ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gucUGGACUCAUCGCGUUCCac 5' |: | | || |||||| Target 5' ggaATGTCAACAGAGCAAGGag 3'	138 - 159	131.00	-9.50
2	miRNA 3' guCUGGACUCAUCGCGUUCCAc 5' ||::| | || |||| || Target 5' taGATTT-ATTATGGCAATGTt 3'	1213 - 1233	123.00	-5.50
3	miRNA 3' gucUGGACUCAUCG-CGUUCCac 5' |:|| |:|| |:|||| Target 5' gtaATCT--TTGGCTGTAAGGca 3'	466 - 486	115.00	-11.00

Mutant ID	Mutant Position	Mutant Source
COSM1200307	7	COSMIC
COSM7889261	17	COSMIC
COSM9879920	34	COSMIC
COSM7815677	48	COSMIC
COSN30151387	67	COSMIC
COSN30625325	129	COSMIC
COSN5200941	177	COSMIC
COSN31581669	182	COSMIC
COSN5364166	422	COSMIC
COSN21916075	751	COSMIC
COSN8430223	990	COSMIC
COSN29458661	1082	COSMIC
COSN21129828	1188	COSMIC
COSN14454526	1339	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs56018936	7	dbSNP
rs897563274	8	dbSNP
rs1018022142	10	dbSNP
rs762806651	11	dbSNP
rs768397816	12	dbSNP
rs1193190547	14	dbSNP
rs1268362312	17	dbSNP
rs765073271	20	dbSNP
rs774209732	20	dbSNP
rs1352250699	25	dbSNP
rs12024498	28	dbSNP
rs1042390	30	dbSNP
rs1191845904	35	dbSNP
rs766621630	36	dbSNP
rs1240073632	38	dbSNP
rs1282708164	39	dbSNP
rs753867903	41	dbSNP
rs759650301	42	dbSNP
rs765768553	43	dbSNP
rs753202580	44	dbSNP
rs1293713371	45	dbSNP
rs758957459	48	dbSNP
rs1438007043	49	dbSNP
rs55788390	51	dbSNP
rs751998623	58	dbSNP
rs191167519	63	dbSNP
rs979087738	65	dbSNP
rs923603798	66	dbSNP
rs781037530	67	dbSNP
rs745343919	72	dbSNP
rs769258176	77	dbSNP
rs1211308379	80	dbSNP
rs148706333	83	dbSNP
rs749126414	86	dbSNP
rs768644578	87	dbSNP
rs28371653	92	dbSNP
rs1031554334	94	dbSNP
rs1440824092	99	dbSNP
rs1180674986	100	dbSNP
rs1163688048	111	dbSNP
rs956898696	112	dbSNP
rs1355083003	117	dbSNP
rs917850605	118	dbSNP
rs989949640	119	dbSNP
rs1415277428	121	dbSNP
rs1403245599	124	dbSNP
rs1322462729	127	dbSNP
rs1438026386	128	dbSNP
rs55884294	137	dbSNP
rs969348903	161	dbSNP
rs1324059566	173	dbSNP
rs1409286552	175	dbSNP
rs55807530	178	dbSNP
rs1170212127	184	dbSNP
rs1450382602	187	dbSNP
rs927884932	196	dbSNP
rs1219390572	199	dbSNP
rs28371672	201	dbSNP
rs1479013063	203	dbSNP
rs1247817260	208	dbSNP
rs1204509946	213	dbSNP
rs939296398	220	dbSNP
rs1334012133	230	dbSNP
rs947900412	231	dbSNP
rs1342470511	233	dbSNP
rs1302150392	239	dbSNP
rs1045337150	256	dbSNP
rs1369175490	259	dbSNP
rs1274919267	264	dbSNP
rs887860580	266	dbSNP
rs556445049	267	dbSNP
rs1333882430	271	dbSNP
rs919044005	279	dbSNP
rs560350919	280	dbSNP
rs1171949080	288	dbSNP
