ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ucUCCGU-CCAAGGACCUAGua 5' || || || |||||||| Target 5' taAGCCAGGGCCCCTGGATCtc 3'	2 - 23	143.00	-20.70
2	miRNA 3' ucuccguccaaGGACCUAGUa 5' |||| |||| Target 5' aacctagcacaCCTGAATCAg 3'	47 - 67	118.00	-8.90
3	miRNA 3' ucUCCGUC--CAAGGACC-UAGUa 5' :| :|| ||||||| |||: Target 5' ggGGATAGTCCTTCCTGGCATCGt 3'	111 - 134	113.00	-18.70

Mutant ID	Mutant Position	Mutant Source
COSN30523510	10	COSMIC
COSN20073994	11	COSMIC
COSN8862384	31	COSMIC
COSN30475358	33	COSMIC
COSN31486838	37	COSMIC
COSN30534835	66	COSMIC
COSN23014393	107	COSMIC
COSN20600401	201	COSMIC
COSN20094847	408	COSMIC
COSN1105977	508	COSMIC
COSN20094848	641	COSMIC
COSN20851530	941	COSMIC
COSN23018512	1068	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs372795381	11	dbSNP
rs1264431704	13	dbSNP
rs927345070	15	dbSNP
rs1323884186	16	dbSNP
rs781029282	18	dbSNP
rs745364705	19	dbSNP
rs755741954	20	dbSNP
rs779722787	22	dbSNP
rs764887122	27	dbSNP
rs372383383	28	dbSNP
rs774154563	29	dbSNP
rs747931957	30	dbSNP
rs41297863	31	dbSNP
rs1470427940	33	dbSNP
rs1471511469	34	dbSNP
rs1175897596	36	dbSNP
rs200376441	37	dbSNP
rs1037954428	38	dbSNP
rs760735709	39	dbSNP
rs766375868	40	dbSNP
rs776701548	42	dbSNP
rs760053092	46	dbSNP
rs536748609	54	dbSNP
rs561140330	59	dbSNP
rs1270019996	62	dbSNP
rs1480552386	77	dbSNP
rs995842404	78	dbSNP
rs916256634	84	dbSNP
rs1357624749	88	dbSNP
rs1409089729	103	dbSNP
rs763631171	104	dbSNP
rs890137117	106	dbSNP
rs948308486	108	dbSNP
rs1338842095	112	dbSNP
rs1008571121	115	dbSNP
rs376699364	117	dbSNP
rs1330953532	124	dbSNP
rs1389853636	127	dbSNP
rs1411634603	133	dbSNP
rs1397078740	134	dbSNP
rs1044376967	139	dbSNP
rs1030713716	141	dbSNP
rs1188299939	142	dbSNP
rs1472252772	143	dbSNP
rs956524654	148	dbSNP
rs1304723237	151	dbSNP
rs1052638716	157	dbSNP
rs1257919988	168	dbSNP
rs901912591	175	dbSNP
rs1337315287	183	dbSNP
rs1367748397	185	dbSNP
rs1274190261	187	dbSNP
rs998030081	188	dbSNP
rs1354475983	189	dbSNP
rs530019461	190	dbSNP
rs1442963364	191	dbSNP
rs1336294071	197	dbSNP
rs1022201826	200	dbSNP
rs889127675	207	dbSNP
rs1006776673	209	dbSNP
rs1165350302	212	dbSNP
rs1016811216	217	dbSNP
rs1411127109	227	dbSNP
rs962644539	227	dbSNP
rs546229754	228	dbSNP
rs980732954	229	dbSNP
rs1177384282	234	dbSNP
rs1450945497	235	dbSNP
rs1254067234	244	dbSNP
rs1025461291	247	dbSNP
rs1450110695	248	dbSNP
rs960469572	262	dbSNP
rs1350133873	267	dbSNP
rs927251517	282	dbSNP
rs1062701	288	dbSNP
rs960036701	293	dbSNP
rs1237931084	294	dbSNP
rs1373053562	296	dbSNP
rs992873273	301	dbSNP
rs1435428886	311	dbSNP
rs1347767974	320	dbSNP
rs1319803849	336	dbSNP
rs907997662	339	dbSNP
rs566506848	348	dbSNP
rs77941984	349	dbSNP
rs17131750	353	dbSNP
rs569086027	355	dbSNP
rs1156277156	367	dbSNP
rs796389755	368	dbSNP
rs1455994202	376	dbSNP
rs534290857	392	dbSNP
rs187324691	395	dbSNP
rs1190997772	399	dbSNP
rs34946952	399	dbSNP
rs1204044756	403	dbSNP
rs935596044	416	dbSNP
rs945	450	dbSNP
rs1050647135	461	dbSNP
rs554756460	465	dbSNP
rs951	468	dbSNP
rs754258939	469	dbSNP
rs1213062145	478	dbSNP
rs948	479	dbSNP
rs1349987149	484	dbSNP
rs1052584942	485	dbSNP
rs1008517297	489	dbSNP
rs1052130302	503	dbSNP
rs933390606	504	dbSNP
rs947	518	dbSNP
rs892241780	531	dbSNP
rs946	538	dbSNP
rs1010722530	547	dbSNP
rs889085716	549	dbSNP
rs191174302	559	dbSNP
