>TMEM251|NM_001098621|3'UTR
   1 AATCAGTCACCGTTTTTTCCCTACGATTACAAAACTGCCAGTCCTATATGGAGTCTGATCACAAGACTGCAGTTTCTTCA
  81 CAGATCTCAGGAAGTTGTCGTGGGGCAGAGGCTTTTTAAAAACATGTGATTAGGGAGCTATCTTTATCTGAATAATAACG
 161 AATTTTTAGGTAAAACCTGAGATAGAGTACTACAAAATCATGTTGATGACTTCAGATTTTGGAAGTTAAATCATGTCTGT
 241 TATTTGCATTCTTTAGAAACTTGACTAAGTACCTGAATTCATATTTCTATTCTACTGTGCAACATAGTGATGATTCAGAA
 321 ATTTTTCCTTTGGGGAAAAAAATGAATATGAACATTTCCATTGTGTTAAGTGTAAAAAGGTCCAGACATGATCATAAAAT
 401 TTAAATTTTATACAATTAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' uucCAUCUU-UCUCCGGAcu 5' ||:|:: ||||||:| Target 5' gtcGTGGGGCAGAGGCTTtt 3'	97 - 116	124.00	-14.10
2	miRNA 3' uucCAUCUUUCUCCGGacu 5' ||: ||| |||:| Target 5' taaGTGTAAAAAGGTCcag 3'	367 - 385	104.00	-7.22
3	miRNA 3' uuCCAUC--UUU-CUCCGGACu 5' || || ||| | |:||| Target 5' ttGGAAGTTAAATCATGTCTGt 3'	219 - 240	103.00	-5.50

Mutant ID	Mutant Position	Mutant Source
COSN30133289	7	COSMIC
COSN26999008	19	COSMIC
COSN26999009	19	COSMIC
COSN30142115	26	COSMIC
COSN30118221	70	COSMIC
COSN30101364	103	COSMIC
COSN30492153	130	COSMIC
COSN30140610	160	COSMIC
COSN30120868	161	COSMIC
COSN31515314	162	COSMIC
COSN30187630	182	COSMIC
COSN31480578	200	COSMIC
COSN31485192	214	COSMIC
COSN30119226	231	COSMIC
COSN30534824	233	COSMIC
COSN30114253	398	COSMIC
COSN22097685	659	COSMIC
COSN16638185	770	COSMIC
COSN17714415	984	COSMIC
COSN21695602	1357	COSMIC
COSN5210944	1413	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs745564025	9	dbSNP
rs1310020581	11	dbSNP
rs1344625828	12	dbSNP
rs1198918869	13	dbSNP
rs769224822	15	dbSNP
rs1299247508	17	dbSNP
rs774992621	20	dbSNP
rs1197706698	21	dbSNP
rs762504169	25	dbSNP
rs764576645	26	dbSNP
rs774884285	29	dbSNP
rs200503787	31	dbSNP
rs1393933645	35	dbSNP
rs762065266	36	dbSNP
rs767949879	46	dbSNP
rs1217359836	49	dbSNP
rs1317090743	55	dbSNP
rs566463433	56	dbSNP
rs554355546	59	dbSNP
rs1225803927	66	dbSNP
rs982975754	84	dbSNP
rs1434989403	91	dbSNP
rs1267664488	96	dbSNP
rs981725194	100	dbSNP
rs764326014	118	dbSNP
rs369313359	120	dbSNP
rs199810758	124	dbSNP
rs908703089	124	dbSNP
rs1038612071	141	dbSNP
rs1222823291	143	dbSNP
rs1267708894	147	dbSNP
rs116029458	149	dbSNP
rs1184024519	153	dbSNP
rs1427816722	154	dbSNP
rs916139706	156	dbSNP
rs752334828	160	dbSNP
rs948710831	161	dbSNP
rs1187799510	163	dbSNP
rs1261735416	170	dbSNP
rs1361224941	180	dbSNP
rs1292924305	192	dbSNP
rs1049724968	200	dbSNP
rs1306215052	215	dbSNP
rs907287231	216	dbSNP
rs1382779690	234	dbSNP