rs930511422	293	dbSNP
rs55806327	298	dbSNP
rs55812205	299	dbSNP
rs1226877295	305	dbSNP
rs1176662094	317	dbSNP
rs1289423805	327	dbSNP
rs772912689	335	dbSNP
rs530112421	339	dbSNP
rs998155778	352	dbSNP
rs1485515465	357	dbSNP
rs1030562508	358	dbSNP
rs191637741	374	dbSNP
rs1313552459	378	dbSNP
rs878923988	383	dbSNP
rs1007717774	399	dbSNP
rs1222663116	404	dbSNP
rs576830350	411	dbSNP
rs1040097631	412	dbSNP
rs28371654	415	dbSNP
rs1354647561	418	dbSNP
rs1310843699	419	dbSNP
rs1188083913	420	dbSNP
rs998805560	424	dbSNP
rs1369758473	427	dbSNP
rs1471523142	428	dbSNP
rs1398956789	433	dbSNP
rs770437357	442	dbSNP
rs1052722545	452	dbSNP
rs1030643524	454	dbSNP
rs759426042	455	dbSNP
rs532365170	456	dbSNP
rs956416737	461	dbSNP
rs1183938220	471	dbSNP
rs1173315066	472	dbSNP
rs1484040328	478	dbSNP
rs1237658405	485	dbSNP
rs1214468850	486	dbSNP
rs1326393656	493	dbSNP
rs1398474338	503	dbSNP
rs28371655	504	dbSNP
rs917833366	505	dbSNP
rs948005969	506	dbSNP
rs980534578	507	dbSNP
rs1002149880	519	dbSNP
rs1288449521	522	dbSNP
rs55993635	533	dbSNP
rs942091645	539	dbSNP
rs1445872167	545	dbSNP
rs752499941	550	dbSNP
rs1283871336	555	dbSNP
rs960740198	558	dbSNP
rs1318899716	571	dbSNP
rs1167394915	575	dbSNP
rs1424694561	577	dbSNP
rs1414090034	597	dbSNP
rs1185634920	600	dbSNP
rs1249390965	608	dbSNP
rs762805341	608	dbSNP
rs534381219	612	dbSNP
rs752470521	612	dbSNP
rs1467997572	613	dbSNP
rs1258552915	627	dbSNP
rs1263535424	629	dbSNP
rs1246733399	630	dbSNP
rs557820530	631	dbSNP
rs919193837	636	dbSNP
rs1255920353	645	dbSNP
rs1036425850	656	dbSNP
rs554147467	657	dbSNP
rs951957812	667	dbSNP
rs1298448852	677	dbSNP
rs1440210163	683	dbSNP
rs984645543	685	dbSNP
rs1295744326	693	dbSNP
rs910300483	694	dbSNP
rs567765015	696	dbSNP
rs55925182	702	dbSNP
rs36016182	703	dbSNP
rs1168739153	708	dbSNP
rs1447336269	715	dbSNP
rs1042662	717	dbSNP
rs41277228	723	dbSNP
rs1440249271	727	dbSNP
rs1264635703	728	dbSNP
rs1211636052	730	dbSNP
rs527604156	731	dbSNP
rs1250593622	732	dbSNP
rs1202697606	733	dbSNP
rs201373838	734	dbSNP
rs55662115	738	dbSNP
rs1275541743	739	dbSNP
rs1052231304	754	dbSNP
rs889371646	756	dbSNP
rs540000468	765	dbSNP
rs556475078	768	dbSNP
rs1329480736	775	dbSNP
rs759422665	777	dbSNP
rs934357402	779	dbSNP
rs779620816	783	dbSNP
rs1422002688	789	dbSNP
rs1306589822	800	dbSNP
rs1053105358	802	dbSNP
rs1372036279	803	dbSNP
rs1461791586	805	dbSNP
rs34906513	814	dbSNP
rs1173713584	817	dbSNP
rs1168897030	838	dbSNP
rs1404950354	839	dbSNP
rs1465229246	854	dbSNP
