ID	Duplex structure	Position	Score	MFE
1	miRNA 3' acaaUUACGAUUAUACAUCCuc 5' ||||:| | |||||| Target 5' tcagAATGTTCTTTTGTAGGca 3'	995 - 1016	142.00	-10.60
2	miRNA 3' acaauuacgauuauaCAUCCUc 5' |||||| Target 5' accttctcttagaggGTAGGAa 3'	530 - 551	120.00	-8.90
3	miRNA 3' acaAUUA-CGAUUAU-ACAUCCUc 5' |::| ||: |: ||||| | Target 5' ccaTGGTCCCTGTTGTTGTAGTAa 3'	733 - 756	115.00	-5.92

Mutant ID	Mutant Position	Mutant Source
COSN30145682	9	COSMIC
COSN31514256	23	COSMIC
COSN30520482	71	COSMIC
COSN31596187	101	COSMIC
COSN30526651	130	COSMIC
COSN9915714	216	COSMIC
COSN9812394	244	COSMIC
COSN19279847	256	COSMIC
COSN17861118	804	COSMIC
COSN7902450	1425	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1249534661	11	dbSNP
rs1234912549	14	dbSNP
rs1376629325	20	dbSNP
rs1186627956	25	dbSNP
rs376769434	26	dbSNP
rs1480228282	30	dbSNP
rs755951078	30	dbSNP
rs763753333	31	dbSNP
rs371916116	32	dbSNP
rs369872742	34	dbSNP
rs573802295	35	dbSNP
rs1421645768	37	dbSNP
rs1182561970	45	dbSNP
rs375215574	45	dbSNP
rs1450777561	61	dbSNP
rs1054703951	69	dbSNP
rs1167334779	74	dbSNP
rs1372941480	87	dbSNP
rs1405808003	90	dbSNP
rs1037585856	91	dbSNP
rs1400376462	91	dbSNP
rs1332677372	95	dbSNP
rs934877845	96	dbSNP
rs1452245304	105	dbSNP
rs555455231	107	dbSNP
rs1367517805	109	dbSNP
rs1416603224	112	dbSNP
rs1226274187	116	dbSNP
rs780047968	118	dbSNP
rs1403548975	119	dbSNP
rs1233742693	125	dbSNP
rs1172615787	129	dbSNP
rs981049559	134	dbSNP
rs1002117305	136	dbSNP
rs1459795498	140	dbSNP
rs756061151	144	dbSNP
rs949734733	152	dbSNP
rs533864464	154	dbSNP
rs991688008	155	dbSNP
rs951906677	158	dbSNP
rs1027867757	161	dbSNP
rs1434221121	163	dbSNP
rs1044407277	179	dbSNP
rs566719859	191	dbSNP
rs17735787	201	dbSNP
rs1376336746	203	dbSNP
rs1374421849	210	dbSNP
rs1160271983	215	dbSNP
rs191947125	216	dbSNP
rs1444027877	221	dbSNP
rs1433013813	234	dbSNP
rs539755691	242	dbSNP
rs1368349585	243	dbSNP
rs186185287	246	dbSNP
rs564055257	247	dbSNP
rs1018889656	248	dbSNP
rs1391904494	249	dbSNP
rs1053575646	267	dbSNP
rs1340097608	280	dbSNP
rs1268432974	281	dbSNP
rs1330746677	283	dbSNP
rs1276946841	284	dbSNP
rs934847120	285	dbSNP
rs781098657	286	dbSNP
rs978917282	299	dbSNP
rs1480350515	315	dbSNP
rs11539372	327	dbSNP
rs1282723220	334	dbSNP
rs149940708	341	dbSNP
rs1414522513	346	dbSNP
rs891145367	346	dbSNP
rs1028403804	350	dbSNP
rs142714115	354	dbSNP
rs540318378	354	dbSNP
rs1158598327	359	dbSNP
rs987172012	360	dbSNP
rs1459449906	364	dbSNP
rs1295291346	369	dbSNP
rs1343552846	371	dbSNP
rs180805152	372	dbSNP
rs1307936873	374	dbSNP
rs954497647	380	dbSNP
rs1352054895	383	dbSNP
rs1221735809	385	dbSNP
rs749147380	393	dbSNP
rs1321794290	399	dbSNP
rs1223117075	413	dbSNP
rs1290285852	416	dbSNP
rs997372608	417	dbSNP
rs1490321926	422	dbSNP
rs1206450202	435	dbSNP
rs893226126	440	dbSNP
rs1054989912	445	dbSNP
rs1468874738	446	dbSNP
rs993614935	448	dbSNP
rs1414795689	453	dbSNP
rs561858703	464	dbSNP
rs751269848	465	dbSNP
