ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gaacacaaucUUGUCUCCGUua 5' ||::||||:| Target 5' gctccagggaAATGGAGGTAtt 3'	341 - 362	116.00	-8.30
2	miRNA 3' gaacacaaUCU--UGUCUCCGUUa 5' ||| |||||| :|| Target 5' agtcaggaAGAAGACAGAGCTAAt 3'	155 - 178	112.00	-9.30
3	miRNA 3' gaacacaAUCU---UGUCUCCGUUa 5' |:|| | |||| || Target 5' tcgacccTGGACCTCCTGAGGGAAa 3'	15 - 39	111.00	-7.00

Mutant ID	Mutant Position	Mutant Source
COSN30180650	12	COSMIC
COSN24314545	16	COSMIC
COSN31590259	17	COSMIC
COSN30469883	27	COSMIC
COSN30449081	34	COSMIC
COSN30479945	57	COSMIC
COSN31499674	93	COSMIC
COSN30121427	94	COSMIC
COSN31519489	94	COSMIC
COSN21405784	115	COSMIC
COSN30149003	116	COSMIC
COSN25838223	134	COSMIC
COSN1729104	258	COSMIC
COSN16088324	271	COSMIC
COSN21630437	755	COSMIC
COSN27432409	755	COSMIC
COSN20966298	756	COSMIC
COSN20290548	876	COSMIC
COSN1201463	996	COSMIC
COSN27450627	1058	COSMIC
COSN27899767	1463	COSMIC
COSN27589122	1538	COSMIC
COSN7455642	1660	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1449249002	1	dbSNP
rs1414421084	5	dbSNP
rs1183572442	6	dbSNP
rs369499551	7	dbSNP
rs774701095	8	dbSNP
rs769444294	10	dbSNP
rs747959955	11	dbSNP
rs1260353064	14	dbSNP
rs768586995	16	dbSNP
rs746465775	17	dbSNP
rs1469437538	20	dbSNP
rs1314060442	21	dbSNP
rs1000266899	24	dbSNP
rs1386780026	27	dbSNP
rs779418880	29	dbSNP
rs866612665	32	dbSNP
rs1376989103	34	dbSNP
rs958436838	35	dbSNP
rs747379300	36	dbSNP
rs1402756108	37	dbSNP
rs1286690900	39	dbSNP
rs1329621583	40	dbSNP
rs1464882999	42	dbSNP
rs1350326297	43	dbSNP
rs1166818862	44	dbSNP
rs1422001452	45	dbSNP
rs574670660	45	dbSNP
rs1006355342	51	dbSNP
rs1346046078	68	dbSNP
rs952283662	80	dbSNP
rs1203344506	86	dbSNP
rs1280765468	93	dbSNP
rs904547170	97	dbSNP
rs1228565378	99	dbSNP
rs1026951740	102	dbSNP
rs1490233477	107	dbSNP
rs1353381847	112	dbSNP
rs9498	117	dbSNP
rs555487992	127	dbSNP
rs1490644093	128	dbSNP
rs997224921	128	dbSNP
rs1339825550	134	dbSNP
rs1480234340	139	dbSNP
rs1182884233	146	dbSNP
rs76614501	151	dbSNP
rs1040903350	154	dbSNP
rs1007632013	156	dbSNP
rs1157749934	160	dbSNP
rs1366150074	170	dbSNP
rs60794745	171	dbSNP
rs1332362251	182	dbSNP
rs939899580	185	dbSNP
rs1391464343	188	dbSNP
rs1308775109	189	dbSNP
rs1333588083	194	dbSNP
rs1237368511	195	dbSNP
rs533747635	200	dbSNP
rs1360805999	203	dbSNP
rs1303191755	217	dbSNP
rs1290210004	219	dbSNP
rs1490223493	222	dbSNP
rs184269458	223	dbSNP
rs147094679	226	dbSNP
rs1436252110	235	dbSNP
rs1363271389	238	dbSNP
rs571065764	240	dbSNP
rs1385571673	241	dbSNP
rs931094899	243	dbSNP
