>ZDHHC5|NM_015457|3'UTR
   1 GCCTTCGGCACCTCCCCTCCCCAACGCCTCTGCGCCTACACCAAAGGGCCCCAGGTGGCCACCTTCCTTCCCTCAAGGGG
  81 CTCCCCTCCCGTGCATGGACATTTTTTAAACCACCGATTCCAAGAGGATGAGGAGTGTTTTCTAAAATGCAGTAGGCTTG
 161 GGGAGTCGGAGAGTTGGGGCCCTGAGACTGGGGTAGCAACCCCCCCTTTTATCTTTTAAGACCTTCCCTTCCTTGATCCC
 241 TGGACCAGACTCAGTGGACATTTGTGCAATTGCTCGCCCTGGAGGGAACCAGATCATTTTTAAACCAGAAATAATTTTTT
 321 TTATTATTGTTACGGATTCTATTTTTTTCCTCTTCTGCGTTACCAGGTGTGTGTGTACATATAATATATATATATATATA
 401 TTATAAATATCAAAGAAATTATATATCTATCCTGGGATGGGAAAATGAGGGAGGGATACATATACGGAGGGGGATCTTAC
 481 TCTTCCCATTCCTCAGACCAGCAGGAAAAGAGGGGAGACGTCAGTCTTTTTCCTGTGGTTCCCTCTCATTTGTCCCAGTT
 561 ACTAACTACGGAAATAGCATCCTCTGCTGGTGCTAAGTGTGATTAGGAAGAAGCCTGGGGAGAGGTGAGTCTGGAATTTT
 641 GGTCACAAGAGGGAAGGACTTGGAGAGGAGAATTAGTTTTCTAGGCTCATTGGCATTTAGTTTCCCTAGGAAAGGGGTCA
 721 AAACTTCAAGACACTGGTGGTGGTGGGAGATCAGGAAAATAACTTGGCCTAGCTCAAACAATATTGGATAATCCCCTCCT
 801 TGGGGGAGAGGGATTAGAGTGTGCTCCTACTGGCCCCTTGGAGCCTCCCCTAGCTTACACAGTTAACTTGATTTTAAAAT
 881 CCAAGGCCAGGAGAGAAGAATCCAAAAAGCAATATTTTTCATCACATGCCAAAAACGGGGGATAGAGAGAAGGAGTGGCA
 961 GGCCTAGGCCCCTCCGATTGTCCCTTGGGGGTTACCCCTCAGCCCACCTCACTATGGTGCTGGGTAGAGGGGATACCTGG
1041 GTTCTAACCTCTAAATAGGGGAGATCCCAGCCTCCACAAAGAGGCCCTTTTATTTTTTATTCTGATTAGCCATTTTAAAC
1121 CAACGAGGAATAAAAAGAAATCCTGATCTAACCAGCAAAAAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ucUGUGUAAAC---C----UCUCCCUUGg 5' :::|| ||| | :|||||||| Target 5' ttGTGCAATTGCTCGCCCTGGAGGGAACc 3'	262 - 290	150.00	-18.10
2	miRNA 3' ucuguguAAACC-----UCUCCCUUgg 5' ||||| |||||||| Target 5' ctggaatTTTGGTCACAAGAGGGAAgg 3'	631 - 657	139.00	-14.50
3	miRNA 3' ucUGUGUAAACCUCUCCCUUGg 5' |||:|| ||||:|||| | Target 5' atACATATACGGAGGGGGATCt 3'	456 - 477	132.00	-21.60

Mutant ID	Mutant Position	Mutant Source
COSN28861570	29	COSMIC
COSN30164211	31	COSMIC
COSN30761986	35	COSMIC
COSN30145065	36	COSMIC
COSN28758325	187	COSMIC
COSN29467966	277	COSMIC
COSN26643687	278	COSMIC
COSN32062025	402	COSMIC
COSN7014773	467	COSMIC
COSN31539470	521	COSMIC
COSN24900733	525	COSMIC
COSN31590600	614	COSMIC
COSN28709076	682	COSMIC
COSN8584270	682	COSMIC
COSN31603633	702	COSMIC
COSN31596324	794	COSMIC
COSN24823874	845	COSMIC
COSN28758008	894	COSMIC
COSN28638248	1127	COSMIC
COSN31513712	1137	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs760716857	2	dbSNP
rs926864588	4	dbSNP
rs764199512	6	dbSNP
rs754070531	7	dbSNP
rs530650676	8	dbSNP
rs200117655	11	dbSNP
rs765382865	13	dbSNP
rs750225456	18	dbSNP
rs1488481131	23	dbSNP
rs376192237	24	dbSNP
rs1208590491	25	dbSNP
rs779883003	25	dbSNP
rs370314176	26	dbSNP
rs374038596	27	dbSNP
rs367986917	34	dbSNP
rs747814809	35	dbSNP
rs1042423140	37	dbSNP
rs1003018673	38	dbSNP
rs769574039	40	dbSNP
rs1300617283	41	dbSNP
rs544848422	45	dbSNP
rs746256502	51	dbSNP
rs1482979842	53	dbSNP
rs113438323	54	dbSNP
rs1187067974	55	dbSNP
rs1358077662	64	dbSNP
rs563072034	72	dbSNP
rs1417008240	76	dbSNP
rs1021542860	82	dbSNP
rs578260699	84	dbSNP
rs996246810	91	dbSNP
