>ELFN1|NM_001128636|3'UTR
   1 GCCCCCCAAGACCGGCGATGCCCACTGGACCAAAAAGGATGCAGGATCCACCCAGAGACTCAGCACCAAACCCAACACAC
  81 GCACGCCACCACAGCAACTGTGACAGCGGGGGGCCCTGCAGAGGCGAGGGGGGAGCGAGTGGGGACAGACAAGGGGGACA
 161 CGTCCCGAGCTCCTGTGGCCGGTCCTGGGATGCGCTTGTCGCCCCGGGTGGCACGTGTCCACACACACACACACACACAC
 241 ACACACACACACGAGGGACTTCGGAAAACTGTGTCTTAGGGATGGGGGGTGGGGGTGGGGATTTTTTTTTCATTATCTTT
 321 CCTCTTTTGAGTCTTCTCTGCCTTTTCTTTTCCTCTCTATCTCTTTACTTTCTTCCTTTTTTAAAAAAATATAATAAAAG
 401 ACAAGTTATTTTAAAAAGACATAAAATGCCATCCGTGGGGGGTGTGGCCGGCGTGGCCACCTCGGGGCCCCTCACGTGAT
 481 CTCCTCGGTCCGTGGTTTTCTGTGGATTCTCTGTCCAGTCCGTCTCTTCATTGCCGCCTCCGGAGTCCACTGCAGAGGGG
 561 CAGAGTGAATGCCGGCGGCCAAGTGGCCTCCGGGACAGGTCCTGGAGCCCTGCTGGACTCAGGGTGGGTGGAGGCTGTGC
 641 CTGTGGACGGCCGGGGTGGCCAGGACGGCCAAGGGCTGGGAGGCACGTCCCCCAGCCCAGCCCCCATGTACACTGTAGTC
 721 GTTCTATTGTACAGAAAAAAATATTTCTATATTTGCAATGTTTGCTGTAAAATGAGAAAGAAAAAAAGACTATGTCTACT
 801 AAAAAAAAAAAAAAAAAGACTATGTCTACTTAAAAAAAAATCTGCAAAGGAAAACAAATCAAATGCTTGTTAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gacgccuuuCUCUUCGUGCACc 5' |:| :||||||| Target 5' tgtcgccccGGGTGGCACGTGt 3'	197 - 218	149.00	-15.50
2	miRNA 3' gacgCCUUUCUCUUCGUGCAcc 5' ||: |:||:|||||| Target 5' ccaaGGGCTGGGAGGCACGTcc 3'	669 - 690	142.00	-19.90
3	miRNA 3' gaCGCCUUUCUCUUCGUGCACc 5' || ||::|:|:|||: ||| Target 5' agGC-GAGGGGGGAGCGAGTGg 3'	122 - 142	123.00	-25.20

Mutant ID	Mutant Position	Mutant Source
COSN30162164	18	COSMIC
COSN30541951	82	COSMIC
COSN23586378	206	COSMIC
COSN15623919	231	COSMIC
COSN30132294	233	COSMIC
COSN20103677	234	COSMIC
COSN17153600	235	COSMIC
COSN27207419	253	COSMIC
COSN27415745	253	COSMIC
COSN30129421	263	COSMIC
COSN30116291	383	COSMIC
COSN30139146	384	COSMIC
COSN30121824	387	COSMIC
COSN30136279	401	COSMIC
COSN30121843	419	COSMIC
COSN15623920	434	COSMIC
COSN25356936	436	COSMIC
COSN15623921	440	COSMIC
COSN28380188	450	COSMIC
COSN31590881	485	COSMIC
COSN32199572	510	COSMIC
COSN15623922	579	COSMIC
COSN31483999	624	COSMIC
COSN30143404	656	COSMIC
COSN30136087	673	COSMIC
COSN30143003	675	COSMIC
COSN15623923	710	COSMIC
COSN30536142	782	COSMIC
COSN20103678	818	COSMIC
COSN27275996	818	COSMIC
COSN31846818	819	COSMIC
COSN30130248	837	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1279692586	4	dbSNP
rs372692511	6	dbSNP
rs1217494201	7	dbSNP
rs1450765796	8	dbSNP
rs1273189825	11	dbSNP
rs1290156861	13	dbSNP
rs776355461	14	dbSNP
rs542293020	15	dbSNP
rs769139773	16	dbSNP
rs148122916	17	dbSNP
rs763339339	18	dbSNP
rs530916643	22	dbSNP
rs1476926443	26	dbSNP
rs1170099994	28	dbSNP
rs1418608046	30	dbSNP
rs1459427547	37	dbSNP
rs1161363800	41	dbSNP
rs142744207	50	dbSNP
rs946179754	60	dbSNP
rs1300332104	65	dbSNP
rs1434773506	66	dbSNP
rs1349589290	69	dbSNP
rs1197944257	72	dbSNP
rs1426728468	75	dbSNP
rs1041887956	77	dbSNP
rs907407036	79	dbSNP
rs192078216	81	dbSNP
rs926291905	82	dbSNP
rs1488053590	83	dbSNP
rs758849960	85	dbSNP
rs1056066077	86	dbSNP
rs894101510	90	dbSNP
rs377601393	95	dbSNP
rs1284774111	96	dbSNP
rs76371074	100	dbSNP
rs1318136350	107	dbSNP
rs1217934399	108	dbSNP
rs1309787050	108	dbSNP
rs1320812211	109	dbSNP
