909526	1390	dbSNP
rs1007148550	1395	dbSNP
rs1223774079	1400	dbSNP
rs1022103809	1412	dbSNP
rs778479588	1424	dbSNP
rs1218737263	1426	dbSNP
rs72934975	1427	dbSNP
rs114549146	1432	dbSNP
rs1371185428	1434	dbSNP
rs371941018	1436	dbSNP
rs960357972	1439	dbSNP
rs991798347	1439	dbSNP
rs1456680122	1441	dbSNP
rs1412665220	1445	dbSNP
rs1023814669	1448	dbSNP
rs1394075163	1448	dbSNP
rs969137520	1472	dbSNP
rs985384593	1473	dbSNP
rs564402650	1475	dbSNP
rs1432426306	1477	dbSNP
rs533465446	1484	dbSNP
rs909366158	1489	dbSNP
rs1465371716	1500	dbSNP
rs931085422	1503	dbSNP
rs540186196	1508	dbSNP
rs940951211	1509	dbSNP
rs1323274704	1517	dbSNP
rs1047130936	1525	dbSNP
rs1375446603	1531	dbSNP
rs1302403615	1532	dbSNP
rs972302147	1533	dbSNP
rs376636599	1536	dbSNP
rs886793168	1546	dbSNP
rs1008120577	1547	dbSNP
rs1433748094	1552	dbSNP
rs560127324	1553	dbSNP
rs1388657363	1561	dbSNP
rs1040971087	1562	dbSNP
rs899776606	1574	dbSNP
rs1328633430	1580	dbSNP
rs1468163802	1588	dbSNP
rs997084004	1591	dbSNP
rs1176496575	1594	dbSNP
rs757688253	1608	dbSNP
rs568862969	1610	dbSNP
rs969170999	1612	dbSNP
rs947476276	1620	dbSNP
rs1043980886	1622	dbSNP
rs149755484	1623	dbSNP
rs1182358749	1626	dbSNP
rs998950331	1633	dbSNP
rs529331177	1636	dbSNP
rs549208545	1637	dbSNP
rs1306082545	1644	dbSNP
rs1270467353	1648	dbSNP
rs960042220	1659	dbSNP
rs569363414	1660	dbSNP
rs992816828	1662	dbSNP
rs1023278267	1674	dbSNP
rs916144866	1674	dbSNP
rs146460934	1676	dbSNP
rs1016475625	1687	dbSNP
rs1467411781	1692	dbSNP
rs755409357	1692	dbSNP
rs1448566944	1693	dbSNP
rs1352485529	1697	dbSNP
rs973946321	1698	dbSNP
rs1193656435	1702	dbSNP
rs1252102160	1706	dbSNP
rs1430635598	1714	dbSNP
rs1452189048	1715	dbSNP
rs1392163731	1716	dbSNP
rs111844146	1718	dbSNP
rs920776144	1720	dbSNP
rs551618467	1722	dbSNP
rs1046824697	1723	dbSNP
rs1452429870	1728	dbSNP
rs908322356	1731	dbSNP
rs1184053237	1741	dbSNP
rs1479867891	1743	dbSNP
rs779264942	1748	dbSNP
rs879724571	1751	dbSNP
rs1251540732	1754	dbSNP
rs1157385191	1760	dbSNP
rs923525458	1761	dbSNP
rs1342408957	1771	dbSNP
rs746169633	1773	dbSNP
rs1387751995	1774	dbSNP
rs1040774237	1795	dbSNP
rs1313361628	1796	dbSNP
rs1397641418	1803	dbSNP
rs540292293	1804	dbSNP
rs1369151638	1806	dbSNP
rs1307163320	1808	dbSNP
rs1410717864	1814	dbSNP
rs1372678412	1815	dbSNP
rs910539968	1816	dbSNP
rs947490284	1817	dbSNP
rs1369068090	1826	dbSNP
rs899745566	1842	dbSNP
rs1043141788	1848	dbSNP
rs74809589	1849	dbSNP
rs756598898	1857	dbSNP
rs1043241202	1858	dbSNP
rs1183310697	1870	dbSNP
rs1484217520	1872	dbSNP
rs935172246	1876	dbSNP
rs758543869	1878	dbSNP
rs1487875494	1880	dbSNP
rs999315780	1881	dbSNP
rs11227182	1882	dbSNP
rs1246971371	1885	dbSNP
rs1326965073	1890	dbSNP
rs896427292	1891	dbSNP
rs778001236	1892	dbSNP
rs1287530723	1918	dbSNP
rs1236944183	1919	dbSNP
rs1262514702	1923	dbSNP
rs1031703034	1925	dbSNP
rs1352782144	1926	dbSNP
rs1205574685	1936	dbSNP
rs1252159455	1937	dbSNP
rs534083815	1943	dbSNP
rs1391616016	1945	dbSNP
rs1295340237	1949	dbSNP
rs554148438	1954	dbSNP
rs771737050	1955	dbSNP
rs567146834	1960	dbSNP
