>CHRFAM7A|NM_139320|3'UTR
   1 CCACGCCTGGTTCTGTACATGTGGAAAACTCACAGATGGGCAAGGCCTTTGGCTTGGCGAGATTTGGGGGTGCTAATCCA
  81 GGACAGCATTACACGCCACAACTCCAGTGTTCCCTTCTGGCTGTCAGTCGTGTTGCTTACGGTTTCTTTGTTACTTTAGG
 161 TAGTAGAATCTCAGCACTTTGTTTCATATTCTCAGATGGGCTGATAGATATCCTTGGCACATCCGTACCATCGGTCAGCA
 241 GGGCCACTGAGTAGTCATTTTGCCCATTAGCCCACTGCCTGGAAAGCCCTTCGGAGAGCTCCCCATGGCTCCTCACCACC
 321 GAGACAGTTGGTTTTGCATGTCTGCATGAAGGTCTACCTGAAAATTCAACATTTGCTTTTTGCTTGTGTACAAACCCAGA
 401 TTGAAGCTAAAATAAACCAGACTCACTAAATCCTTTCCAATAATTGACTGGTGGAAGGAAAACAAAAAACAAAAACTAAA
 481 AACCTCTTAGCTTTTCTGCAATTCAACTTTTTATTTTTATTTTTATTTCTATCAAAGACGGTAGAGAGAAACAGCTTGAT
 561 GCTGTTTCTACATCAAAAAAAAAAAAAAAAAAGACAGACTGTTGGTCTTACTAAGGATGTTTTTACCAGCCTGCCTGACT
 641 TCTGCAAACCTACCCTGTCAAGGAGATCAAAGGGACGCAGGTTTCTGTTTATTCTGAACAAGGGCCAGGCCCCGCGGAGT
 721 GTCTTTGGTGGATCCCAGATAACTCCTAGGTGCTGCTCTCAGACACTGAGGAGTTGAGCAAATCTGTTCTATTCTGCAGA
 801 ACCCATAGGACAAATAAGAGTTCTACTAGAATTAACAGCCCAAAAGAATAGCTACAGCTAAGTGAAGCCACTTACGTGGG
 881 CTTTAAAAAAATAATGTGTTAGCTGATTCACATGCACTGGAGTTAATTAGTCTTAGAAATGTGTGCATCCATACAAATGC
 961 ACAACATAAAGTGAACATATTCCTAGGCCCTTTCTGCCTGTGTCAGGGCCAGGAAGTAGAGGCTGGGAACTCTTCTGGTC
1041 CCCAGTATGGCAG

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' aggUAGU-CCUCAGUACCUUCga 5' || | || | :|||||| Target 5' ccaATAATTGACTGGTGGAAGga 3'	437 - 459	131.00	-9.70
2	miRNA 3' agGUAGUC--CUCA-GUACC-UUCGa 5' |||:|| | | | ||| |||| Target 5' ccCATTAGCCCACTGCCTGGAAAGCc 3'	263 - 288	122.00	-12.70
3	miRNA 3' agguaguccucagUACCUUCGa 5' || ||||| Target 5' tgtacaaacccagATTGAAGCt 3'	387 - 408	113.00	-7.20

Mutant ID	Mutant Position	Mutant Source
COSN30164712	540	COSMIC
COSN28027909	597	COSMIC
COSN31559888	616	COSMIC
COSN28755887	714	COSMIC
COSN7042466	760	COSMIC
COSN24202838	804	COSMIC
COSN31569968	846	COSMIC
COSN31579852	884	COSMIC
COSN30170922	893	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1171084932	4	dbSNP
rs1477644887	5	dbSNP
rs1390693243	30	dbSNP
rs1421688801	35	dbSNP
rs1201718419	45	dbSNP
rs1488807540	48	dbSNP
rs986563921	59	dbSNP
rs1173736220	196	dbSNP
rs1358314198	208	dbSNP
rs1465740939	211	dbSNP
rs1303571355	232	dbSNP
rs1408470636	234	dbSNP
rs1432970479	242	dbSNP
rs1320530813	281	dbSNP
rs955325153	289	dbSNP
rs1254461323	293	dbSNP
rs1299669660	308	dbSNP
rs1311910396	311	dbSNP
rs1233606389	314	dbSNP
rs1264603772	320	dbSNP
rs1463199331	321	dbSNP
rs1213829942	324	dbSNP
rs1320580756	328	dbSNP
rs1486821455	331	dbSNP
rs1189343169	332	dbSNP
rs1424207328	346	dbSNP
rs1433548196	356	dbSNP
rs1028194281	357	dbSNP
rs1287720713	367	dbSNP
rs113285763	376	dbSNP
rs1320010053	381	dbSNP
rs1345811873	385	dbSNP
rs1433516990	439	dbSNP
rs1216185834	462	dbSNP
rs996493713	465	dbSNP
rs1296531378	469	dbSNP
rs1226503862	471	dbSNP
rs1387686599	471	dbSNP
rs1284853824	473	dbSNP
rs1326679805	476	dbSNP
rs1227349395	478	dbSNP
rs1268230295	486	dbSNP
rs1318127498	501	dbSNP
rs1373517564	507	dbSNP
rs1488710405	517	dbSNP
rs1201276688	518	dbSNP
rs957046553	520	dbSNP
rs112633028	523	dbSNP
rs1158628709	529	dbSNP
rs1326799713	529	dbSNP
rs1408893995	529	dbSNP
rs1435919163	539	dbSNP
rs542078948	540	dbSNP
rs1033061294	542	dbSNP
rs1348133854	550	dbSNP
rs1331476965	564	dbSNP
