>LFNG|NM_001040167|3'UTR
   1 TGGCCATGGCTGAGACCCAATCCCTGGGCGCCCCTGGTATCCAAAGGGCCCAGGGACCCTGTTGCGCTGCCCTGGCCTCG
  81 GCATTCGAGGCTCCCCTAGGGCCGTGCCTGTGCGTGTGCGTGTGCGTGTGTGTGTGTGTGTACTGCATGCCCACCCGGGT
 161 AGCAGGCTGCTGGGCAGTTCTGCTCTGTGGAGGGGCGGGCACCAGCGCCACTTATGTGCCTCTGCTCCGAGGGCCAGTGG
 241 GCTGCAGGGCCTGCTTGGAGGAAGGATTTGTGTGTCGGAGGCCACTCCGAGGGCAATTCTGTTAGGATTTTTGGATCTTT
 321 CTACAGCTACGGGGCTCCGGGCTACTTTGCAGGGATGCGATGCGTAGGTGCCTTTCTCTTCCTGCTGACCACAAGCTCTG
 401 TGCTGGGGGTACCTGTGCCCTGAAGTCCTGGCCCCTGTGTCATAGCCCCAAGTACGACTCACTGAGCCATGCTCATTGCA
 481 GGGGAGGCTGGGTCTGGGGGTGCGTGACCCAATCCCCTTCCTCCTGGCCTGGACGCTGTGGCTTAAGAGTAACAGCAGCC
 561 ACCGCCCAGTTCCAGTGGCCCCACGAAGCCCCCAGTGGCTGGCTGTCCAGCTGGGCAAACAGTGGCACCCCTCCCAGCTC
 641 TTCTGAGTGGGGAGTCTTCCAGGCCTCCTCAGAGGTCTTCCCTTTGCCTCCCCAGGACAGGGTGAGTCAGAGCTCAGCAT
 721 TTAATCTCCTCTCCAAAGTAGAGAGCAAGTCGCCCACAGTGGGCGTGTCTGTAAATATTGTGACAGTATTTTTTTACTGT
 801 GCTGTTTTTTTTGAAAGGGGATGGGTAAAAAGTAGGGTGTTCTTGTTTTTTGCTTGGGAGGGTGGGGGTGGGGGAGGGTC
 881 TTATTTTATCTTATCTTTTCTGTGGATCAGAAAAAACAGAAGCCAAACTCGGGGTCATCTTTGTTTTTAAAGCTGAAGTG
 961 GGACTGTCTGGCACTCTGTGTATTTATGCGTTCCAGCATCTGGAACCTCCCATCCCTGCCCTCCTCCTGTGTAGCTGCCA
1041 CCTCCCCGCTGGGCCCAGCATGGCTCACCTGTCCCGTGGGCTGTGTTTCTTGTTGTTTTTCTCTTTGCAAAGACATAGCT
1121 AGGAAAGCGAATGATAAGGGAAAAGTTCTCAGGGAATTGAAGTGTTGTTGCTATGGTGACGTCCTTTTGCTGTGAATAAA
1201 GGTGCTCTTTGCAGCAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gaGUGGACU-CGAG--------GGCACGGAc 5' ||:: || |||| |||||||| Target 5' ggCATTCGAGGCTCCCCTAGGGCCGTGCCTg 3'	80 - 110	154.00	-27.20
2	miRNA 3' gaGUGGACUC---GAGGGCACGGAc 5' |||| | | ||: :|||||| Target 5' ggCACCAGCGCCACTTATGTGCCTc 3'	198 - 222	144.00	-18.60
3	miRNA 3' gaguGGACUCGAGGGCACGGAc 5' || ||: ||||:|| Target 5' tcgcCCACAGTGGGCGTGTCTg 3'	750 - 771	130.00	-19.90

Mutant ID	Mutant Position	Mutant Source
COSN20061109	12	COSMIC
COSN28888634	31	COSMIC
COSN31589536	66	COSMIC
COSN17583555	80	COSMIC
COSN30530835	81	COSMIC
COSN28416732	88	COSMIC
COSN23261075	109	COSMIC
COSN18746355	126	COSMIC
COSN1347736	127	COSMIC
COSN32057765	132	COSMIC
COSN23089422	141	COSMIC
COSN31560651	158	COSMIC
COSN1347737	292	COSMIC
COSN7975814	373	COSMIC
COSN28823720	682	COSMIC
COSN25476678	684	COSMIC
COSN7975816	700	COSMIC
COSN28813330	759	COSMIC
COSN31583833	792	COSMIC
COSN26570684	929	COSMIC
COSN31583262	1129	COSMIC
COSN31481071	1208	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1253795638	4	dbSNP
rs759059115	7	dbSNP
rs760874474	8	dbSNP
rs1191433857	10	dbSNP
rs1375163891	11	dbSNP
rs1475973215	18	dbSNP
rs1477744602	19	dbSNP
rs766513167	22	dbSNP
rs764643641	29	dbSNP