rs1309463817	253	dbSNP
rs748595545	254	dbSNP
rs980468043	264	dbSNP
rs949029429	272	dbSNP
rs1226118390	275	dbSNP
rs570431223	298	dbSNP
rs1054218734	301	dbSNP
rs141704657	318	dbSNP
rs1474686664	318	dbSNP
rs1331101141	336	dbSNP
rs537831847	341	dbSNP
rs924570723	342	dbSNP
rs993071325	345	dbSNP
rs1313616362	356	dbSNP
rs1321610888	362	dbSNP
rs1200154634	376	dbSNP
rs1228285291	382	dbSNP
rs113544449	392	dbSNP
rs1337714382	394	dbSNP
rs1031824490	396	dbSNP
rs949985122	401	dbSNP
rs978902314	403	dbSNP
rs1462535697	404	dbSNP
rs537790281	413	dbSNP
rs991170536	421	dbSNP
rs1428996018	438	dbSNP
rs937078804	440	dbSNP
rs1370775132	449	dbSNP
rs1461039243	451	dbSNP
rs549058970	458	dbSNP
rs1407816050	460	dbSNP
rs1454952504	466	dbSNP
rs1335094704	467	dbSNP
rs1379111626	470	dbSNP
rs1271994786	482	dbSNP
rs1297824816	489	dbSNP
rs748258297	501	dbSNP
rs1305908929	504	dbSNP
rs143389763	512	dbSNP
rs1194024397	520	dbSNP
rs115605418	521	dbSNP
rs1283367327	525	dbSNP
rs754043764	534	dbSNP
rs1486154835	548	dbSNP
rs879830374	553	dbSNP
rs1259557469	565	dbSNP
rs1004074508	568	dbSNP
rs1289881158	577	dbSNP
rs569040232	580	dbSNP
rs766598235	582	dbSNP
rs781340967	583	dbSNP
rs995712209	593	dbSNP
rs904940963	598	dbSNP
rs972753049	603	dbSNP
rs1045210254	604	dbSNP
rs1454628655	606	dbSNP
rs1291207637	610	dbSNP
rs966310703	614	dbSNP
rs1360468001	615	dbSNP
rs1399524636	617	dbSNP
rs548989624	634	dbSNP
rs149151180	638	dbSNP
rs1221840022	640	dbSNP
rs1427252372	649	dbSNP
rs751404469	654	dbSNP
rs1057409853	660	dbSNP
rs533647417	663	dbSNP
rs1179220144	664	dbSNP
rs1007474918	666	dbSNP
rs1487898792	668	dbSNP
rs1470605832	669	dbSNP
rs12601381	678	dbSNP
rs1479255533	680	dbSNP
rs1179311009	722	dbSNP
rs1198327485	724	dbSNP
rs1408252255	726	dbSNP
rs1420106904	728	dbSNP
rs934919568	736	dbSNP
rs1343985637	740	dbSNP
rs1462605715	749	dbSNP
rs1263757640	751	dbSNP
rs1202927112	752	dbSNP
rs1320865319	754	dbSNP
rs1285691402	755	dbSNP
rs1224026115	756	dbSNP
rs1367598076	756	dbSNP
rs112773986	768	dbSNP
rs1274533210	773	dbSNP
rs1297423742	773	dbSNP
rs1374289259	773	dbSNP
rs753373862	773	dbSNP
rs75646857	773	dbSNP
rs924829870	773	dbSNP
rs1012286778	780	dbSNP
rs960816815	782	dbSNP
rs1246539227	783	dbSNP
rs1035462703	785	dbSNP
rs889205894	788	dbSNP
rs1293854603	790	dbSNP
rs1489672700	791	dbSNP
rs1372079144	792	dbSNP
rs421612	793	dbSNP
rs1481380443	794	dbSNP
rs868457729	798	dbSNP
rs921400411	808	dbSNP
rs1385429582	833	dbSNP
rs1338004801	834	dbSNP
rs1469717247	837	dbSNP
rs1439460451	855	dbSNP
rs975897798	856	dbSNP
rs965438336	857	dbSNP