rs546727537	475	dbSNP
rs1016087542	477	dbSNP
rs1423967192	478	dbSNP
rs1308507128	483	dbSNP
rs1001981297	484	dbSNP
rs1045990315	490	dbSNP
rs1412659464	497	dbSNP
rs1278655457	498	dbSNP
rs866020569	502	dbSNP
rs763636934	503	dbSNP
rs1379423493	504	dbSNP
rs1229580925	511	dbSNP
rs139090303	516	dbSNP
rs564366577	524	dbSNP
rs1312321953	531	dbSNP
rs1024827110	535	dbSNP
rs762587478	537	dbSNP
rs949702586	544	dbSNP
rs895763198	546	dbSNP
rs1473641364	551	dbSNP
rs1436501820	555	dbSNP
rs1204253257	559	dbSNP
rs1237880399	561	dbSNP
rs1238318500	562	dbSNP
rs1053121683	565	dbSNP
rs1181934750	571	dbSNP
rs1384709737	571	dbSNP
rs1482067695	583	dbSNP
rs1254001202	584	dbSNP
rs934774487	585	dbSNP
rs915597487	593	dbSNP
rs1205968228	596	dbSNP
rs546062454	600	dbSNP
rs991180310	601	dbSNP
rs1454270959	602	dbSNP
rs1334224603	603	dbSNP
rs1381414392	605	dbSNP
rs904593586	613	dbSNP
rs1230295433	619	dbSNP
rs1337992435	621	dbSNP
rs752078665	630	dbSNP
rs1214391218	641	dbSNP
rs1357464136	642	dbSNP
rs1314257757	645	dbSNP
rs1288192909	646	dbSNP
rs575908205	647	dbSNP
rs1242688733	648	dbSNP
rs879173950	667	dbSNP
rs1408472726	671	dbSNP
rs930350562	681	dbSNP
rs563800441	682	dbSNP
rs1243820314	690	dbSNP
rs1474406148	692	dbSNP
rs1167212856	694	dbSNP
rs766883263	695	dbSNP
rs1470796669	698	dbSNP
rs1173896262	705	dbSNP
rs1404885932	715	dbSNP
rs971864291	715	dbSNP
rs910820826	716	dbSNP
rs961903728	722	dbSNP
rs1430670162	726	dbSNP
rs1275899055	729	dbSNP
rs1347583447	730	dbSNP
rs1018856990	734	dbSNP
rs1222059923	738	dbSNP
rs1262815819	749	dbSNP
rs1330056293	750	dbSNP
rs933004870	752	dbSNP
rs988094333	752	dbSNP
rs918958109	754	dbSNP
rs761119925	756	dbSNP
rs773597726	772	dbSNP
rs1406800780	773	dbSNP
rs1196992187	776	dbSNP
rs1428215193	777	dbSNP
rs79324308	784	dbSNP
rs1015951783	785	dbSNP
rs74484150	785	dbSNP
rs963128740	785	dbSNP
rs980593492	785	dbSNP
rs1347922229	788	dbSNP
rs370756731	792	dbSNP
rs539370008	792	dbSNP
rs969158310	792	dbSNP
rs1351438808	797	dbSNP
rs544197666	799	dbSNP
rs1024893018	803	dbSNP
rs996858188	808	dbSNP
rs1013959555	811	dbSNP
rs893184556	814	dbSNP
rs1210496839	816	dbSNP
rs573639629	820	dbSNP
rs1220110532	828	dbSNP
rs555400040	830	dbSNP
rs1033070172	840	dbSNP
rs1472762868	843	dbSNP
rs998966107	845	dbSNP
rs1361701177	850	dbSNP
rs1469231033	858	dbSNP
rs7682	862	dbSNP
rs1045954259	863	dbSNP
rs1423325619	870	dbSNP
rs1224046452	871	dbSNP
rs1303018607	876	dbSNP
rs950315924	878	dbSNP
rs1043133057	891	dbSNP
rs894729748	892	dbSNP
rs1267822427	895	dbSNP
rs9451258	896	dbSNP
rs889249088	897	dbSNP
rs1357312809	898	dbSNP
rs1051937241	899	dbSNP
rs933602710	904	dbSNP
rs762071199	905	dbSNP
rs919506078	918	dbSNP
rs564549897	920	dbSNP
rs1436830357	921	dbSNP
rs1187759314	930	dbSNP
rs189318000	933	dbSNP
rs1386576234	937	dbSNP
rs539230999	952	dbSNP
rs1163588739	962	dbSNP
rs552256163	962	dbSNP
rs1463897056	963	dbSNP
rs1291342411	967	dbSNP
rs908981968	973	dbSNP
rs569138032	974	dbSNP