rs887940571	236	dbSNP
rs758183928	244	dbSNP
rs1039057182	246	dbSNP
rs200715503	247	dbSNP
rs1406970351	248	dbSNP
rs901861310	250	dbSNP
rs1366469257	260	dbSNP
rs1163936774	266	dbSNP
rs892282558	270	dbSNP
rs1172441438	274	dbSNP
rs997899262	285	dbSNP
rs1022186935	290	dbSNP
rs543135912	293	dbSNP
rs899731711	297	dbSNP
rs1269185328	306	dbSNP
rs1195530002	313	dbSNP
rs1372335575	335	dbSNP
rs147298582	336	dbSNP
rs554630763	336	dbSNP
rs777618225	347	dbSNP
rs1029706102	354	dbSNP
rs1020891442	356	dbSNP
rs955191410	358	dbSNP
rs982924425	360	dbSNP
rs556605980	366	dbSNP
rs1363978787	372	dbSNP
rs533609211	373	dbSNP
rs1389955968	375	dbSNP
rs1394052637	380	dbSNP
rs1299722184	386	dbSNP
rs74984385	389	dbSNP
rs962888139	394	dbSNP
rs959188492	412	dbSNP
rs990570622	425	dbSNP
rs556201455	427	dbSNP
rs771017064	428	dbSNP
rs1180635949	439	dbSNP
rs1416994602	444	dbSNP
rs1253074490	455	dbSNP
rs372910344	456	dbSNP
rs192397446	457	dbSNP
rs541698597	458	dbSNP
rs1461227492	471	dbSNP
rs1384057298	473	dbSNP
rs1205568776	481	dbSNP
rs1324369889	486	dbSNP
rs916173825	487	dbSNP
rs1237127861	497	dbSNP
rs948910579	498	dbSNP
rs1308834135	503	dbSNP
rs970431675	510	dbSNP
rs1289999342	516	dbSNP
rs1334610585	526	dbSNP
rs928617743	528	dbSNP
rs1406151391	530	dbSNP
rs1157530592	533	dbSNP
rs972785784	544	dbSNP
rs561485929	561	dbSNP
rs1365216413	566	dbSNP
rs1182920163	584	dbSNP
rs77126471	588	dbSNP
rs985007354	595	dbSNP
rs1241757126	598	dbSNP
rs1485239482	598	dbSNP
rs1283616256	612	dbSNP
rs1462194455	612	dbSNP
rs893196911	613	dbSNP
rs10133344	634	dbSNP
rs1261545658	639	dbSNP
rs77387017	642	dbSNP
rs1381759640	646	dbSNP
rs114666512	647	dbSNP
rs1182755391	649	dbSNP
rs899764990	650	dbSNP
rs552536771	651	dbSNP
rs145858927	654	dbSNP
rs923337439	656	dbSNP
rs1398473784	659	dbSNP
rs933399176	663	dbSNP
rs570285588	665	dbSNP
rs1029365622	667	dbSNP
rs1411560308	669	dbSNP
rs1160097458	673	dbSNP
rs572408742	674	dbSNP
rs115760200	679	dbSNP
rs116076713	682	dbSNP
rs1001228668	683	dbSNP
rs1053663369	691	dbSNP
rs567931387	695	dbSNP
rs1357616323	696	dbSNP
rs1289281099	697	dbSNP
rs1247938495	699	dbSNP
rs1356903288	701	dbSNP
rs1012058921	703	dbSNP
rs1024747282	713	dbSNP
rs1379562961	730	dbSNP
rs1403921435	731	dbSNP
rs1363368338	736	dbSNP
rs1395311822	743	dbSNP
rs982087182	747	dbSNP
rs1406336681	748	dbSNP
rs1307232554	750	dbSNP
rs970912581	751	dbSNP
rs1419349927	754	dbSNP
rs1166654864	763	dbSNP
rs576032535	764	dbSNP
rs993924400	765	dbSNP
rs111381620	769	dbSNP