rs1387598383	858	dbSNP
rs1422875076	859	dbSNP
rs1322920188	864	dbSNP
rs1019557210	865	dbSNP
rs1444550208	875	dbSNP
rs903044529	877	dbSNP
rs1375950946	881	dbSNP
rs1041545182	882	dbSNP
rs1161325463	883	dbSNP
rs1356504757	885	dbSNP
rs1004138561	886	dbSNP
rs1227262669	886	dbSNP
rs763001251	896	dbSNP
rs1202079988	902	dbSNP
rs951306994	904	dbSNP
rs1457632877	906	dbSNP
rs1175683216	912	dbSNP
rs192366270	922	dbSNP
rs530511457	926	dbSNP
rs1245537566	933	dbSNP
rs995389126	943	dbSNP
rs1182938824	944	dbSNP
rs561713185	947	dbSNP
rs1420243879	949	dbSNP
rs1411715914	951	dbSNP
rs867950982	952	dbSNP
rs1055477809	956	dbSNP
rs1013733439	972	dbSNP
rs764908099	973	dbSNP
rs1338396852	974	dbSNP
rs1215812523	976	dbSNP
rs936964243	978	dbSNP
rs1052115534	983	dbSNP
rs1315799771	983	dbSNP
rs909649519	984	dbSNP
rs983892274	985	dbSNP
rs929697112	988	dbSNP
rs1323742443	994	dbSNP
rs527890212	1002	dbSNP
rs1362099128	1012	dbSNP
rs1187532278	1018	dbSNP
rs1243194467	1019	dbSNP
rs1476454048	1020	dbSNP
rs972254558	1024	dbSNP
rs541863730	1025	dbSNP
rs558686797	1031	dbSNP
rs145175647	1035	dbSNP
rs1290720603	1036	dbSNP
rs1431643302	1048	dbSNP
rs1011130110	1049	dbSNP
rs1399878085	1050	dbSNP
rs1344658296	1055	dbSNP
rs1157264261	1056	dbSNP
rs1426735863	1058	dbSNP
rs1385671499	1059	dbSNP
rs75182655	1059	dbSNP
rs1318943668	1065	dbSNP
rs1162623630	1068	dbSNP
rs1442719025	1069	dbSNP
rs139971030	1071	dbSNP
rs35037723	1071	dbSNP
rs1421637242	1073	dbSNP
rs1224908172	1074	dbSNP
rs1187033421	1076	dbSNP
rs921421569	1077	dbSNP
rs1019159042	1083	dbSNP
rs538997534	1084	dbSNP
rs144332897	1090	dbSNP
rs965454308	1093	dbSNP
rs6501884	1097	dbSNP
rs982747149	1098	dbSNP
rs953403325	1100	dbSNP
rs1480799615	1105	dbSNP
rs1224277001	1107	dbSNP
rs1477604320	1108	dbSNP
rs1158882524	1109	dbSNP
rs139633040	1120	dbSNP
rs1000272203	1121	dbSNP
rs1297055632	1123	dbSNP
rs1365721609	1127	dbSNP
rs903265242	1130	dbSNP
rs536992533	1137	dbSNP
rs1245623354	1144	dbSNP
rs1321219368	1145	dbSNP
rs1320273688	1146	dbSNP
rs1298456393	1169	dbSNP
rs1330125433	1174	dbSNP
rs1233010182	1179	dbSNP
rs1280460993	1180	dbSNP
rs866742668	1182	dbSNP
rs1215650407	1183	dbSNP
rs1020540991	1184	dbSNP
rs575193697	1188	dbSNP
rs969271509	1190	dbSNP
rs1296378544	1197	dbSNP
rs1265565307	1200	dbSNP
rs1014056944	1201	dbSNP
rs1023907729	1202	dbSNP
rs1407002073	1209	dbSNP
rs555484522	1219	dbSNP
rs1302769018	1221	dbSNP
rs895737136	1236	dbSNP
rs1422588972	1239	dbSNP
rs770640822	1244	dbSNP
rs1385751519	1248	dbSNP
rs746574498	1253	dbSNP
rs1374553271	1259	dbSNP
