>GXYLT2|NM_001080393|3'UTR
   1 ATATTTTGTCTTGTTGCAAGTCAATTAGGTGTCTTGTGACCAAGGAAATACTAATCTCTAAGCTGCCTGGGTCTTTTTGT
  81 GTGAATATTTAATGGTGCTCCATGACTGTTGAGTTTTAAAAACCTCGTTAAATTTTGCCAAATCAGTTGCCCCCAAAAGG
 161 GAATATGCTTTTCCTTATTTTTTTTTCTAAAATGCTATTTATCTCTAAGGAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ucUCGUUCUGGGGCAGAGAUUu 5' || || |: ||||||| Target 5' caAGGAAATACTAATCTCTAAg 3'	41 - 62	148.00	-12.10
2	miRNA 3' ucucgUUCUG--GGGCAGAGAUUu 5' || :| ::: ||||||| Target 5' tctaaAATGCTATTTATCTCTAAg 3'	186 - 209	143.00	-7.70
3	miRNA 3' ucucGUUCUGGGGCAGAGAUUu 5' :|| | || || :||| Target 5' gtttTAAAAACC--TCGTTAAa 3'	113 - 132	102.00	-8.40

Mutant ID	Mutant Position	Mutant Source
COSN15660863	18	COSMIC
COSN30183391	18	COSMIC
COSN28615358	41	COSMIC
COSN30480179	101	COSMIC
COSN31532020	119	COSMIC
COSN5047002	150	COSMIC
COSN30138086	170	COSMIC
COSN28887888	187	COSMIC
COSN20098658	223	COSMIC
COSN1280699	322	COSMIC
COSN17913305	415	COSMIC
COSN1280700	456	COSMIC
COSN22752075	513	COSMIC
COSN17197859	652	COSMIC
COSN17201121	655	COSMIC
COSN32174501	1089	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs377447427	9	dbSNP
rs531179063	12	dbSNP
rs7613265	14	dbSNP
rs1340711401	25	dbSNP
rs1227334459	33	dbSNP
rs1052278	41	dbSNP
rs373822031	44	dbSNP
rs1199053089	50	dbSNP
rs1247153605	51	dbSNP
rs1295588215	52	dbSNP
rs915760674	55	dbSNP
rs1362691622	71	dbSNP
rs1045429287	80	dbSNP
rs906969201	88	dbSNP
rs1348046190	90	dbSNP
rs756871716	93	dbSNP
rs1034185780	111	dbSNP
rs1338221196	114	dbSNP
rs957467981	115	dbSNP
rs1166292915	125	dbSNP
rs1011480785	127	dbSNP
rs928534263	128	dbSNP
rs571197973	137	dbSNP
rs1020637533	141	dbSNP
rs939361109	142	dbSNP
rs1271606394	147	dbSNP
rs1223688401	150	dbSNP
rs1482908303	178	dbSNP
rs988120906	178	dbSNP
rs1230950814	179	dbSNP
rs1279661444	180	dbSNP
rs1308266235	181	dbSNP
rs1300758111	182	dbSNP
rs1217537170	184	dbSNP
rs1375399140	187	dbSNP
rs913880066	187	dbSNP
rs1222050224	188	dbSNP
rs1267241679	189	dbSNP
rs1324081938	198	dbSNP
rs528773735	200	dbSNP
rs1205351770	205	dbSNP
rs1261448930	206	dbSNP
rs1369668634	207	dbSNP
rs1442095233	207	dbSNP
rs201394105	209	dbSNP
rs371869973	209	dbSNP
rs386662267	209	dbSNP
rs374666255	210	dbSNP
rs1174758376	211	dbSNP
rs1250114330	211	dbSNP
rs397819913	211	dbSNP
rs5850090	211	dbSNP
rs869285852	211	dbSNP
rs1258824563	224	dbSNP
rs1481116030	226	dbSNP
rs930562915	226	dbSNP
rs1255571160	228	dbSNP
rs967341879	232	dbSNP
rs547287698	233	dbSNP
rs1313986302	240	dbSNP
rs1264954829	252	dbSNP
rs1234725831	256	dbSNP
rs1224103617	259	dbSNP