rs1022930159	1962	dbSNP
rs658794	1974	dbSNP
rs1418055895	1989	dbSNP
rs1179078558	1992	dbSNP
rs1160489687	1993	dbSNP
rs1473783221	2008	dbSNP
rs1427556300	2012	dbSNP
rs1364991135	2013	dbSNP
rs1196387772	2014	dbSNP
rs1432217731	2015	dbSNP
rs1454768639	2019	dbSNP
rs749363707	2021	dbSNP
rs904850639	2025	dbSNP
rs781003709	2032	dbSNP
rs973700108	2033	dbSNP
rs1209210630	2034	dbSNP
rs138796491	2035	dbSNP
rs1272844264	2036	dbSNP
rs1016025244	2038	dbSNP
rs1331869479	2039	dbSNP
rs1303628767	2056	dbSNP
rs1387923647	2057	dbSNP
rs576101012	2059	dbSNP
rs1463315352	2074	dbSNP
rs538019094	2078	dbSNP
rs1404431901	2081	dbSNP
rs1172332907	2082	dbSNP
rs1465266948	2083	dbSNP
rs768757334	2088	dbSNP
rs993684226	2091	dbSNP
rs1200481453	2094	dbSNP
rs1447138671	2101	dbSNP
rs908290474	2108	dbSNP
rs1030485021	2111	dbSNP
rs1189209587	2117	dbSNP
rs1309242112	2117	dbSNP
rs1466181977	2118	dbSNP
rs1276293284	2119	dbSNP
rs1199696203	2121	dbSNP
rs955158650	2124	dbSNP
rs1257995522	2128	dbSNP
rs1226373100	2134	dbSNP
rs1364632741	2146	dbSNP
rs1228994850	2150	dbSNP
rs557929847	2155	dbSNP
rs943805538	2158	dbSNP
rs986391057	2159	dbSNP
rs976378696	2160	dbSNP
rs1332473097	2161	dbSNP
rs187939378	2177	dbSNP
rs1208397548	2185	dbSNP
rs1396989687	2187	dbSNP
rs1404721757	2193	dbSNP
rs910580183	2201	dbSNP
rs1427414193	2209	dbSNP
rs540518055	2222	dbSNP
rs1168637515	2225	dbSNP
rs1450751349	2227	dbSNP
rs1235687688	2228	dbSNP
rs560890090	2233	dbSNP
rs1480124466	2234	dbSNP
rs1258005799	2242	dbSNP
rs1193653177	2244	dbSNP
rs1252068435	2251	dbSNP
rs1203352558	2255	dbSNP
rs1341691762	2261	dbSNP
rs1275488558	2262	dbSNP
rs978698119	2273	dbSNP
rs924710811	2275	dbSNP
rs1284133276	2283	dbSNP
rs1449394823	2284	dbSNP
rs1419148875	2286	dbSNP
rs191979795	2288	dbSNP
rs1306541625	2291	dbSNP
rs932536302	2293	dbSNP
rs1308210751	2294	dbSNP
rs112866560	2295	dbSNP
rs1370025952	2299	dbSNP
rs904466975	2301	dbSNP
rs1044987143	2302	dbSNP
rs1252836553	2303	dbSNP
rs1207480023	2314	dbSNP
rs905071059	2323	dbSNP
rs1289228506	2326	dbSNP
rs1229447922	2327	dbSNP
rs775276544	2329	dbSNP
rs562808279	2330	dbSNP
rs756231186	2335	dbSNP
rs1286958838	2339	dbSNP
rs934492006	2343	dbSNP
rs762948976	2345	dbSNP
rs1166138265	2352	dbSNP
rs895896280	2357	dbSNP
rs1354240478	2358	dbSNP
rs1014295555	2362	dbSNP
rs1005894306	2363	dbSNP
rs1347669016	2374	dbSNP
rs1037343084	2378	dbSNP
rs1322281432	2378	dbSNP
rs1022897794	2379	dbSNP
rs993232740	2381	dbSNP
rs768091667	2398	dbSNP
rs1412434204	2400	dbSNP
rs551334961	2401	dbSNP
rs1292654831	2403	dbSNP
rs1477150318	2414	dbSNP
rs1353512216	2416	dbSNP
rs1027890091	2419	dbSNP
rs773867512	2422	dbSNP
rs531855088	2426	dbSNP
rs1235019941	2442	dbSNP
rs1453355336	2446	dbSNP
rs954898030	2447	dbSNP
rs1313166776	2453	dbSNP
rs551554870	2463	dbSNP
rs760206209	2465	dbSNP
rs1290582429	2468	dbSNP
rs1225163040	2474	dbSNP
rs1365009028	2478	dbSNP
rs1008098845	2479	dbSNP
rs1017862673	2480	dbSNP
rs969346624	2491	dbSNP
rs1483124978	2493	dbSNP
rs978752161	2498	dbSNP
rs1019134070	2501	dbSNP
rs565064270	2504	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.