rs776136278	30	dbSNP
rs201970001	31	dbSNP
rs368992076	32	dbSNP
rs1394680539	35	dbSNP
rs1381338416	36	dbSNP
rs1293120845	37	dbSNP
rs1327960812	41	dbSNP
rs751878647	42	dbSNP
rs545931165	46	dbSNP
rs767664190	50	dbSNP
rs1204733509	58	dbSNP
rs1232383559	62	dbSNP
rs760735207	66	dbSNP
rs559796856	67	dbSNP
rs374747670	70	dbSNP
rs1343738851	72	dbSNP
rs1309496451	75	dbSNP
rs893558226	78	dbSNP
rs983508434	80	dbSNP
rs947604312	81	dbSNP
rs1342126757	83	dbSNP
rs1332194819	87	dbSNP
rs528621625	88	dbSNP
rs1485684686	92	dbSNP
rs950204135	94	dbSNP
rs548750010	101	dbSNP
rs1379929535	108	dbSNP
rs1187517401	109	dbSNP
rs1286054463	109	dbSNP
rs201574373	109	dbSNP
rs937552928	109	dbSNP
rs1218189448	112	dbSNP
rs1350980544	114	dbSNP
rs7457877	115	dbSNP
rs1282335218	120	dbSNP
rs1447253614	120	dbSNP
rs559555929	120	dbSNP
rs150935549	121	dbSNP
rs79129905	121	dbSNP
rs1254869229	122	dbSNP
rs1360126244	122	dbSNP
rs1010545178	125	dbSNP
rs1009096886	126	dbSNP
rs1227557260	126	dbSNP
rs1280088831	126	dbSNP
rs1491549227	126	dbSNP
rs3074378	126	dbSNP
rs563595289	127	dbSNP
rs985218349	127	dbSNP
rs758371551	128	dbSNP
rs878855343	128	dbSNP
rs895829027	129	dbSNP
rs545875243	130	dbSNP
rs71026526	131	dbSNP
rs7456343	132	dbSNP
rs964544558	138	dbSNP
rs1023043165	139	dbSNP
rs1476542161	142	dbSNP
rs996062142	145	dbSNP
rs1191302541	151	dbSNP
rs573462131	155	dbSNP
rs1244637540	156	dbSNP
rs147211886	157	dbSNP
rs952004053	158	dbSNP
rs1026586395	165	dbSNP
rs1353735129	166	dbSNP
rs1414460467	170	dbSNP
rs907898897	178	dbSNP
rs950542802	195	dbSNP
rs987396267	197	dbSNP
rs570412528	198	dbSNP
rs964413650	200	dbSNP
rs981933551	203	dbSNP
rs1447969701	204	dbSNP
rs927478554	207	dbSNP
rs10259275	208	dbSNP
rs1212328250	210	dbSNP
rs1360274676	211	dbSNP
rs1277643717	215	dbSNP
rs868099397	216	dbSNP
rs990345524	220	dbSNP
rs946471260	221	dbSNP
rs546656087	226	dbSNP
rs924775675	228	dbSNP
rs934796069	229	dbSNP
rs1042022259	230	dbSNP
rs1233795149	242	dbSNP
rs1196550699	245	dbSNP
rs1480234890	246	dbSNP
rs1256520165	247	dbSNP
rs544105369	248	dbSNP
rs535224381	250	dbSNP
rs896067750	252	dbSNP
rs1279855613	254	dbSNP
rs1379441448	255	dbSNP
rs1307472203	257	dbSNP
rs1012892369	271	dbSNP
rs555114380	277	dbSNP
rs1175885112	278	dbSNP
rs944468712	280	dbSNP
rs1044360688	282	dbSNP
rs899143224	283	dbSNP
rs995335755	284	dbSNP
rs1419876508	289	dbSNP
rs1026366526	290	dbSNP
rs1418355793	292	dbSNP
rs996032742	294	dbSNP
rs950645256	296	dbSNP
rs1008733890	307	dbSNP
rs1373783057	318	dbSNP
rs1217470847	324	dbSNP
rs1434315943	330	dbSNP
rs571516312	331	dbSNP
rs1018897859	332	dbSNP
rs1322746570	334	dbSNP