rs1349767407	263	dbSNP
rs1469043498	264	dbSNP
rs1182176629	265	dbSNP
rs1392854080	266	dbSNP
rs568378621	284	dbSNP
rs1040403418	297	dbSNP
rs1108154	300	dbSNP
rs557220829	303	dbSNP
rs975936977	304	dbSNP
rs569325055	310	dbSNP
rs1184446633	314	dbSNP
rs1419980237	320	dbSNP
rs1328918963	326	dbSNP
rs1180290796	331	dbSNP
rs1355830474	332	dbSNP
rs1462810920	338	dbSNP
rs1003860235	344	dbSNP
rs1208185162	354	dbSNP
rs1328406455	357	dbSNP
rs1407911740	358	dbSNP
rs1258819757	360	dbSNP
rs920091944	360	dbSNP
rs1240949209	362	dbSNP
rs536879029	363	dbSNP
rs186402074	368	dbSNP
rs1225081196	378	dbSNP
rs541015796	384	dbSNP
rs1023098130	385	dbSNP
rs1433639590	387	dbSNP
rs940327363	388	dbSNP
rs772739069	390	dbSNP
rs780359598	391	dbSNP
rs1436085082	395	dbSNP
rs1163089997	400	dbSNP
rs540940623	403	dbSNP
rs969957184	405	dbSNP
rs906919847	407	dbSNP
rs553188361	411	dbSNP
rs200024754	412	dbSNP
rs2101614	415	dbSNP
rs1463566742	432	dbSNP
rs563282921	441	dbSNP
rs1206873091	443	dbSNP
rs1486135854	445	dbSNP
rs955958271	456	dbSNP
rs1377469033	457	dbSNP
rs1477482358	459	dbSNP
rs988698202	463	dbSNP
rs1020163560	465	dbSNP
rs913909468	467	dbSNP
rs1362336821	480	dbSNP
rs946659044	482	dbSNP
rs1383313153	486	dbSNP
rs903102323	489	dbSNP
rs1390643670	490	dbSNP
rs1421208868	490	dbSNP
rs1427212468	497	dbSNP
rs1168138423	500	dbSNP
rs1386124161	500	dbSNP
rs1447860705	505	dbSNP
rs1374902436	509	dbSNP
rs979578668	516	dbSNP
rs1008187455	521	dbSNP
rs189674788	534	dbSNP
rs543524034	537	dbSNP
rs1490768413	538	dbSNP
rs1292082257	541	dbSNP
rs182590069	544	dbSNP
rs1321325564	546	dbSNP
rs1271500618	553	dbSNP
rs1227506410	560	dbSNP
rs1331050808	566	dbSNP
rs940291304	567	dbSNP
rs1227891702	571	dbSNP
rs1027503691	580	dbSNP
rs1307772521	589	dbSNP
rs188106257	594	dbSNP
rs983363526	596	dbSNP
rs1292640898	602	dbSNP
rs908759993	607	dbSNP
rs1490977211	612	dbSNP
rs1220973832	616	dbSNP
rs949637152	619	dbSNP
rs546988041	630	dbSNP
rs1481365437	631	dbSNP
rs539422916	636	dbSNP
rs2087662	649	dbSNP
rs937028532	650	dbSNP
rs536634608	659	dbSNP
rs1243454229	663	dbSNP
rs1435781379	683	dbSNP
rs1447331707	694	dbSNP
rs1274610970	710	dbSNP
rs1195901560	725	dbSNP
rs528861409	730	dbSNP
rs892883543	741	dbSNP
rs373625527	742	dbSNP
rs1260678629	747	dbSNP
rs1225929499	754	dbSNP
rs947199046	755	dbSNP
rs1385384695	756	dbSNP
rs1451456450	760	dbSNP
rs1426470715	761	dbSNP
rs1329744127	764	dbSNP
rs1413999580	764	dbSNP
rs879089930	764	dbSNP
rs1404064611	767	dbSNP
rs1178640220	768	dbSNP
rs1182135383	768	dbSNP
rs1204999351	768	dbSNP
rs1222454390	768	dbSNP
rs1234274218	768	dbSNP