rs201913768	770	dbSNP
rs934677753	770	dbSNP
rs556808426	771	dbSNP
rs1224365191	773	dbSNP
rs1451970048	783	dbSNP
rs1272099902	784	dbSNP
rs914667488	788	dbSNP
rs750385164	791	dbSNP
rs1341437838	796	dbSNP
rs749384369	800	dbSNP
rs947437974	803	dbSNP
rs1461721910	812	dbSNP
rs1222400181	816	dbSNP
rs541328271	818	dbSNP
rs576862193	819	dbSNP
rs564325275	822	dbSNP
rs1175738828	826	dbSNP
rs1051470221	838	dbSNP
rs1200406792	842	dbSNP
rs1178047107	843	dbSNP
rs1232061493	846	dbSNP
rs909441180	848	dbSNP
rs539120836	850	dbSNP
rs964870115	857	dbSNP
rs1272242492	861	dbSNP
rs974907675	867	dbSNP
rs1004292159	874	dbSNP
rs1258649026	876	dbSNP
rs866122208	890	dbSNP
rs1417516855	897	dbSNP
rs1178688068	901	dbSNP
rs552934840	903	dbSNP
rs923448203	916	dbSNP
rs1284711048	918	dbSNP
rs768803041	927	dbSNP
rs138336214	931	dbSNP
rs1278105310	942	dbSNP
rs1356689923	942	dbSNP
rs1444841786	944	dbSNP
rs200951165	946	dbSNP
rs1297919424	949	dbSNP
rs923938428	953	dbSNP
rs1372161228	961	dbSNP
rs1408362104	961	dbSNP
rs995246400	961	dbSNP
rs936651007	964	dbSNP
rs1284712388	972	dbSNP
rs1175211394	973	dbSNP
rs1053716014	974	dbSNP
rs970196314	981	dbSNP
rs1238638592	984	dbSNP
rs1182902257	985	dbSNP
rs1323620037	989	dbSNP
rs1003021095	997	dbSNP
rs774499069	1000	dbSNP
rs1261154503	1002	dbSNP
rs1315906383	1003	dbSNP
rs10135777	1008	dbSNP
rs1012151932	1015	dbSNP
rs377092203	1018	dbSNP
rs1314861504	1020	dbSNP
rs1046297220	1023	dbSNP
rs1205001255	1025	dbSNP
rs1232029289	1030	dbSNP
rs1479789654	1033	dbSNP
rs906363768	1035	dbSNP
rs1343590016	1039	dbSNP
rs1161553069	1040	dbSNP
rs1420607950	1041	dbSNP
rs1201847109	1042	dbSNP
rs994326906	1047	dbSNP
rs1025359013	1048	dbSNP
rs1480135583	1053	dbSNP
rs1258205228	1055	dbSNP
rs561546134	1065	dbSNP
rs952498508	1070	dbSNP
rs1005153871	1071	dbSNP
rs1410951911	1072	dbSNP
rs1239927936	1073	dbSNP
rs1170204428	1081	dbSNP
rs1354022280	1082	dbSNP
rs1291448982	1103	dbSNP
rs1353105191	1111	dbSNP
rs914574416	1120	dbSNP
rs1407682770	1123	dbSNP
rs1304549042	1124	dbSNP
rs1345649288	1125	dbSNP
rs1017880232	1132	dbSNP
rs1272533430	1144	dbSNP
rs1341394510	1151	dbSNP
rs1215032382	1153	dbSNP
rs1272102485	1154	dbSNP
rs974787035	1159	dbSNP
rs1365216216	1160	dbSNP
rs964962691	1168	dbSNP
rs974955135	1169	dbSNP
rs1269892204	1174	dbSNP
rs1490235382	1176	dbSNP
rs1197364764	1177	dbSNP
rs1243857619	1179	dbSNP
rs1476059746	1185	dbSNP
rs921994886	1195	dbSNP
rs772365272	1196	dbSNP
rs1370050552	1203	dbSNP
rs1417864221	1209	dbSNP
