ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ucGUUGU-GG-CG--UCGCUGUUcg 5' || :| || || ||:||||| Target 5' gaCACTAGCCAGCAAAGTGACAAtg 3'	143 - 167	121.00	-13.90
2	miRNA 3' ucgUUGUGGCGUCGCUGUUCg 5' || || |||:| |||| Target 5' gtgAAAAC--CAGTGCCAAGc 3'	483 - 501	114.00	-12.70
3	miRNA 3' ucguuguggCGUCGCUGUUCg 5' |:|| |||:|| Target 5' atatttttaGTAGAGACGAGg 3'	675 - 695	108.00	-11.50

Mutant ID	Mutant Position	Mutant Source
COSN30126958	22	COSMIC
COSN30458971	27	COSMIC
COSN30462741	32	COSMIC
COSN26638411	52	COSMIC
COSN30137569	67	COSMIC
COSN30117178	68	COSMIC
COSN30763719	92	COSMIC
COSN30191263	106	COSMIC
COSN21884547	539	COSMIC
COSN10048841	746	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1053681219	2	dbSNP
rs1223045461	8	dbSNP
rs1305323624	12	dbSNP
rs1294751896	16	dbSNP
rs777174197	17	dbSNP
rs377094399	18	dbSNP
rs747442241	20	dbSNP
rs1439924276	23	dbSNP
rs111918624	24	dbSNP
rs1294345351	29	dbSNP
rs1163831209	32	dbSNP
rs752120681	33	dbSNP
rs1459499086	35	dbSNP
rs888149379	42	dbSNP
rs1427594767	43	dbSNP
rs756948744	45	dbSNP
rs1323579390	49	dbSNP
rs1326407606	56	dbSNP
rs1429200791	57	dbSNP
rs1272391851	68	dbSNP
rs1340524792	79	dbSNP
rs1232991989	96	dbSNP
rs574085932	100	dbSNP
rs1450706430	109	dbSNP
rs1337216121	115	dbSNP
rs1214455949	120	dbSNP
rs1261095550	126	dbSNP
rs1054958793	159	dbSNP
rs937958561	162	dbSNP
rs1243720622	164	dbSNP
rs1191582811	167	dbSNP
rs765297009	183	dbSNP
rs910251031	191	dbSNP
rs1462672416	196	dbSNP
rs554290535	203	dbSNP
rs1046233329	224	dbSNP
rs1398400849	238	dbSNP
rs1320863828	240	dbSNP
rs954659041	250	dbSNP
rs1428326965	263	dbSNP
rs1414619596	264	dbSNP
rs1268437928	265	dbSNP
rs759809735	269	dbSNP
rs989846710	271	dbSNP
rs753984075	272	dbSNP
rs1291216848	276	dbSNP
rs1348650350	280	dbSNP
rs1206906895	281	dbSNP
rs1286340988	290	dbSNP
rs1488569199	299	dbSNP
rs910588480	300	dbSNP
rs961527425	303	dbSNP
rs1344332057	313	dbSNP
rs954962680	314	dbSNP
rs1468158333	316	dbSNP
rs1198976	324	dbSNP
rs972235586	326	dbSNP
rs961379480	336	dbSNP
rs1005729659	337	dbSNP
rs760420294	339	dbSNP
rs1303100781	352	dbSNP
rs1033664833	358	dbSNP
rs547534970	366	dbSNP
rs74469123	368	dbSNP
rs1310049911	379	dbSNP
rs767578954	384	dbSNP
rs558854690	394	dbSNP
rs1278037972	395	dbSNP
rs1484118809	404	dbSNP
rs1763696	405	dbSNP
rs1249459464	406	dbSNP
rs140541882	409	dbSNP
rs1435700574	409	dbSNP
rs1380416485	424	dbSNP
rs556805281	433	dbSNP
rs892277126	440	dbSNP
rs1461902701	443	dbSNP
rs1397359522	452	dbSNP
rs1378614111	454	dbSNP
rs1394667977	456	dbSNP
rs1393330983	459	dbSNP
rs945230921	474	dbSNP
rs1370368188	475	dbSNP
rs191414803	485	dbSNP
rs1301162703	494	dbSNP
rs1053864822	497	dbSNP
rs1233775387	499	dbSNP
rs1268463333	502	dbSNP
rs1183079722	505	dbSNP
rs936594717	514	dbSNP