rs892744635	854	dbSNP
rs1333625588	872	dbSNP
rs757320964	877	dbSNP
rs576643280	892	dbSNP
rs1433720581	894	dbSNP
rs1249680723	896	dbSNP
rs1179750243	897	dbSNP
rs1483882735	898	dbSNP
rs1252261194	900	dbSNP
rs1210523462	916	dbSNP
rs1011491387	922	dbSNP
rs904704652	923	dbSNP
rs1043909366	924	dbSNP
rs1316877006	928	dbSNP
rs765257454	931	dbSNP
rs1000592925	935	dbSNP
rs1412204497	937	dbSNP
rs1030738440	940	dbSNP
rs1351559420	947	dbSNP
rs905374780	955	dbSNP
rs1402091699	963	dbSNP
rs956695368	968	dbSNP
rs28371656	969	dbSNP
rs1466042424	975	dbSNP
rs1025065641	989	dbSNP
rs1156930407	991	dbSNP
rs1473531556	992	dbSNP
rs1257492764	996	dbSNP
rs993540155	998	dbSNP
rs752553003	1000	dbSNP
rs1440931118	1005	dbSNP
rs1258485090	1009	dbSNP
rs980670434	1027	dbSNP
rs1201114243	1030	dbSNP
rs1485616567	1048	dbSNP
rs1266308743	1053	dbSNP
rs1342825392	1053	dbSNP
rs147469126	1055	dbSNP
rs560196622	1058	dbSNP
rs1293083034	1063	dbSNP
rs971898906	1070	dbSNP
rs1338338675	1076	dbSNP
rs1488977214	1076	dbSNP
rs139963064	1082	dbSNP
rs1317926074	1084	dbSNP
rs910347906	1084	dbSNP
rs919340306	1094	dbSNP
rs933437992	1098	dbSNP
rs1458804532	1104	dbSNP
rs1412560634	1110	dbSNP
rs964559084	1113	dbSNP
rs1051727704	1118	dbSNP
rs1428342314	1120	dbSNP
rs1471651433	1125	dbSNP
rs910550483	1131	dbSNP
rs975802429	1136	dbSNP
rs74877368	1141	dbSNP
rs574920252	1142	dbSNP
rs1210611182	1145	dbSNP
rs904799770	1147	dbSNP
rs1361311814	1149	dbSNP
rs1273028693	1154	dbSNP
rs1208442978	1158	dbSNP
rs1358978710	1159	dbSNP
rs1285154759	1171	dbSNP
rs145479193	1173	dbSNP
rs1363987270	1182	dbSNP
rs1053320326	1185	dbSNP
rs563621356	1186	dbSNP
rs753994405	1191	dbSNP
rs1322750322	1197	dbSNP
rs1387527581	1200	dbSNP
rs1303143372	1202	dbSNP
rs368469534	1211	dbSNP
rs1163599605	1215	dbSNP
rs1449115273	1217	dbSNP
rs1388505764	1218	dbSNP
rs1232515795	1232	dbSNP
rs1013761510	1236	dbSNP
rs1450097952	1241	dbSNP
rs1246186578	1248	dbSNP
rs1024615506	1249	dbSNP
rs1197459244	1252	dbSNP
rs1453805510	1283	dbSNP
rs1291104275	1286	dbSNP
rs1195546855	1289	dbSNP
rs946933564	1290	dbSNP
rs1043956865	1297	dbSNP
rs28371657	1309	dbSNP
rs938193939	1310	dbSNP
rs1355277424	1312	dbSNP
rs1332705524	1313	dbSNP
rs1323997429	1319	dbSNP
rs552358820	1321	dbSNP
rs1430644878	1325	dbSNP
rs1424602294	1330	dbSNP
rs1284623448	1339	dbSNP
rs1170875324	1340	dbSNP
rs1479305878	1341	dbSNP
rs1247760427	1344	dbSNP
rs371954089	1352	dbSNP
rs750563951	1354	dbSNP
rs1049972377	1355	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.