>TAF13|NM_005645|3'UTR
   1 CACTTTTTGTAGTTTCCGAAAATTACCATCTGGGGAAACCATATATAATAATTGTATATTTTCTAAAGTAAGATTCTGAT
  81 ATCTAGCCATGTAAATGAAAGATGGAGAAACACAAAGTTTTCAGCCTTTATTTTTATGCCTTTGATT

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ucguccucccGACCCGUccgc 5' ||||| | Target 5' aaattaccatCTGGGGAaacc 3'	20 - 40	63.00	-7.50

Mutant ID	Mutant Position	Mutant Source
COSN30493607	21	COSMIC
COSN31498107	33	COSMIC
COSN30191578	35	COSMIC
COSN24398832	58	COSMIC
COSN30187931	76	COSMIC
COSN30119960	83	COSMIC
COSN30068199	91	COSMIC
COSN29263587	180	COSMIC
COSN22371248	379	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1051388965	1	dbSNP
rs1176113543	3	dbSNP
rs1468217786	7	dbSNP
rs997773389	9	dbSNP
rs765786346	13	dbSNP
rs759586910	17	dbSNP
rs201718167	18	dbSNP
rs1473336242	21	dbSNP
rs771099747	27	dbSNP
rs1213526359	28	dbSNP
rs1173844910	29	dbSNP
rs6604757	30	dbSNP
rs1182303082	33	dbSNP
rs1349211152	35	dbSNP
rs753210706	42	dbSNP
rs747252248	43	dbSNP
rs537495241	48	dbSNP
rs1466914938	53	dbSNP
rs1305092256	65	dbSNP
rs775041895	70	dbSNP
rs1377931018	71	dbSNP
rs1325465870	72	dbSNP
rs1439234712	73	dbSNP
rs522193	76	dbSNP
rs1053050597	78	dbSNP
rs191835272	89	dbSNP
rs925429729	94	dbSNP
rs955862030	96	dbSNP
rs1322523617	101	dbSNP
rs1233768740	104	dbSNP
rs1294669427	110	dbSNP
rs771567797	111	dbSNP
rs1479580158	115	dbSNP
rs1195173002	117	dbSNP
rs1251850101	136	dbSNP
rs1483769940	138	dbSNP
rs1196801567	140	dbSNP
rs187001365	147	dbSNP
rs111650544	150	dbSNP
rs948100755	151	dbSNP
rs917924528	153	dbSNP
rs992092277	159	dbSNP
rs1461867807	164	dbSNP
rs1309192917	166	dbSNP
rs960248601	169	dbSNP
rs1403224336	172	dbSNP
rs919206973	180	dbSNP
rs1368644882	183	dbSNP
rs968527466	184	dbSNP
rs1303064195	186	dbSNP
rs1305574969	191	dbSNP
rs1226554458	194	dbSNP
rs1275316745	195	dbSNP
rs1023119096	204	dbSNP
rs963278838	210	dbSNP
rs1267721625	211	dbSNP
rs1253364982	212	dbSNP
rs1192579805	213	dbSNP
rs553691876	217	dbSNP
rs143959539	220	dbSNP
rs565608824	228	dbSNP
rs1392621489	241	dbSNP
rs756524684	249	dbSNP
rs953072163	251	dbSNP
rs748393997	256	dbSNP
rs181478310	257	dbSNP
rs1438818423	263	dbSNP
rs7412176	263	dbSNP
rs755598484	270	dbSNP
rs1359567600	273	dbSNP
rs1303011274	276	dbSNP
rs569270520	279	dbSNP
rs1232328110	281	dbSNP
rs1434161334	283	dbSNP
rs1037188213	291	dbSNP
rs1006113917	311	dbSNP
rs1243683930	314	dbSNP
rs1302436970	317	dbSNP
rs1321813544	325	dbSNP
rs888575826	332	dbSNP
rs1258625913	334	dbSNP
rs1360498604	335	dbSNP
rs1485732779	336	dbSNP
rs1291139648	337	dbSNP
rs1410787325	340	dbSNP
rs1178355232	341	dbSNP
rs1050262080	342	dbSNP
rs1171410761	343	dbSNP
rs1436236637	344	dbSNP
rs1377782581	346	dbSNP
rs1443260698	347	dbSNP
rs1183540361	348	dbSNP
rs1192204544	348	dbSNP
rs1426509663	349	dbSNP
rs1263835607	355	dbSNP
rs1414573441	356	dbSNP
rs1194269462	358	dbSNP
rs1488681340	359	dbSNP
rs1279743194	362	dbSNP
rs1157162168	367	dbSNP
rs1229586367	367	dbSNP
rs1283561318	367	dbSNP
rs1304397704	367	dbSNP
rs1328134633	367	dbSNP
rs1344886448	367	dbSNP
rs1379226663	367	dbSNP
rs1390584075	367	dbSNP
rs1450301464	367	dbSNP
rs1456501101	367	dbSNP
rs1464741611	367	dbSNP
rs1488321988	367	dbSNP
rs35296800	367	dbSNP
rs71069642	367	dbSNP
rs1245360462	368	dbSNP
rs1468077059	368	dbSNP
rs138603694	369	dbSNP
rs1490421451	370	dbSNP
rs1333406217	372	dbSNP
rs1359731936	373	dbSNP
rs1449579358	379	dbSNP
rs1295880247	380	dbSNP
rs932678798	381	dbSNP
rs1349361088	382	dbSNP
rs1350342464	383	dbSNP
rs922560705	384	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.