rs551937318	114	dbSNP
rs1454379477	119	dbSNP
rs565678260	126	dbSNP
rs1534789	127	dbSNP
rs554145292	129	dbSNP
rs1425662935	133	dbSNP
rs993246490	134	dbSNP
rs1201315536	136	dbSNP
rs568015707	137	dbSNP
rs1188522011	140	dbSNP
rs1030116357	145	dbSNP
rs1193842983	147	dbSNP
rs1446539583	148	dbSNP
rs919308533	149	dbSNP
rs1181764881	151	dbSNP
rs1486577240	153	dbSNP
rs1253692361	157	dbSNP
rs1413164785	158	dbSNP
rs954555192	162	dbSNP
rs1208698823	163	dbSNP
rs536770487	167	dbSNP
rs889139410	168	dbSNP
rs1007796632	170	dbSNP
rs1040677830	173	dbSNP
rs1382942749	174	dbSNP
rs757431354	181	dbSNP
rs902005739	182	dbSNP
rs1465545560	185	dbSNP
rs910480167	194	dbSNP
rs964047812	195	dbSNP
rs1463867701	196	dbSNP
rs79870618	201	dbSNP
rs914599487	202	dbSNP
rs940310999	202	dbSNP
rs1454507871	206	dbSNP
rs946108349	215	dbSNP
rs1312350553	216	dbSNP
rs1483242166	218	dbSNP
rs1433538481	219	dbSNP
rs1163561535	220	dbSNP
rs1168247574	220	dbSNP
rs1173761185	220	dbSNP
rs1186018515	220	dbSNP
rs1366336466	220	dbSNP
rs1386509846	220	dbSNP
rs1399332397	220	dbSNP
rs143376319	220	dbSNP
rs1444720379	220	dbSNP
rs1463260366	220	dbSNP
rs1491496013	220	dbSNP
rs1491359419	221	dbSNP
rs1224034980	225	dbSNP
rs1308646980	226	dbSNP
rs1456801891	227	dbSNP
rs1238025908	229	dbSNP
rs3077247	231	dbSNP
rs61188936	231	dbSNP
rs74671825	231	dbSNP
rs746290433	233	dbSNP
rs570881196	234	dbSNP
rs5019477	235	dbSNP
rs1033285887	241	dbSNP
rs1392931374	243	dbSNP
rs1388226599	251	dbSNP
rs1463105708	253	dbSNP
rs57908849	253	dbSNP
rs959058757	254	dbSNP
rs1156303188	255	dbSNP
rs1438453977	256	dbSNP
rs576848644	263	dbSNP
rs1183087073	264	dbSNP
rs1421286265	268	dbSNP
rs1265644031	270	dbSNP
rs1222084668	278	dbSNP
rs540068317	279	dbSNP
rs1179190984	280	dbSNP
rs1405987095	281	dbSNP
rs1471489953	283	dbSNP
rs1280069888	284	dbSNP
rs1353004598	284	dbSNP
rs1534788	285	dbSNP
rs573583192	286	dbSNP
rs542501778	290	dbSNP
rs1406522753	291	dbSNP
rs1418568945	291	dbSNP
rs1385005625	292	dbSNP
rs938833661	293	dbSNP
rs1376323237	294	dbSNP
rs1199138956	295	dbSNP
rs1332079623	296	dbSNP
rs1191691499	298	dbSNP
rs1271336251	298	dbSNP
rs1446532671	301	dbSNP
rs562079004	301	dbSNP
rs919766752	302	dbSNP
rs930722352	302	dbSNP
rs1342782368	303	dbSNP
rs1255254715	304	dbSNP
rs1223911403	309	dbSNP
rs1347093230	318	dbSNP
rs1049635978	323	dbSNP
rs1326550571	325	dbSNP
rs894707191	325	dbSNP
rs1319678268	331	dbSNP
rs943386623	337	dbSNP
rs1400670771	340	dbSNP
rs1040648126	342	dbSNP
rs1470509517	353	dbSNP
rs1006497653	355	dbSNP
rs1207389214	356	dbSNP
rs1168825153	358	dbSNP
rs1475190753	360	dbSNP
rs902059606	367	dbSNP
rs1299541192	376	dbSNP
rs1440716484	378	dbSNP
rs1204181573	383	dbSNP
rs1325457126	383	dbSNP
rs575564723	383	dbSNP
rs1042534081	384	dbSNP
rs904040576	387	dbSNP
rs1271485711	390	dbSNP
rs897524028	390	dbSNP
rs763331496	391	dbSNP
rs1445191484	393	dbSNP
rs1339303218	394	dbSNP
rs1370643945	416	dbSNP
rs1453943068	417	dbSNP
rs1227399431	421	dbSNP
rs1408811574	421	dbSNP
rs1409669414	422	dbSNP
rs375628942	426	dbSNP
rs1420512942	430	dbSNP
rs1284397939	434	dbSNP
rs1326079481	435	dbSNP