rs1410972377	568	dbSNP
rs1348958370	570	dbSNP
rs1389984830	571	dbSNP
rs286102	574	dbSNP
rs112808378	575	dbSNP
rs1455839950	575	dbSNP
rs1396572269	576	dbSNP
rs867278418	576	dbSNP
rs67960668	577	dbSNP
rs866400111	577	dbSNP
rs1322289105	590	dbSNP
rs1193870504	592	dbSNP
rs1272224892	593	dbSNP
rs1471222637	593	dbSNP
rs201193172	593	dbSNP
rs3865088	593	dbSNP
rs59383178	593	dbSNP
rs1413108265	594	dbSNP
rs377742720	594	dbSNP
rs1244411769	595	dbSNP
rs889219448	595	dbSNP
rs1425863897	610	dbSNP
rs1206560062	612	dbSNP
rs1369163589	616	dbSNP
rs1329181183	617	dbSNP
rs1438284120	617	dbSNP
rs998632981	626	dbSNP
rs1445304066	662	dbSNP
rs1283112821	672	dbSNP
rs1273785819	676	dbSNP
rs1202820365	677	dbSNP
rs1248083877	681	dbSNP
rs1349764471	688	dbSNP
rs1295299512	706	dbSNP
rs1304451229	709	dbSNP
rs1218811819	713	dbSNP
rs1439803627	714	dbSNP
rs1208217325	715	dbSNP
rs1365610868	721	dbSNP
rs902892716	723	dbSNP
rs1281314881	739	dbSNP
rs1045937331	747	dbSNP
rs1388829835	755	dbSNP
rs1168883478	768	dbSNP
rs1442985073	785	dbSNP
rs1014421123	786	dbSNP
rs1412413131	802	dbSNP
rs373424302	806	dbSNP
rs1406255621	807	dbSNP
rs1454099221	811	dbSNP
rs1318507500	816	dbSNP
rs894767527	817	dbSNP
rs1376371988	819	dbSNP
rs1176347185	831	dbSNP
rs1271733535	838	dbSNP
rs573069056	843	dbSNP
rs1217760976	847	dbSNP
rs1262732936	851	dbSNP
rs1422479284	857	dbSNP
rs1205603796	858	dbSNP
rs1464858383	875	dbSNP
rs930855235	875	dbSNP
rs1194446745	876	dbSNP
rs553037721	880	dbSNP
rs1375144106	896	dbSNP
rs1477241651	900	dbSNP
rs1171688452	909	dbSNP
rs899184290	925	dbSNP
rs1470178737	930	dbSNP
rs1387207427	947	dbSNP
rs1036734835	951	dbSNP
rs1329195096	953	dbSNP
rs1251060535	959	dbSNP
rs1179920239	960	dbSNP
rs1324570436	963	dbSNP
rs1225525556	964	dbSNP
rs1266328488	978	dbSNP
rs1486538303	982	dbSNP
rs1206306403	990	dbSNP
rs1264459839	996	dbSNP
rs1450285951	1002	dbSNP
rs940796487	1006	dbSNP
rs1269988403	1009	dbSNP
rs1280719627	1016	dbSNP
rs1179491216	1023	dbSNP
rs539408244	1048	dbSNP
rs1310708165	1055	dbSNP
rs1286587910	1056	dbSNP
rs1388445927	1063	dbSNP
rs1404652298	1066	dbSNP
rs1224464544	1070	dbSNP
rs1347097036	1078	dbSNP
rs1406998312	1081	dbSNP
rs1286675335	1102	dbSNP
rs911956967	1107	dbSNP
rs1239825204	1130	dbSNP
rs1262530026	1138	dbSNP
rs986636031	1139	dbSNP
rs1287004878	1151	dbSNP
rs1292970388	1178	dbSNP
rs1490942977	1198	dbSNP
rs1193407807	1206	dbSNP
rs1249358014	1257	dbSNP
rs1419191070	1260	dbSNP
rs1183392884	1306	dbSNP
rs781778021	1384	dbSNP
rs1472432044	1393	dbSNP
rs2651442	1440	dbSNP
rs933808714	1481	dbSNP
rs1427565282	1508	dbSNP
rs1306456889	1523	dbSNP
rs921209743	1525	dbSNP
rs975314382	1557	dbSNP
rs1309257302	1559	dbSNP
rs1464830930	1566	dbSNP
rs1245981984	1572	dbSNP
rs1357117097	1588	dbSNP
rs957492315	1593	dbSNP
rs1203413612	1617	dbSNP
rs1251065121	1626	dbSNP
rs1480765018	1634	dbSNP
rs1032681433	1654	dbSNP
rs1253467704	1657	dbSNP
rs977455875	1659	dbSNP
rs1184193977	1660	dbSNP
rs1386989001	1671	dbSNP
rs1447539739	1672	dbSNP
rs967186018	1695	dbSNP
rs1024056928	1701	dbSNP
rs200792307	1701	dbSNP
rs1300115070	1708	dbSNP
rs1400233968	1715	dbSNP
rs1451984133	1718	dbSNP
rs1338009698	1725	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.