ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ugacccAAGUGGAAAUUCCcgu 5' | | :|||||||| Target 5' tatattTCCTTCTTTAAGGtaa 3'	600 - 621	120.00	-9.20
2	miRNA 3' ugaccCAAGUGG---AAAUUCccgu 5' ||||||: |||||| Target 5' tgtatGTTCACTTTGTTTAAGttgt 3'	372 - 396	109.00	-8.20
3	miRNA 3' ugACCC----AAGUGG-AAAUUCccgu 5' |||| ||:|:| | |||| Target 5' caTGGGACTTTTTATCATCTAAGtaac 3'	84 - 110	102.00	-7.50

Mutant ID	Mutant Position	Mutant Source
COSN30150849	8	COSMIC
COSN31613717	12	COSMIC
COSN31501491	14	COSMIC
COSN31593608	15	COSMIC
COSN19732476	39	COSMIC
COSN30489821	40	COSMIC
COSN30101154	53	COSMIC
COSN30178339	77	COSMIC
COSN30186959	111	COSMIC
COSN28869091	121	COSMIC
COSN28816528	128	COSMIC
COSN31525895	133	COSMIC
COSN19386857	390	COSMIC
COSN20113874	568	COSMIC
COSN1718730	599	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1051938457	13	dbSNP
rs755425778	14	dbSNP
rs1265722305	19	dbSNP
rs754162621	24	dbSNP
rs780539908	29	dbSNP
rs370967139	30	dbSNP
rs749935471	39	dbSNP
rs1485778789	40	dbSNP
rs377610296	40	dbSNP
rs1398242535	41	dbSNP
rs1329776039	42	dbSNP
rs1181078920	43	dbSNP
rs1325738760	51	dbSNP
rs188856616	54	dbSNP
rs1473490854	57	dbSNP
rs1323827779	58	dbSNP
rs892752969	60	dbSNP
rs1054183407	66	dbSNP
rs1413926861	85	dbSNP
rs1174079325	90	dbSNP
rs1377392883	101	dbSNP
rs8072207	102	dbSNP
rs905213102	106	dbSNP
rs1307721741	110	dbSNP
rs948966605	111	dbSNP
rs917456383	115	dbSNP
rs753042066	120	dbSNP
rs1344965185	125	dbSNP
rs1218024750	129	dbSNP
rs929087332	151	dbSNP
rs918986662	152	dbSNP
rs1204001615	169	dbSNP
rs973499285	179	dbSNP
rs949481895	180	dbSNP
rs917744640	183	dbSNP
rs594415	185	dbSNP
rs986079287	194	dbSNP
rs954604941	195	dbSNP
rs1192900141	221	dbSNP
rs1030192035	226	dbSNP
rs1396951555	228	dbSNP
rs1009390020	232	dbSNP
rs551863145	233	dbSNP
rs1368972839	239	dbSNP
rs929867898	241	dbSNP
rs1411963714	243	dbSNP
rs956333080	245	dbSNP
rs1434931266	249	dbSNP
rs1306365375	255	dbSNP
rs1371013586	262	dbSNP
rs1227041677	266	dbSNP
rs1031731893	268	dbSNP
rs555985271	285	dbSNP
rs1385601514	297	dbSNP
rs539543102	314	dbSNP
rs755453959	323	dbSNP
rs1449710676	327	dbSNP
rs1215482301	332	dbSNP
rs919875360	337	dbSNP
rs1444222136	339	dbSNP
rs1454727959	343	dbSNP
rs1188041736	358	dbSNP
rs1388445317	363	dbSNP
rs1476501500	369	dbSNP
rs750098782	369	dbSNP
rs1390463468	376	dbSNP
rs184155803	395	dbSNP
rs1328450757	396	dbSNP
rs1395879257	403	dbSNP
rs1044790376	406	dbSNP
rs1195428025	415	dbSNP
rs1013145456	427	dbSNP
rs151224893	433	dbSNP
rs765024576	435	dbSNP
rs1227686012	437	dbSNP
rs1283304480	452	dbSNP
rs1353913668	455	dbSNP
rs192679400	455	dbSNP
rs1215349775	460	dbSNP
rs1273694777	463	dbSNP
rs1017959842	465	dbSNP
rs1464362802	466	dbSNP
rs1206800930	479	dbSNP
rs1429162860	480	dbSNP
rs896059642	490	dbSNP
rs986507752	517	dbSNP
rs1368132996	546	dbSNP
rs1474400801	550	dbSNP
rs955147946	552	dbSNP
rs1167584972	559	dbSNP
rs761386773	561	dbSNP
rs1203874174	565	dbSNP
rs199733207	567	dbSNP
rs201417957	569	dbSNP
rs200964012	571	dbSNP
rs3760153	571	dbSNP
rs1009767169	576	dbSNP
rs1386486088	578	dbSNP
rs892692895	579	dbSNP
rs200352802	580	dbSNP
rs1172368046	582	dbSNP
rs1234792813	582	dbSNP
rs1338370584	582	dbSNP
rs3834564	582	dbSNP
rs397840955	582	dbSNP
rs398058699	582	dbSNP
rs763599921	582	dbSNP
rs1205820741	586	dbSNP
rs1001540019	594	dbSNP
rs1037422988	596	dbSNP
rs1255680678	596	dbSNP
rs941766206	596	dbSNP
rs1258635408	601	dbSNP
rs1356841337	605	dbSNP
rs1472506688	608	dbSNP
rs748425756	614	dbSNP
rs561660234	616	dbSNP
rs910255894	617	dbSNP
rs1366071987	624	dbSNP
rs985772962	625	dbSNP
rs905159908	628	dbSNP
rs374374893	630	dbSNP
rs1325329519	636	dbSNP
rs933251042	637	dbSNP
rs1416232247	641	dbSNP
rs1045082188	646	dbSNP
rs1293400276	647	dbSNP
rs35705041	648	dbSNP
rs546457983	650	dbSNP
rs923154008	651	dbSNP
rs1407786043	656	dbSNP
rs1309002297	666	dbSNP
rs987991398	678	dbSNP
rs956526145	692	dbSNP
rs1009161216	710	dbSNP
rs1302327024	716	dbSNP
rs1032180566	717	dbSNP
rs1213285928	717	dbSNP
rs1281310370	722	dbSNP
rs1422449569	730	dbSNP
rs796899187	734	dbSNP
rs528290298	744	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.