rs1471870912	435	dbSNP
rs1033421340	436	dbSNP
rs1278474463	438	dbSNP
rs993175225	442	dbSNP
rs1030042777	443	dbSNP
rs954523217	448	dbSNP
rs1438126259	449	dbSNP
rs1482885169	449	dbSNP
rs1007362154	450	dbSNP
rs1017465583	451	dbSNP
rs958174943	453	dbSNP
rs544256627	454	dbSNP
rs1307637331	456	dbSNP
rs914547399	462	dbSNP
rs564635935	464	dbSNP
rs973078967	464	dbSNP
rs977463581	465	dbSNP
rs1403796036	466	dbSNP
rs1026801851	471	dbSNP
rs1424306595	474	dbSNP
rs1164285438	476	dbSNP
rs928721777	477	dbSNP
rs1378418973	479	dbSNP
rs1176486991	481	dbSNP
rs183382856	484	dbSNP
rs551998661	487	dbSNP
rs145027156	488	dbSNP
rs769801972	492	dbSNP
rs1291946031	493	dbSNP
rs1037967410	502	dbSNP
rs923283030	517	dbSNP
rs9177	518	dbSNP
rs928993820	522	dbSNP
rs548053993	528	dbSNP
rs1281600957	532	dbSNP
rs568292798	536	dbSNP
rs535686762	537	dbSNP
rs1303929061	541	dbSNP
rs566543608	542	dbSNP
rs1007285316	543	dbSNP
rs1017850585	549	dbSNP
rs893672393	557	dbSNP
rs550299945	561	dbSNP
rs1401196292	574	dbSNP
rs1011205140	575	dbSNP
rs1274778375	577	dbSNP
rs372136617	577	dbSNP
rs1020873395	578	dbSNP
rs1201082782	582	dbSNP
rs967346999	583	dbSNP
rs866350047	592	dbSNP
rs1341506494	593	dbSNP
rs1035718159	595	dbSNP
rs1222085608	599	dbSNP
rs1024573532	603	dbSNP
rs1284204240	604	dbSNP
rs1406943554	608	dbSNP
rs1360016938	610	dbSNP
rs1288333062	616	dbSNP
rs896837949	618	dbSNP
rs1027351851	621	dbSNP
rs994085989	621	dbSNP
rs1469128790	622	dbSNP
rs1271257557	627	dbSNP
rs960110068	629	dbSNP
rs1178202721	637	dbSNP
rs952575156	642	dbSNP
rs1260508625	643	dbSNP
rs1196402010	644	dbSNP
rs991622504	649	dbSNP
rs749060384	650	dbSNP
rs1323302339	653	dbSNP
rs942216701	654	dbSNP
rs1225625330	657	dbSNP
rs974042881	662	dbSNP
rs976185694	667	dbSNP
rs1295052939	668	dbSNP
rs919523850	669	dbSNP
rs1475735427	670	dbSNP
rs929591192	683	dbSNP
rs1051358523	687	dbSNP
rs570575915	688	dbSNP
rs1338445919	689	dbSNP
rs796074810	690	dbSNP
rs539495157	693	dbSNP
rs1372164195	694	dbSNP
rs1428481978	696	dbSNP
rs1429811521	706	dbSNP
rs139011991	708	dbSNP
rs936945567	709	dbSNP
rs3187572	713	dbSNP
rs1038787372	721	dbSNP
rs866882889	722	dbSNP
rs3187573	725	dbSNP
rs1010758384	729	dbSNP
rs116312610	741	dbSNP
rs1327364366	742	dbSNP
rs902417563	756	dbSNP
rs949121424	758	dbSNP
rs1046160046	761	dbSNP
rs1245234446	767	dbSNP
rs1295992249	774	dbSNP
rs1317009956	777	dbSNP
rs1447240892	781	dbSNP
rs920839512	781	dbSNP
rs1364577100	784	dbSNP
rs929526674	789	dbSNP
rs1298418232	791	dbSNP
rs1463181003	794	dbSNP
rs1363214486	800	dbSNP
rs1162373192	801	dbSNP
rs1171929196	801	dbSNP
rs1178035895	801	dbSNP
rs1289752063	801	dbSNP
rs1444625327	801	dbSNP
rs1481736365	801	dbSNP
rs5881906	801	dbSNP
rs1221853902	818	dbSNP
rs1246731103	821	dbSNP
rs1294225127	824	dbSNP
rs1236736817	827	dbSNP
rs896811173	829	dbSNP
rs1307403672	832	dbSNP
rs1343242837	832	dbSNP
rs994279357	832	dbSNP
rs1302070111	837	dbSNP
rs1424782298	841	dbSNP
rs1209454700	843	dbSNP
rs1288942254	851	dbSNP
rs1048063009	855	dbSNP
rs3829824	856	dbSNP
rs1195281542	859	dbSNP
rs1246051356	861	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.