rs1160896450	1263	dbSNP
rs1171114253	1265	dbSNP
rs1427798555	1268	dbSNP
rs937221082	1269	dbSNP
rs1329981367	1270	dbSNP
rs535908458	1275	dbSNP
rs773638186	1277	dbSNP
rs1048081082	1278	dbSNP
rs772411377	1279	dbSNP
rs566874699	1293	dbSNP
rs1030718859	1294	dbSNP
rs999231711	1295	dbSNP
rs1267801050	1298	dbSNP
rs1219786426	1299	dbSNP
rs765950319	1300	dbSNP
rs367778459	1302	dbSNP
rs1252922542	1303	dbSNP
rs547099040	1308	dbSNP
rs539629354	1309	dbSNP
rs373596945	1310	dbSNP
rs571097615	1311	dbSNP
rs1243697098	1318	dbSNP
rs1276400521	1320	dbSNP
rs1184781060	1322	dbSNP
rs1367317042	1325	dbSNP
rs1169333163	1326	dbSNP
rs1462035063	1326	dbSNP
rs146807899	1343	dbSNP
rs144098290	1348	dbSNP
rs139125109	1349	dbSNP
rs386799305	1350	dbSNP
rs1384189379	1354	dbSNP
rs150808462	1356	dbSNP
rs1311192270	1357	dbSNP
rs528164889	1359	dbSNP
rs141343381	1360	dbSNP
rs953622153	1362	dbSNP
rs1461423646	1363	dbSNP
rs1316241555	1373	dbSNP
rs947610614	1374	dbSNP
rs925995763	1384	dbSNP
rs545922509	1385	dbSNP
rs1469924424	1387	dbSNP
rs1180101387	1388	dbSNP
rs1427946512	1393	dbSNP
rs1428649161	1403	dbSNP
rs576622422	1404	dbSNP
rs1421064762	1407	dbSNP
rs967875843	1408	dbSNP
rs563143945	1414	dbSNP
rs1170429873	1418	dbSNP
rs1407375045	1419	dbSNP
rs1020341552	1427	dbSNP
rs543271079	1428	dbSNP
rs1178084147	1429	dbSNP
rs982820732	1430	dbSNP
rs148618483	1432	dbSNP
rs1256788562	1433	dbSNP
rs1218183291	1434	dbSNP
rs1206090131	1440	dbSNP
rs1324425736	1450	dbSNP
rs959921664	1452	dbSNP
rs974078009	1463	dbSNP
rs969722837	1468	dbSNP
rs1023518854	1475	dbSNP
rs1206387673	1479	dbSNP
rs1260335062	1481	dbSNP
rs1487669585	1498	dbSNP
rs1199782274	1501	dbSNP
rs1337687232	1502	dbSNP
rs1034169546	1514	dbSNP
rs1307456139	1516	dbSNP
rs991996236	1530	dbSNP
rs960527847	1532	dbSNP
rs1374374856	1535	dbSNP
rs1338662384	1537	dbSNP
rs1470214604	1538	dbSNP
rs1454698372	1541	dbSNP
rs1300129099	1543	dbSNP
rs1030790968	1547	dbSNP
rs1399469956	1550	dbSNP
rs1217298978	1552	dbSNP
rs1300258279	1552	dbSNP
rs1304037352	1552	dbSNP
rs1491054623	1552	dbSNP
rs202223634	1552	dbSNP
rs565552454	1552	dbSNP
rs1170227560	1555	dbSNP
rs999264496	1559	dbSNP
rs1189843723	1561	dbSNP
rs755095203	1563	dbSNP
rs749405883	1571	dbSNP
rs1420033571	1582	dbSNP
rs1161041608	1586	dbSNP
rs1157913061	1594	dbSNP
rs369206308	1599	dbSNP
rs903546118	1610	dbSNP
rs1022398770	1613	dbSNP
rs1351842984	1619	dbSNP
rs1293147909	1628	dbSNP
rs995830600	1628	dbSNP
rs888360972	1629	dbSNP
rs1373875402	1640	dbSNP
rs1048092898	1641	dbSNP
rs900084592	1644	dbSNP
rs1462124400	1659	dbSNP