rs949	560	dbSNP
rs1442680474	563	dbSNP
rs950	568	dbSNP
rs13046	569	dbSNP
rs748373961	579	dbSNP
rs898406004	582	dbSNP
rs994069337	594	dbSNP
rs1034937527	596	dbSNP
rs150157001	600	dbSNP
rs1187439748	619	dbSNP
rs758444378	620	dbSNP
rs1477635854	625	dbSNP
rs1261239150	628	dbSNP
rs960837510	629	dbSNP
rs1394519820	637	dbSNP
rs35173267	638	dbSNP
rs397864157	638	dbSNP
rs377397102	639	dbSNP
rs1023801623	643	dbSNP
rs1310340746	655	dbSNP
rs992861941	659	dbSNP
rs1218967088	669	dbSNP
rs969199459	682	dbSNP
rs1275843907	685	dbSNP
rs979079385	697	dbSNP
rs1329613801	699	dbSNP
rs1465019585	701	dbSNP
rs1356747029	715	dbSNP
rs1014996493	716	dbSNP
rs1465376094	724	dbSNP
rs1421762455	725	dbSNP
rs962461132	731	dbSNP
rs41297865	733	dbSNP
rs1317731094	736	dbSNP
rs1360643853	738	dbSNP
rs1234481137	756	dbSNP
rs1199046820	757	dbSNP
rs1317146507	760	dbSNP
rs546304854	765	dbSNP
rs1234802726	766	dbSNP
rs138614051	769	dbSNP
rs1311428636	770	dbSNP
rs1481406008	776	dbSNP
rs986356773	781	dbSNP
rs1376183037	783	dbSNP
rs1195933751	785	dbSNP
rs1446687507	789	dbSNP
rs36036202	797	dbSNP
rs879684752	797	dbSNP
rs986304041	797	dbSNP
rs11803547	798	dbSNP
rs11803548	799	dbSNP
rs573209457	808	dbSNP
rs1037648194	809	dbSNP
rs1385726381	811	dbSNP
rs897848471	818	dbSNP
rs765604273	823	dbSNP
rs929867689	824	dbSNP
rs1052076694	826	dbSNP
rs1457246475	830	dbSNP
rs35707547	835	dbSNP
rs149294525	841	dbSNP
rs1168057117	842	dbSNP
rs529941118	853	dbSNP
rs1013828852	856	dbSNP
rs1318269404	863	dbSNP
rs1023497403	866	dbSNP
rs904920523	867	dbSNP
rs1375284739	868	dbSNP
rs1328379168	870	dbSNP
rs1387651859	875	dbSNP
rs1390297750	879	dbSNP
rs1168611714	881	dbSNP
rs756489628	885	dbSNP
rs1401627952	889	dbSNP
rs1381053189	893	dbSNP
rs1158092745	895	dbSNP
rs1439045819	896	dbSNP
rs546911808	901	dbSNP
rs559874729	902	dbSNP
rs1195280097	903	dbSNP
rs1031980968	906	dbSNP
rs1450480383	909	dbSNP
rs1266402290	913	dbSNP
rs956367069	916	dbSNP
rs1486628626	919	dbSNP
rs1339282538	925	dbSNP
rs532160978	927	dbSNP
rs1215207181	935	dbSNP
rs1352171722	938	dbSNP
rs1306190211	941	dbSNP
rs1384090107	951	dbSNP
rs946432083	961	dbSNP
rs1330947780	968	dbSNP
rs1299615852	969	dbSNP
rs1384176446	973	dbSNP
rs1361369444	980	dbSNP
rs769575194	981	dbSNP
rs146616469	983	dbSNP
rs904985988	985	dbSNP
rs955018965	992	dbSNP
rs182864818	993	dbSNP
rs1174314587	996	dbSNP
rs187461226	998	dbSNP
rs193271976	999	dbSNP
rs1320821985	1001	dbSNP
rs1263390641	1002	dbSNP
rs910747575	1005	dbSNP
rs1487062335	1013	dbSNP
rs1281830789	1017	dbSNP
rs12086065	1019	dbSNP
rs757675304	1020	dbSNP
rs1254660125	1029	dbSNP
rs919227407	1031	dbSNP
rs1015314515	1034	dbSNP
rs1277728390	1041	dbSNP
rs962081215	1044	dbSNP
rs973861165	1054	dbSNP
rs773944560	1056	dbSNP
rs1357513415	1060	dbSNP
rs1057165567	1070	dbSNP
rs896377712	1075	dbSNP
rs1263552930	1076	dbSNP
rs975977132	1078	dbSNP
rs1428856257	1082	dbSNP
rs1424070386	1083	dbSNP
rs1476625173	1084	dbSNP
rs1171427217	1088	dbSNP
rs1428784872	1090	dbSNP
rs139115973	1096	dbSNP
rs1178669083	1097	dbSNP
rs905039688	1099	dbSNP
rs1407541053	1101	dbSNP
rs1453647547	1103	dbSNP
rs1187590643	1106	dbSNP
rs1245578135	1111	dbSNP
rs1134128	1114	dbSNP
rs1364561299	1121	dbSNP
rs1383078512	1133	dbSNP
rs1300174374	1134	dbSNP
rs1032095319	1139	dbSNP
rs76069442	1145	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.