rs1315395945	338	dbSNP
rs568729000	339	dbSNP
rs887662947	340	dbSNP
rs974630580	342	dbSNP
rs1439666467	345	dbSNP
rs1400083108	347	dbSNP
rs537707909	349	dbSNP
rs140627680	352	dbSNP
rs1156521032	355	dbSNP
rs201654623	360	dbSNP
rs778669543	361	dbSNP
rs1166693920	364	dbSNP
rs191731191	365	dbSNP
rs1236487590	366	dbSNP
rs1256740340	372	dbSNP
rs1277529718	373	dbSNP
rs1014926212	374	dbSNP
rs1261273427	381	dbSNP
rs971839428	384	dbSNP
rs1488944945	393	dbSNP
rs532692599	401	dbSNP
rs1243086476	403	dbSNP
rs373324573	407	dbSNP
rs1274627339	410	dbSNP
rs778723010	413	dbSNP
rs546173366	414	dbSNP
rs1202801286	416	dbSNP
rs1341889184	420	dbSNP
rs553129764	430	dbSNP
rs573268734	433	dbSNP
rs541981597	434	dbSNP
rs1057208590	436	dbSNP
rs182423865	439	dbSNP
rs779494937	446	dbSNP
rs1459685811	447	dbSNP
rs1417077363	456	dbSNP
rs1171355775	457	dbSNP
rs752467042	461	dbSNP
rs1421517441	463	dbSNP
rs1192586216	464	dbSNP
rs948992933	467	dbSNP
rs1455083592	468	dbSNP
rs1044613996	469	dbSNP
rs1269743512	470	dbSNP
rs1208424490	472	dbSNP
rs1468363910	478	dbSNP
rs1259243231	482	dbSNP
rs1201119239	488	dbSNP
rs1196106110	489	dbSNP
rs990250209	490	dbSNP
rs1267849198	499	dbSNP
rs1226080689	500	dbSNP
rs899171692	501	dbSNP
rs149714904	503	dbSNP
rs1048317674	504	dbSNP
rs1438430246	505	dbSNP
rs185900482	510	dbSNP
rs1008765081	522	dbSNP
rs752571497	525	dbSNP
rs544863067	535	dbSNP
rs145579363	536	dbSNP
rs996842879	541	dbSNP
rs944397191	545	dbSNP
rs996096993	546	dbSNP
rs1022178791	559	dbSNP
rs900227816	562	dbSNP
rs1239128995	564	dbSNP
rs533489651	565	dbSNP
rs1272935117	567	dbSNP
rs977780732	568	dbSNP
rs1048890381	582	dbSNP
rs887651620	584	dbSNP
rs1031189723	585	dbSNP
rs1231570575	586	dbSNP
rs1004797206	597	dbSNP
rs1227438107	599	dbSNP
rs550893787	608	dbSNP
rs1309636775	624	dbSNP
rs1271447963	625	dbSNP
rs1448722687	629	dbSNP
rs546553353	630	dbSNP
rs1333903063	639	dbSNP
rs1015286557	640	dbSNP
rs1415086202	646	dbSNP
rs907184304	650	dbSNP
rs1257791740	655	dbSNP
rs1381166775	656	dbSNP
rs1160759190	664	dbSNP
rs1003263822	672	dbSNP
rs1034327450	681	dbSNP
rs4721752	682	dbSNP
rs1215973587	702	dbSNP
rs1208114603	707	dbSNP
rs990196489	709	dbSNP
rs746722168	714	dbSNP
rs1451545861	719	dbSNP
rs748765275	726	dbSNP
rs1374927276	732	dbSNP
rs1474530778	737	dbSNP
rs770532937	744	dbSNP
rs1170292111	750	dbSNP
rs977687608	752	dbSNP
rs1462783983	753	dbSNP
rs1323652405	765	dbSNP
rs1361411417	769	dbSNP
rs528949020	773	dbSNP
rs1160741936	776	dbSNP
rs1399302898	782	dbSNP
rs1389860435	787	dbSNP
rs912828999	793	dbSNP
rs965673761	796	dbSNP
rs917419125	803	dbSNP
rs780894491	804	dbSNP