rs900407308	92	dbSNP
rs1256508960	110	dbSNP
rs1210977181	116	dbSNP
rs1030861577	117	dbSNP
rs954552900	131	dbSNP
rs983325336	133	dbSNP
rs907788028	134	dbSNP
rs1341536861	145	dbSNP
rs963259473	154	dbSNP
rs886246094	159	dbSNP
rs777279157	161	dbSNP
rs545695706	168	dbSNP
rs186968752	169	dbSNP
rs971090599	172	dbSNP
rs1352219254	175	dbSNP
rs947738137	180	dbSNP
rs749685518	181	dbSNP
rs1001192526	182	dbSNP
rs1465762791	189	dbSNP
rs1377676938	191	dbSNP
rs1185609907	193	dbSNP
rs1033964953	198	dbSNP
rs1256830915	200	dbSNP
rs959869519	200	dbSNP
rs371268180	201	dbSNP
rs1316245157	205	dbSNP
rs1260224393	206	dbSNP
rs751150913	206	dbSNP
rs112723301	212	dbSNP
rs938844527	221	dbSNP
rs548684500	223	dbSNP
rs1314103542	224	dbSNP
rs1053181653	245	dbSNP
rs560675239	246	dbSNP
rs1330004758	253	dbSNP
rs978188101	259	dbSNP
rs1402090556	261	dbSNP
rs1215942473	263	dbSNP
rs1243741271	264	dbSNP
rs374462812	270	dbSNP
rs531302092	271	dbSNP
rs1043716218	277	dbSNP
rs549605761	278	dbSNP
rs571117196	287	dbSNP
rs1166851623	290	dbSNP
rs1417163697	301	dbSNP
rs900488382	303	dbSNP
rs1237493904	306	dbSNP
rs1039429921	315	dbSNP
rs1178173845	315	dbSNP
rs1383734054	315	dbSNP
rs996605129	318	dbSNP
rs1030415377	321	dbSNP
rs1182734956	323	dbSNP
rs890580895	324	dbSNP
rs1208244559	329	dbSNP
rs1385640460	332	dbSNP
rs921932944	334	dbSNP
rs1004981210	338	dbSNP
rs1309152390	342	dbSNP
rs1315729921	342	dbSNP
rs1048938231	348	dbSNP
rs1407598981	352	dbSNP
rs761292789	356	dbSNP
rs1320447388	359	dbSNP
rs781157668	360	dbSNP
rs1452567831	363	dbSNP
rs1004714801	367	dbSNP
rs1337726052	367	dbSNP
rs1045540894	368	dbSNP
rs1159149822	373	dbSNP
rs149110165	376	dbSNP
rs1001229607	381	dbSNP
rs1197036708	383	dbSNP
rs1491513075	383	dbSNP
rs10633679	384	dbSNP
rs1231890022	384	dbSNP
rs759646421	384	dbSNP
rs963217704	384	dbSNP
rs34110973	385	dbSNP
rs1331389906	388	dbSNP
rs138094238	392	dbSNP
rs1247653126	399	dbSNP
rs1491478335	401	dbSNP
rs1491299857	402	dbSNP
rs1326538217	403	dbSNP
rs868633633	403	dbSNP
rs1298753509	404	dbSNP
rs1023995996	405	dbSNP
rs1022543555	412	dbSNP
rs1223845237	416	dbSNP
rs969078407	419	dbSNP
rs1378475480	423	dbSNP
rs190229110	424	dbSNP
rs1477060027	426	dbSNP
rs912000651	430	dbSNP
rs966120493	441	dbSNP
rs767029045	445	dbSNP
rs1489595011	450	dbSNP
rs182445440	458	dbSNP
rs1199440262	461	dbSNP
rs921936858	464	dbSNP
rs1176590786	466	dbSNP
rs1278525312	467	dbSNP
rs1401608449	479	dbSNP
rs866148578	481	dbSNP
rs1333403068	483	dbSNP
rs1227183926	486	dbSNP
rs1049487179	487	dbSNP
rs1402944226	489	dbSNP
rs1174550832	495	dbSNP
rs907783455	500	dbSNP
rs2956980	520	dbSNP
rs1045569950	523	dbSNP
rs913374157	528	dbSNP
rs1469701840	538	dbSNP
rs1442516928	543	dbSNP
rs534233979	544	dbSNP
rs1177813725	546	dbSNP
rs1409004448	548	dbSNP
rs1257583608	559	dbSNP
rs1196367195	564	dbSNP
rs947585743	570	dbSNP
rs745756836	571	dbSNP
rs1220290094	575	dbSNP
rs900791625	579	dbSNP
rs1448595390	580	dbSNP
rs1341149184	582	dbSNP