rs1242612937	1667	dbSNP
rs189035576	1668	dbSNP
rs896910473	1688	dbSNP
rs944243135	1690	dbSNP
rs1291318038	1692	dbSNP
rs891279970	1697	dbSNP
rs1220442699	1698	dbSNP
rs1251522286	1699	dbSNP
rs1352913863	1702	dbSNP
rs1180850493	1720	dbSNP
rs1236920653	1721	dbSNP
rs1439555490	1722	dbSNP
rs1182538568	1723	dbSNP
rs1040774710	1726	dbSNP
rs1403672820	1733	dbSNP
rs1164399524	1740	dbSNP
rs535459050	1750	dbSNP
rs756365629	1751	dbSNP
rs750557130	1752	dbSNP
rs912096220	1758	dbSNP
rs1467011370	1761	dbSNP
rs113242360	1767	dbSNP
rs1453212417	1771	dbSNP
rs919993601	1771	dbSNP
rs1285864110	1779	dbSNP
rs1376419167	1782	dbSNP
rs1316845873	1786	dbSNP
rs1295906978	1793	dbSNP
rs553182995	1794	dbSNP
rs1453299099	1797	dbSNP
rs932239109	1798	dbSNP
rs1200923591	1801	dbSNP
rs1256500670	1805	dbSNP
rs183997541	1806	dbSNP
rs1381878781	1812	dbSNP
rs192015803	1818	dbSNP
rs764041784	1822	dbSNP
rs916525382	1823	dbSNP
rs992069941	1824	dbSNP
rs1424643893	1834	dbSNP
rs758267492	1839	dbSNP
rs1168288724	1840	dbSNP
rs1383482609	1842	dbSNP
rs1385014245	1852	dbSNP
rs1470117157	1852	dbSNP
rs753414356	1853	dbSNP
rs1336133331	1858	dbSNP
rs1287975673	1862	dbSNP
rs1357334492	1863	dbSNP
rs1417429124	1864	dbSNP
rs752722071	1867	dbSNP
rs1446695954	1870	dbSNP
rs1270207901	1871	dbSNP
rs1378885378	1871	dbSNP
rs1165788319	1873	dbSNP
rs115757475	1876	dbSNP
rs1368452899	1878	dbSNP
rs1186040076	1882	dbSNP
rs1216480310	1882	dbSNP
rs1030823463	1884	dbSNP
rs1448852670	1884	dbSNP
rs1262485710	1887	dbSNP
rs1204811244	1889	dbSNP
rs977897962	1889	dbSNP
rs543024264	1891	dbSNP
rs1281377461	1898	dbSNP
rs1293693076	1904	dbSNP
rs1022003848	1907	dbSNP
rs1209509134	1908	dbSNP
rs1263924021	1910	dbSNP
rs913208261	1913	dbSNP
rs992953168	1915	dbSNP
rs960101692	1917	dbSNP
rs147135352	1918	dbSNP
rs1001328094	1919	dbSNP
rs952614881	1920	dbSNP
rs1174060166	1921	dbSNP
rs1018508290	1924	dbSNP
rs1008414635	1932	dbSNP
rs866222799	1948	dbSNP
rs568682880	1950	dbSNP
rs763775484	1951	dbSNP
rs117418912	1954	dbSNP
rs1397554853	1976	dbSNP
rs1297251227	1985	dbSNP
rs1345698703	1988	dbSNP
rs1437669823	1989	dbSNP
rs776238606	1992	dbSNP
rs1343508014	2000	dbSNP
rs1397753737	2001	dbSNP
rs1219215825	2005	dbSNP
rs1366987700	2009	dbSNP
rs1047231957	2016	dbSNP
rs896842052	2026	dbSNP
rs1355992048	2030	dbSNP
rs994261746	2034	dbSNP
rs1019691125	2036	dbSNP
rs1008017569	2037	dbSNP
rs1200754210	2044	dbSNP
rs1477574052	2045	dbSNP
rs1159222350	2048	dbSNP
rs1303364680	2055	dbSNP
rs528061408	2058	dbSNP
rs1417347037	2059	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.