rs975715780	805	dbSNP
rs948857194	806	dbSNP
rs980798639	817	dbSNP
rs920855895	818	dbSNP
rs930663012	820	dbSNP
rs1047710927	821	dbSNP
rs780704892	833	dbSNP
rs1444957327	835	dbSNP
rs1283238707	838	dbSNP
rs1382770218	838	dbSNP
rs770637091	840	dbSNP
rs1228688036	842	dbSNP
rs1358298289	844	dbSNP
rs1319715928	846	dbSNP
rs931678252	846	dbSNP
rs886411917	848	dbSNP
rs1226083602	852	dbSNP
rs944792140	856	dbSNP
rs1341264779	859	dbSNP
rs1300245512	860	dbSNP
rs1428829943	864	dbSNP
rs1344842801	868	dbSNP
rs1261553273	869	dbSNP
rs1407499630	870	dbSNP
rs1164890195	871	dbSNP
rs909034917	872	dbSNP
rs1293483923	876	dbSNP
rs879475220	877	dbSNP
rs745680396	889	dbSNP
rs1040441711	892	dbSNP
rs1474189547	895	dbSNP
rs940545349	896	dbSNP
rs1036218683	910	dbSNP
rs1213038156	911	dbSNP
rs1271175897	911	dbSNP
rs1336494756	913	dbSNP
rs1318537050	918	dbSNP
rs1235459039	919	dbSNP
rs1271729219	920	dbSNP
rs907087134	929	dbSNP
rs900342548	931	dbSNP
rs745471465	932	dbSNP
rs1392791215	933	dbSNP
rs1325686930	934	dbSNP
rs1466556947	935	dbSNP
rs1206281189	940	dbSNP
rs1022670848	973	dbSNP
rs1407782425	974	dbSNP
rs1445306613	977	dbSNP
rs1191464606	983	dbSNP
rs903750904	985	dbSNP
rs1002800939	987	dbSNP
rs1250867836	990	dbSNP
rs1193081613	991	dbSNP
rs1253072859	998	dbSNP
rs1202506911	1002	dbSNP
rs1258412111	1007	dbSNP
rs1279560742	1015	dbSNP
rs1476317826	1019	dbSNP
rs1055683393	1024	dbSNP
rs1303060890	1030	dbSNP
rs1447993479	1037	dbSNP
rs879679836	1038	dbSNP
rs894519870	1039	dbSNP
rs1367747964	1042	dbSNP
rs1011608122	1043	dbSNP
rs1021692602	1047	dbSNP
rs769360562	1048	dbSNP
rs1392880018	1049	dbSNP
rs548679551	1050	dbSNP
rs1440142991	1057	dbSNP
rs1019791929	1058	dbSNP
rs1175450170	1061	dbSNP
rs1480286405	1066	dbSNP
rs960325791	1067	dbSNP
rs1213130643	1071	dbSNP
rs190614229	1076	dbSNP
rs1312969177	1077	dbSNP
rs975661914	1087	dbSNP
rs921592285	1090	dbSNP
rs1305454833	1093	dbSNP
rs1380561904	1096	dbSNP
rs1412614732	1096	dbSNP
rs953055803	1096	dbSNP
rs1416156833	1100	dbSNP
rs1373224271	1102	dbSNP
rs1311940380	1103	dbSNP
rs537648051	1106	dbSNP
rs1340296996	1114	dbSNP
rs774825225	1115	dbSNP
rs970239713	1120	dbSNP
rs1365282732	1122	dbSNP
rs908933730	1128	dbSNP
rs774707251	1129	dbSNP
rs1414452024	1130	dbSNP
rs940466040	1138	dbSNP
rs1484765950	1141	dbSNP
rs1036571400	1154	dbSNP
rs928491666	1158	dbSNP
rs557575315	1168	dbSNP
rs1259285740	1177	dbSNP
rs1055673434	1181	dbSNP
rs1322842180	1182	dbSNP
rs930925079	1183	dbSNP
rs879409820	1184	dbSNP
rs762101666	1193	dbSNP
rs907876900	1195	dbSNP
rs1292167070	1213	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.