rs1328677429	583	dbSNP
rs931994591	586	dbSNP
rs1052167981	588	dbSNP
rs1442498982	590	dbSNP
rs1467543916	599	dbSNP
rs1280749006	600	dbSNP
rs1163200563	612	dbSNP
rs555777289	614	dbSNP
rs937098947	615	dbSNP
rs186895390	620	dbSNP
rs1456913882	625	dbSNP
rs1783979	627	dbSNP
rs1015043309	647	dbSNP
rs1022533033	647	dbSNP
rs556656677	648	dbSNP
rs191335096	649	dbSNP
rs573240140	661	dbSNP
rs902755790	662	dbSNP
rs1306965548	663	dbSNP
rs539108587	665	dbSNP
rs779756699	667	dbSNP
rs999709573	668	dbSNP
rs1332330018	671	dbSNP
rs1019086466	675	dbSNP
rs995117232	690	dbSNP
rs1323385736	694	dbSNP
rs1023543449	696	dbSNP
rs1406303657	709	dbSNP
rs1368059182	710	dbSNP
rs969676755	728	dbSNP
rs982053898	739	dbSNP
rs545235411	741	dbSNP
rs1380323737	748	dbSNP
rs956386202	753	dbSNP
rs1029074645	760	dbSNP
rs114728264	765	dbSNP
rs1245756993	769	dbSNP
rs749484276	785	dbSNP
rs1464572656	789	dbSNP
rs1167641061	793	dbSNP
rs182641182	795	dbSNP
rs907814425	796	dbSNP
rs1353098981	797	dbSNP
rs968857013	798	dbSNP
rs1309982549	800	dbSNP
rs1225533385	803	dbSNP
rs979374851	805	dbSNP
rs922133571	811	dbSNP
rs981326951	813	dbSNP
rs928459922	817	dbSNP
rs1296910997	819	dbSNP
rs1419568751	819	dbSNP
rs932189029	820	dbSNP
rs542258855	821	dbSNP
rs1361730040	830	dbSNP
rs937150034	835	dbSNP
rs560537280	837	dbSNP
rs531168465	841	dbSNP
rs1052033215	842	dbSNP
rs188783024	846	dbSNP
rs1191377573	861	dbSNP
rs1478900895	865	dbSNP
rs564608565	867	dbSNP
rs1192856806	871	dbSNP
rs940694633	875	dbSNP
rs947065346	883	dbSNP
rs768977808	890	dbSNP
rs1288054683	904	dbSNP
rs143262971	913	dbSNP
rs899282108	914	dbSNP
rs1310485639	927	dbSNP
rs994938426	928	dbSNP
rs1255966472	931	dbSNP
rs2969941	937	dbSNP
rs71484458	938	dbSNP
rs1276775791	942	dbSNP
rs1291114280	944	dbSNP
rs193249911	944	dbSNP
rs1445219567	948	dbSNP
rs999742524	948	dbSNP
rs1034929521	951	dbSNP
rs1490267055	958	dbSNP
rs529943168	959	dbSNP
rs1029518240	962	dbSNP
rs772253660	962	dbSNP
rs549443325	976	dbSNP
rs567675904	977	dbSNP
rs141487300	979	dbSNP
rs1325994791	985	dbSNP
rs984847749	990	dbSNP
rs1009228262	991	dbSNP
rs1318993552	994	dbSNP
rs185330509	1016	dbSNP
rs1298406512	1017	dbSNP
rs147487820	1018	dbSNP
rs1374201234	1023	dbSNP
rs1476576903	1024	dbSNP
rs1302986712	1027	dbSNP
rs1161897835	1029	dbSNP
rs1190400599	1030	dbSNP
rs1454103970	1037	dbSNP
rs879070538	1041	dbSNP
rs1397729432	1045	dbSNP
rs968170081	1047	dbSNP
rs761201097	1049	dbSNP
rs1374533576	1054	dbSNP
rs1162612006	1065	dbSNP
rs1303164597	1067	dbSNP
rs1414432208	1072	dbSNP
rs1472306438	1073	dbSNP
rs922072658	1075	dbSNP
rs539246596	1077	dbSNP
rs1462686730	1093	dbSNP
rs1236616211	1100	dbSNP
rs879722165	1103	dbSNP
rs1481175077	1108	dbSNP
rs1253381884	1109	dbSNP
rs1243068248	1113	dbSNP
rs1321702251	1115	dbSNP
rs958817753	1117	dbSNP
rs991321061	1121	dbSNP
rs988108725	1124	dbSNP
rs190181991	1125	dbSNP
rs554066922	1126	dbSNP
rs924285475	1135	dbSNP
rs1358921693	1148	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.