rs1200170927	518	dbSNP
rs76183127	518	dbSNP
rs1477682600	519	dbSNP
rs397802183	519	dbSNP
rs57070122	519	dbSNP
rs796142347	519	dbSNP
rs1248444250	520	dbSNP
rs76556970	520	dbSNP
rs201812100	521	dbSNP
rs1345627345	522	dbSNP
rs1257608011	525	dbSNP
rs910467379	526	dbSNP
rs567641673	527	dbSNP
rs1438882811	534	dbSNP
rs1327986894	541	dbSNP
rs910534571	545	dbSNP
rs369500594	546	dbSNP
rs1050551041	548	dbSNP
rs933527399	549	dbSNP
rs932970258	551	dbSNP
rs561258324	559	dbSNP
rs1333531982	561	dbSNP
rs867115229	562	dbSNP
rs923017878	563	dbSNP
rs1305568099	565	dbSNP
rs1327565430	566	dbSNP
rs186705460	569	dbSNP
rs961537961	581	dbSNP
rs908745208	585	dbSNP
rs1179137958	586	dbSNP
rs1468566401	587	dbSNP
rs984236108	588	dbSNP
rs1266665273	589	dbSNP
rs953005494	598	dbSNP
rs1428976036	603	dbSNP
rs372896095	605	dbSNP
rs1002618136	606	dbSNP
rs1479008718	615	dbSNP
rs1194836680	616	dbSNP
rs1417480170	628	dbSNP
rs1471266703	633	dbSNP
rs565891875	638	dbSNP
rs983868633	643	dbSNP
rs952587700	646	dbSNP
rs1033277610	647	dbSNP
rs573095643	650	dbSNP
rs377673201	651	dbSNP
rs1009681255	652	dbSNP
rs1258192799	656	dbSNP
rs892534018	659	dbSNP
rs1053656835	660	dbSNP
rs1314371010	662	dbSNP
rs1321807654	663	dbSNP
rs1214372364	668	dbSNP
rs1268503985	670	dbSNP
rs1489547572	674	dbSNP
rs536461513	675	dbSNP
rs1001832410	687	dbSNP
rs1474405867	690	dbSNP
rs145280965	691	dbSNP
rs56911841	692	dbSNP
rs1050325418	699	dbSNP
rs933001142	700	dbSNP
rs1343413980	701	dbSNP
rs901482592	702	dbSNP
rs1421411762	717	dbSNP
rs533314469	722	dbSNP
rs1244898585	723	dbSNP
rs867846032	726	dbSNP
rs940468962	730	dbSNP
rs1285599634	733	dbSNP
rs563476485	745	dbSNP
rs182424448	746	dbSNP
rs908964071	750	dbSNP
rs984288367	754	dbSNP
rs931442218	755	dbSNP
rs1356513480	758	dbSNP
rs1241540872	763	dbSNP
rs1405869869	766	dbSNP
rs1280178519	768	dbSNP
rs369151187	769	dbSNP
rs11210828	773	dbSNP
rs1402720153	782	dbSNP
rs560533052	783	dbSNP
rs1050380378	791	dbSNP
rs971373024	793	dbSNP
rs1158144978	798	dbSNP
rs1024996342	799	dbSNP
rs149562698	801	dbSNP
rs1335922217	802	dbSNP
rs1359427549	811	dbSNP
rs1387118032	813	dbSNP
rs1036603211	817	dbSNP
rs956807948	819	dbSNP
rs1446799151	826	dbSNP
rs549888735	827	dbSNP
rs940963981	828	dbSNP
rs909358107	840	dbSNP
rs1217658681	841	dbSNP
rs1032396862	846	dbSNP
rs1240198048	847	dbSNP
rs1458274150	852	dbSNP
rs749006202	853	dbSNP
rs888933672	854	dbSNP
rs1252359914	857	dbSNP
rs1476986704	857	dbSNP
rs1174143358	859	dbSNP
rs1425645365	861	dbSNP
rs1409101810	863	dbSNP
rs1168107177	866	dbSNP
rs1283120399	869	dbSNP
rs12127513	881	dbSNP
rs926376215	881	dbSNP
rs1324612082	894	dbSNP
rs571997679	897	dbSNP
rs980526398	898	dbSNP
rs565484325	905	dbSNP
rs1275910549	908	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.