ID	Duplex structure	Position	Score	MFE
1	miRNA 3' uagUUC--CAGGCGACACUUGUGc 5' ||| |:| : ||:|||| Target 5' gggAAGCCCTTCCTACTGGACACg 3'	27 - 50	129.00	-13.60
2	miRNA 3' uaguuccaggcgacaCUUGUGc 5' |||||| Target 5' tgaaaaaaaaaaaaaGAACACa 3'	673 - 694	120.00	-5.70
3	miRNA 3' uaguuccAGGCGACACUUGUgc 5' ||||:||||:||: Target 5' aagcaccTCCGTTGTGGACGgt 3'	81 - 102	119.00	-19.40

Mutant ID	Mutant Position	Mutant Source
COSN31576562	7	COSMIC
COSN23014262	24	COSMIC
COSN31534370	28	COSMIC
COSN30499391	50	COSMIC
COSN30169700	58	COSMIC
COSN31578260	79	COSMIC
COSN20073444	114	COSMIC
COSN22876063	598	COSMIC
COSN20096114	674	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs758349029	2	dbSNP
rs750328882	10	dbSNP
rs1180856610	11	dbSNP
rs765075443	18	dbSNP
rs1374738597	21	dbSNP
rs1302728495	23	dbSNP
rs375238321	28	dbSNP
rs1203711936	30	dbSNP
rs753505587	39	dbSNP
rs779604263	41	dbSNP
rs757953704	42	dbSNP
rs932505203	47	dbSNP
rs1258472392	48	dbSNP
rs371401857	49	dbSNP
rs367649384	50	dbSNP
rs1313780975	54	dbSNP
rs371269528	55	dbSNP
rs763453689	58	dbSNP
rs1377246375	60	dbSNP
rs1179723183	61	dbSNP
rs966041162	61	dbSNP
rs773664089	62	dbSNP
rs148005713	64	dbSNP
rs748514199	67	dbSNP
rs1161923855	68	dbSNP
rs768948299	69	dbSNP
rs1467519484	72	dbSNP
rs780213134	74	dbSNP
rs1164512543	76	dbSNP
rs907888807	90	dbSNP
rs1026739258	91	dbSNP
rs1334619017	93	dbSNP
rs983638840	98	dbSNP
rs993958265	99	dbSNP
rs554908658	100	dbSNP
rs1024675548	101	dbSNP
rs1212514540	106	dbSNP
rs1013488756	107	dbSNP
rs145296244	110	dbSNP
rs1281582784	115	dbSNP
rs569043471	121	dbSNP
rs1320672470	123	dbSNP
rs970666051	124	dbSNP
rs746806564	126	dbSNP
rs1177568060	127	dbSNP
rs1379680288	129	dbSNP
rs1460815788	130	dbSNP
rs1296022847	139	dbSNP
rs1214408184	152	dbSNP
rs1395339707	154	dbSNP
rs1024055904	158	dbSNP
rs904575812	159	dbSNP
rs1014018481	160	dbSNP
rs1343543826	161	dbSNP
rs554523102	162	dbSNP
rs955659266	165	dbSNP
rs112289848	166	dbSNP
rs541342993	171	dbSNP
rs141505370	173	dbSNP
rs111403231	174	dbSNP
rs1335542311	179	dbSNP
rs1340406311	179	dbSNP
rs552984198	182	dbSNP
rs1356264306	216	dbSNP
rs987810973	216	dbSNP
rs539526199	230	dbSNP
rs1200727475	241	dbSNP
rs570659614	248	dbSNP
rs920126809	266	dbSNP
rs1417149654	273	dbSNP
rs1372139663	275	dbSNP
rs972464332	277	dbSNP
rs116812446	279	dbSNP
rs901001971	281	dbSNP
rs138776125	283	dbSNP
rs1293984253	289	dbSNP
rs1369714986	290	dbSNP
rs1242728000	297	dbSNP
rs375618175	298	dbSNP
rs1459135077	305	dbSNP
rs907857563	312	dbSNP
rs1289900502	331	dbSNP
rs1358735802	332	dbSNP
rs1047702035	333	dbSNP
rs1204456310	334	dbSNP
rs992249945	341	dbSNP
rs1485216196	343	dbSNP
rs959287320	349	dbSNP