rs1267979063	768	dbSNP
rs1280481735	768	dbSNP
rs1324898488	768	dbSNP
rs1353228323	768	dbSNP
rs1468352070	768	dbSNP
rs200250227	768	dbSNP
rs560026796	768	dbSNP
rs762340731	768	dbSNP
rs780595405	768	dbSNP
rs1389941654	769	dbSNP
rs1447628549	771	dbSNP
rs1380854236	772	dbSNP
rs1382528326	772	dbSNP
rs1320081006	773	dbSNP
rs1022740323	774	dbSNP
rs1363251671	775	dbSNP
rs1434705387	776	dbSNP
rs1315804215	784	dbSNP
rs55888823	785	dbSNP
rs905589610	786	dbSNP
rs1472293801	787	dbSNP
rs10212494	788	dbSNP
rs1242702306	789	dbSNP
rs1265308210	792	dbSNP
rs1352080728	793	dbSNP
rs1207234645	794	dbSNP
rs1260147394	795	dbSNP
rs569279490	796	dbSNP
rs539565210	798	dbSNP
rs1449207211	804	dbSNP
rs1463261195	805	dbSNP
rs1285477026	808	dbSNP
rs1357575253	827	dbSNP
rs557794203	837	dbSNP
rs147927959	842	dbSNP
rs1008135133	843	dbSNP
rs1364606034	845	dbSNP
rs1287154383	846	dbSNP
rs1428628062	848	dbSNP
rs1346876348	849	dbSNP
rs1318740386	858	dbSNP
rs534461651	861	dbSNP
rs1423686279	863	dbSNP
rs1383035888	866	dbSNP
rs1187613294	872	dbSNP
rs367963830	874	dbSNP
rs1418219510	883	dbSNP
rs1184256062	889	dbSNP
rs899809543	890	dbSNP
rs1243143901	898	dbSNP
rs141886091	904	dbSNP
rs192736945	909	dbSNP
rs373634149	922	dbSNP
rs760572439	924	dbSNP
rs1216343024	933	dbSNP
rs1004342370	934	dbSNP
rs1015709438	935	dbSNP
rs1304697247	939	dbSNP
rs970900580	940	dbSNP
rs1424981574	948	dbSNP
rs575285679	950	dbSNP
rs1337555892	957	dbSNP
rs147119548	960	dbSNP
rs958363860	964	dbSNP
rs763769913	965	dbSNP
rs1200579893	971	dbSNP
rs986878083	974	dbSNP
rs367779679	979	dbSNP
rs914280728	987	dbSNP
rs1206751138	992	dbSNP
rs1308101658	999	dbSNP
rs1277974026	1009	dbSNP
rs138518895	1019	dbSNP
rs1328837156	1021	dbSNP
rs1037286141	1023	dbSNP
rs1041516937	1028	dbSNP
rs1405271977	1030	dbSNP
rs35230145	1033	dbSNP
rs1204728012	1059	dbSNP
rs1296055332	1063	dbSNP
rs753580293	1065	dbSNP
rs756996358	1067	dbSNP
rs778670749	1071	dbSNP
rs1175078998	1075	dbSNP
rs1432006408	1078	dbSNP
rs1468752147	1078	dbSNP
rs749960057	1089	dbSNP
rs1177603376	1090	dbSNP
rs1418821965	1094	dbSNP
rs1248710578	1101	dbSNP
rs1179221816	1106	dbSNP
rs757925845	1125	dbSNP
rs1198199596	1126	dbSNP
rs773282306	1128	dbSNP
rs920171503	1129	dbSNP
rs1183986174	1130	dbSNP
rs1201840361	1135	dbSNP
rs899757323	1140	dbSNP
rs1044472629	1150	dbSNP
rs1223928497	1153	dbSNP
rs1409664949	1161	dbSNP
rs905498680	1170	dbSNP
rs1003043551	1176	dbSNP
rs1373585762	1177	dbSNP
rs996820801	1184	dbSNP
rs1335508814	1187	dbSNP
rs1449746069	1193	dbSNP
rs1048873620	1194	dbSNP
rs1176911368	1196	dbSNP