rs1394770335	982	dbSNP
rs1439429255	983	dbSNP
rs532340262	987	dbSNP
rs1396177462	996	dbSNP
rs1319599103	998	dbSNP
rs1396851062	1004	dbSNP
rs550563530	1020	dbSNP
rs1380681566	1023	dbSNP
rs1451998937	1024	dbSNP
rs541510220	1032	dbSNP
rs930341299	1035	dbSNP
rs751545098	1042	dbSNP
rs1159708734	1043	dbSNP
rs1249431095	1049	dbSNP
rs1338447993	1053	dbSNP
rs747735868	1059	dbSNP
rs1459637430	1068	dbSNP
rs184255417	1069	dbSNP
rs1249235132	1072	dbSNP
rs940504326	1077	dbSNP
rs911760476	1078	dbSNP
rs568160678	1080	dbSNP
rs1372883816	1081	dbSNP
rs991991702	1090	dbSNP
rs956858565	1092	dbSNP
rs1404164531	1102	dbSNP
rs1030894718	1103	dbSNP
rs953375899	1111	dbSNP
rs1321261856	1123	dbSNP
rs546565865	1135	dbSNP
rs1364119617	1145	dbSNP
rs1247663793	1150	dbSNP
rs1293275074	1152	dbSNP
rs1325712000	1153	dbSNP
rs921888722	1155	dbSNP
rs1223886439	1158	dbSNP
rs998868877	1159	dbSNP
rs1466505973	1160	dbSNP
rs1260825800	1164	dbSNP
rs968672577	1164	dbSNP
rs975789903	1166	dbSNP
rs1021720934	1169	dbSNP
rs1185289836	1169	dbSNP
rs1481000337	1173	dbSNP
rs1202011922	1176	dbSNP
rs1427506560	1191	dbSNP
rs957421754	1191	dbSNP
rs60315698	1198	dbSNP
rs1310972161	1199	dbSNP
rs1033037564	1200	dbSNP
rs889198889	1208	dbSNP
rs1052394331	1209	dbSNP
rs1298476183	1216	dbSNP
rs1451721228	1216	dbSNP
rs998933607	1224	dbSNP
rs1405377926	1225	dbSNP
rs1284993528	1233	dbSNP
rs766822380	1241	dbSNP
rs997677172	1259	dbSNP
rs967444237	1261	dbSNP
rs796316436	1274	dbSNP
rs528594432	1275	dbSNP
rs1044702822	1278	dbSNP
rs894690894	1283	dbSNP
rs1267234590	1289	dbSNP
rs181084090	1293	dbSNP
rs1432505535	1295	dbSNP
rs1177998896	1302	dbSNP
rs947834466	1312	dbSNP
rs1417462480	1315	dbSNP
rs146198242	1315	dbSNP
rs751529459	1315	dbSNP
rs1390559431	1318	dbSNP
rs1425248559	1321	dbSNP
rs1289292871	1324	dbSNP
rs1465423170	1328	dbSNP
rs1357386550	1331	dbSNP
rs1178262030	1332	dbSNP
rs774702949	1341	dbSNP
rs1304820424	1342	dbSNP
rs189116588	1347	dbSNP
rs1389673747	1349	dbSNP
rs768696117	1354	dbSNP
rs1298447321	1360	dbSNP
rs1375041034	1368	dbSNP
rs1186904111	1373	dbSNP
rs1036108213	1375	dbSNP
rs1359468612	1378	dbSNP
rs763404731	1379	dbSNP
rs979305082	1387	dbSNP
rs967955017	1388	dbSNP
rs1482541058	1396	dbSNP
rs749401863	1397	dbSNP
rs775665272	1398	dbSNP
rs780590115	1399	dbSNP
rs1234857938	1409	dbSNP
rs564018255	1415	dbSNP
rs1007553212	1423	dbSNP
rs911645756	1425	dbSNP
rs1385956601	1428	dbSNP
rs1446453062	1434	dbSNP
rs769886116	1437	dbSNP
rs1051570332	1440	dbSNP
rs542592002	1443	dbSNP
rs921830822	1446	dbSNP
rs989436719	1452	dbSNP
rs575164389	1453	dbSNP
rs1366937482	1458	dbSNP
rs745844453	1461	dbSNP
rs1297183427	1475	dbSNP
rs754470510	1477	dbSNP
rs1382889173	1484	dbSNP
rs572588317	1485	dbSNP
rs1454112888	1487	dbSNP
rs11757474	1488	dbSNP
rs1359316170	1488	dbSNP
rs897962285	1494	dbSNP
rs540513312	1495	dbSNP
rs1275579021	1501	dbSNP
rs1036484190	1507	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.