rs1292504880	351	dbSNP
rs778356364	355	dbSNP
rs1262808696	359	dbSNP
rs930675754	364	dbSNP
rs1451755174	372	dbSNP
rs973156452	373	dbSNP
rs1383021916	374	dbSNP
rs1423442657	375	dbSNP
rs920849246	408	dbSNP
rs1351520259	424	dbSNP
rs1451601406	432	dbSNP
rs757286398	432	dbSNP
rs980802020	440	dbSNP
rs1437009992	447	dbSNP
rs1313113375	450	dbSNP
rs548571386	454	dbSNP
rs144845163	471	dbSNP
rs1314988660	486	dbSNP
rs1315223773	487	dbSNP
rs891899765	487	dbSNP
rs1041020083	491	dbSNP
rs1298197292	493	dbSNP
rs1441422155	506	dbSNP
rs754455645	514	dbSNP
rs992551037	523	dbSNP
rs1472287145	536	dbSNP
rs955795232	537	dbSNP
rs1415267185	538	dbSNP
rs149090747	550	dbSNP
rs944043220	551	dbSNP
rs1458602999	553	dbSNP
rs1334520447	570	dbSNP
rs999854332	583	dbSNP
rs968826703	589	dbSNP
rs1425040486	598	dbSNP
rs753341663	606	dbSNP
rs114501179	607	dbSNP
rs1286206605	611	dbSNP
rs1371193895	613	dbSNP
rs1223305890	620	dbSNP
rs1050424530	623	dbSNP
rs931581936	627	dbSNP
rs900977155	635	dbSNP
rs1040874034	636	dbSNP
rs1004024011	640	dbSNP
rs766898762	646	dbSNP
rs1421045818	647	dbSNP
rs1443371926	648	dbSNP
rs1210328379	649	dbSNP
rs182752321	655	dbSNP
rs1180898914	656	dbSNP
rs939726036	657	dbSNP
rs1479966401	663	dbSNP
rs1271651432	667	dbSNP
rs1223760896	670	dbSNP
rs1428292277	671	dbSNP
rs1335930692	674	dbSNP
rs55911834	675	dbSNP
rs1289957925	686	dbSNP
rs1308760437	688	dbSNP
rs200615269	688	dbSNP
rs5781620	688	dbSNP
rs1243340262	689	dbSNP
rs1305472782	690	dbSNP
rs774057564	690	dbSNP
rs1197108870	691	dbSNP
rs1203772574	691	dbSNP
rs1251968207	691	dbSNP
rs1421623956	693	dbSNP
rs917682959	695	dbSNP
rs940440737	700	dbSNP
rs1478226919	701	dbSNP
rs1174175874	703	dbSNP
rs1047837447	719	dbSNP
rs1033384237	720	dbSNP
rs1169494227	721	dbSNP
rs1372437457	723	dbSNP
rs1371158267	725	dbSNP
rs1303010952	730	dbSNP
rs1422824041	730	dbSNP
rs1332233300	731	dbSNP
rs1439043667	736	dbSNP
rs563333725	739	dbSNP
rs1268826828	740	dbSNP
rs1359401306	756	dbSNP
rs1405402266	763	dbSNP
rs543547943	764	dbSNP
rs920594500	765	dbSNP
rs546877104	769	dbSNP
rs1219692005	771	dbSNP
rs949002573	773	dbSNP
rs917402269	775	dbSNP
rs907661154	783	dbSNP
rs190179688	785	dbSNP
rs954399288	793	dbSNP
rs879124790	796	dbSNP
rs1200709420	797	dbSNP
rs1417382921	799	dbSNP
rs992979526	800	dbSNP
rs756649577	806	dbSNP
rs186836491	808	dbSNP
rs1490314243	811	dbSNP
rs1162808572	813	dbSNP
rs561154299	836	dbSNP
rs1407621525	849	dbSNP
rs1008346493	850	dbSNP
rs889773245	852	dbSNP
rs1207224815	858	dbSNP
rs968376949	870	dbSNP
rs1486666870	872	dbSNP
rs1260926800	894	dbSNP
rs540952327	898	dbSNP
rs1367001703	903	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.