rs888491403	1203	dbSNP
rs1453646039	1225	dbSNP
rs1464779103	1229	dbSNP
rs1161730070	1230	dbSNP
rs1419959704	1231	dbSNP
rs1181833594	1234	dbSNP
rs1462680729	1247	dbSNP
rs1056860960	1248	dbSNP
rs1201019654	1258	dbSNP
rs1302325187	1260	dbSNP
rs1397391486	1266	dbSNP
rs1240846228	1269	dbSNP
rs1353975864	1273	dbSNP
rs1313868054	1274	dbSNP
rs1393220704	1292	dbSNP
rs1243166440	1293	dbSNP
rs540810923	1301	dbSNP
rs527618880	1305	dbSNP
rs891670955	1309	dbSNP
rs1015656918	1314	dbSNP
rs1383423800	1316	dbSNP
rs1021580133	1326	dbSNP
rs183558917	1329	dbSNP
rs1003673593	1342	dbSNP
rs1033852875	1343	dbSNP
rs1365223815	1347	dbSNP
rs996084926	1353	dbSNP
rs1385988047	1354	dbSNP
rs1446649536	1354	dbSNP
rs959885700	1364	dbSNP
rs1350438379	1368	dbSNP
rs780670418	1369	dbSNP
rs1285628007	1379	dbSNP
rs914209080	1381	dbSNP
rs35460639	1385	dbSNP
rs977144368	1388	dbSNP
rs1207657515	1390	dbSNP
rs1290729045	1391	dbSNP
rs924369459	1397	dbSNP
rs1219847575	1398	dbSNP
rs1361146434	1402	dbSNP
rs1284338189	1403	dbSNP
rs1225986992	1404	dbSNP
rs1254897094	1407	dbSNP
rs1325205784	1408	dbSNP
rs1298322812	1412	dbSNP
rs1383150428	1414	dbSNP
rs1480633064	1416	dbSNP
rs1301648116	1426	dbSNP
rs1206694890	1429	dbSNP
rs529567708	1435	dbSNP
rs1366361636	1443	dbSNP
rs576532725	1449	dbSNP
rs961560100	1453	dbSNP
rs747467680	1458	dbSNP
rs1195299605	1460	dbSNP
rs759219645	1463	dbSNP
rs931567908	1464	dbSNP
rs767078854	1469	dbSNP
rs1290073929	1490	dbSNP
rs1194755427	1496	dbSNP
rs550963286	1499	dbSNP
rs1252519638	1504	dbSNP
rs1219831723	1506	dbSNP
rs775864532	1508	dbSNP
rs1175549398	1514	dbSNP
rs370201383	1523	dbSNP
rs1407089172	1524	dbSNP
rs1056935646	1526	dbSNP
rs1306295250	1530	dbSNP
rs1328392844	1551	dbSNP
rs1370453237	1556	dbSNP
rs1398792055	1558	dbSNP
rs1406145397	1564	dbSNP
rs533113395	1568	dbSNP
rs781388361	1570	dbSNP
rs1010097680	1584	dbSNP
rs1042929926	1585	dbSNP
rs546584435	1586	dbSNP
rs904327305	1587	dbSNP
rs1180692228	1594	dbSNP
rs1424697910	1606	dbSNP
rs1219011934	1620	dbSNP
rs1003619772	1635	dbSNP
rs1198717232	1636	dbSNP
rs748460952	1640	dbSNP
rs371979807	1656	dbSNP
rs1261765423	1667	dbSNP
rs1307733807	1671	dbSNP
rs895344878	1677	dbSNP
rs1011556906	1685	dbSNP
rs1271907011	1688	dbSNP
rs1237230196	1692	dbSNP
rs1337750871	1693	dbSNP
rs1332132797	1694	dbSNP
rs1451930795	1696	dbSNP
rs1008177237	1701	dbSNP
rs1341357673	1702	dbSNP
rs1277740133	1703	dbSNP
rs1019688008	1705	dbSNP
rs1223226331	1713	dbSNP
rs1248392033	1737	dbSNP
rs1425666175	1741	dbSNP
rs961458407	1754	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.