rs1427909153	1214	dbSNP
rs773601460	1219	dbSNP
rs1050911675	1223	dbSNP
rs1164553994	1230	dbSNP
rs1488385657	1235	dbSNP
rs1365843439	1240	dbSNP
rs2532894	1256	dbSNP
rs912470304	1258	dbSNP
rs1030954775	1263	dbSNP
rs1489670721	1263	dbSNP
rs369416873	1265	dbSNP
rs954860256	1271	dbSNP
rs1423536644	1274	dbSNP
rs1266465278	1275	dbSNP
rs1321028650	1277	dbSNP
rs144326408	1283	dbSNP
rs939950246	1286	dbSNP
rs1306305241	1292	dbSNP
rs1037138639	1294	dbSNP
rs1219349141	1299	dbSNP
rs1431481090	1307	dbSNP
rs978588957	1309	dbSNP
rs1269493858	1325	dbSNP
rs183270965	1330	dbSNP
rs936673595	1332	dbSNP
rs989505080	1350	dbSNP
rs995277617	1351	dbSNP
rs916577193	1352	dbSNP
rs1208273324	1357	dbSNP
rs1044187045	1362	dbSNP
rs905583358	1367	dbSNP
rs563675667	1371	dbSNP
rs1035824392	1381	dbSNP
rs1477865961	1387	dbSNP
rs1428073817	1388	dbSNP
rs1046273415	1390	dbSNP
rs1434598079	1392	dbSNP
rs956530949	1395	dbSNP
rs1010482146	1396	dbSNP
rs906367494	1405	dbSNP
rs1240887661	1408	dbSNP
rs929799656	1413	dbSNP
rs760895653	1414	dbSNP
rs1184598890	1433	dbSNP
rs1021611104	1434	dbSNP
rs1443696367	1435	dbSNP
rs1331941038	1439	dbSNP
rs1047272205	1443	dbSNP
rs1161093880	1454	dbSNP
rs1301659126	1463	dbSNP
rs1386556029	1468	dbSNP
rs766899592	1472	dbSNP
rs888229396	1475	dbSNP
rs186399120	1476	dbSNP
rs1371007629	1477	dbSNP
rs563826961	1478	dbSNP
rs1404697348	1489	dbSNP
rs1173691402	1496	dbSNP
rs1017927808	1499	dbSNP
rs1377862638	1500	dbSNP
rs1454451593	1508	dbSNP
rs899502876	1509	dbSNP
rs759059604	1511	dbSNP
rs922025833	1520	dbSNP
rs954776039	1525	dbSNP
rs749064986	1528	dbSNP
rs1315533527	1543	dbSNP
rs1345908880	1551	dbSNP
rs1030547790	1574	dbSNP
rs955057672	1580	dbSNP
rs978260020	1592	dbSNP
rs1031569189	1596	dbSNP
rs958137678	1601	dbSNP
rs1311250148	1613	dbSNP
rs1351601863	1616	dbSNP
rs1204635243	1623	dbSNP
rs1334057881	1632	dbSNP
rs1397280191	1637	dbSNP
rs559720566	1644	dbSNP
rs1463068035	1645	dbSNP
rs972625896	1649	dbSNP
rs1204839767	1663	dbSNP
rs189962623	1668	dbSNP
rs919818625	1679	dbSNP
rs948003437	1681	dbSNP
rs982451930	1694	dbSNP
rs1241848344	1698	dbSNP
rs927881329	1700	dbSNP
rs555701347	1703	dbSNP
rs929866392	1709	dbSNP
rs1203595267	1729	dbSNP
rs1489418902	1732	dbSNP
rs144414275	1735	dbSNP
rs1240624323	1737	dbSNP
rs905612501	1738	dbSNP
rs1046923866	1761	dbSNP
rs34954547	1769	dbSNP
rs1057492890	1775	dbSNP
rs888274785	1781	dbSNP
rs941150648	1789	dbSNP
rs1157510006	1790	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.