>DARS2|NM_018122|3'UTR
   1 ATCATGCATACCATGCAGAAAGTTGAGCTTTTAGGTTTTGTCCTCTTTGCTTCCCCAAGGCTAAAGTCAGATCTAGAGTT
  81 CTGCCACAGGTCTAACAATCAAGTCTTTAGATGGAAGGAATCCAGGCAACATTCTTCACCACAACGAAGAAACAGATAAA
 161 AGATACCCAATTTTGACTTGATTTCATGCATCATTTGGATTTTTTTTGGTTAGGACTTTTTTTGAAGTTCCTTTTTACTT
 241 AGGTGTGAAAGATGGTTCTTTGTTGAAATAATATAGTGGTTTAGTGTTTTCAAATCATGTTTCTCATACCCAGATAGTAG
 321 ATTATTCACTTAGGACAGAGGTAATCAAATTATGTGTGAAATGTAGGAAAATGCTTGCCCCTGTAAACTAGTGAGTTGAT
 401 GGAGCATTTGCTTCATCATCCTCATCAAGAGAATCATATAAATTAAGCTTTATAATGACATTTCAACCATCAACATAATA
 481 TAGTGAGGAGTAGCATAATATTTTTTAATAATGCAGAAAACATCACTGAAATGAGAGTCACAAATTTTTCTTCAGTGTTT
 561 CAGCCTGAGTAAGTTACATAAACCTCGCTTAGCCTCCCTTCCTGCTAATGTGTAAAATACATACTTGCCCTGGCTACCTC
 641 ACCGGGCTGTTATTGCTGGAATCAGAGGAGATAACATATATGGAAGATAAAGTGAATAAAAGTACTTTGAAAAACTATAA
 721 AGCATTCCACAAATATGAGATGATGGTATTATCCATCCATAAATAGGTAGATATATCTCTATTTTATAGTTTCAGATTAA
 801 ACAAAACTGATATCAATAGTAAAAGTCATTTTACTTATC

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ucUCCGUC--CAAGGACC-UAGUa 5' :||| | || |||| |||| Target 5' ccGGGCTGTTATTGCTGGAATCAg 3'	642 - 665	125.00	-12.50
2	miRNA 3' ucucCGUCCAAGGACCUAGUa 5' |:: ||| |||| || Target 5' actaGTGAGTTGATGGAGCAt 3'	387 - 407	121.00	-9.70
3	miRNA 3' ucuccguccAAGGACCUAGUa 5' ||| || |||| Target 5' tgacttgatTTCATGCATCAt 3'	174 - 194	120.00	-5.50

Mutant ID	Mutant Position	Mutant Source
873686	153	ClinVar
293831	169	ClinVar
293832	211	ClinVar
293833	432	ClinVar
873687	588	ClinVar
293834	643	ClinVar
873688	645	ClinVar
293835	654	ClinVar
COSN30110940	47	COSMIC
COSN30485735	76	COSMIC
COSN26027493	81	COSMIC
COSN31565862	81	COSMIC
COSN30510893	83	COSMIC
COSN31557921	106	COSMIC
COSN13493866	128	COSMIC
COSN26434579	147	COSMIC
COSN31563997	185	COSMIC
COSN18714183	203	COSMIC
COSN22609339	503	COSMIC
COSN19460399	587	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs759030417	6	dbSNP
rs1249302028	7	dbSNP
rs1482222045	15	dbSNP
rs778418949	17	dbSNP
rs1412846820	24	dbSNP
rs749994971	25	dbSNP
rs755664477	34	dbSNP
rs776183062	35	dbSNP
rs200858499	42	dbSNP
rs1250144800	45	dbSNP
rs1000780590	55	dbSNP
rs1186693143	56	dbSNP
rs908756396	59	dbSNP
rs944313360	66	dbSNP
rs546699392	90	dbSNP
rs145246788	99	dbSNP
rs1289688488	108	dbSNP
rs184458663	110	dbSNP
rs1340958985	126	dbSNP
rs748208338	145	dbSNP
rs1019884556	146	dbSNP
rs555583349	153	dbSNP
rs550840346	169	dbSNP
rs972902827	172	dbSNP
rs1025226694	180	dbSNP
rs952422471	187	dbSNP
rs1392206513	198	dbSNP
rs1166986029	200	dbSNP
rs1211523802	200	dbSNP
rs1448909344	202	dbSNP
rs1043109952	206	dbSNP
rs9425758	211	dbSNP
rs529812512	213	dbSNP
rs998790940	217	dbSNP
rs760958796	222	dbSNP
rs1205593670	229	dbSNP
rs959907335	231	dbSNP
rs1475863617	232	dbSNP
rs1484252696	237	dbSNP
rs1271990511	238	dbSNP
rs1169806879	243	dbSNP
rs1227260821	245	dbSNP
rs771259782	262	dbSNP
rs1347940155	271	dbSNP
rs537759436	279	dbSNP
rs990972782	288	dbSNP
rs557695965	291	dbSNP
rs1013500521	295	dbSNP
rs1314050216	307	dbSNP
rs12084787	314	dbSNP
rs1298704938	315	dbSNP
rs1377760616	316	dbSNP
rs1368522500	317	dbSNP
rs918085957	319	dbSNP
rs1025334902	330	dbSNP
rs1395762454	334	dbSNP
rs969233837	335	dbSNP
rs1178311885	336	dbSNP
rs1318054446	339	dbSNP
rs1250122648	355	dbSNP
rs777034042	367	dbSNP
rs1485831061	378	dbSNP
rs981024604	381	dbSNP
rs1257410846	389	dbSNP
rs1026709899	391	dbSNP
rs760039025	394	dbSNP
rs765636264	397	dbSNP
rs982411647	401	dbSNP
rs1348384065	408	dbSNP
rs908201992	409	dbSNP
rs1272657850	412	dbSNP
rs577636691	412	dbSNP
rs1346551754	415	dbSNP
rs1376230689	418	dbSNP
rs1234344319	421	dbSNP
rs1358693927	422	dbSNP
rs1160436364	425	dbSNP
rs886045592	432	dbSNP
rs1473889738	445	dbSNP
rs1181823768	447	dbSNP
rs1475754206	448	dbSNP
rs936684812	457	dbSNP
rs1282447334	485	dbSNP
rs1482632875	490	dbSNP
rs1053684745	492	dbSNP
rs943743175	495	dbSNP
rs889687541	496	dbSNP
rs1210511469	497	dbSNP
rs1326906347	503	dbSNP
rs1267443896	511	dbSNP
rs1233622969	525	dbSNP
rs1007233612	536	dbSNP
rs372838932	538	dbSNP
rs901005378	556	dbSNP
rs1204404801	565	dbSNP
rs765746998	567	dbSNP
rs921541431	579	dbSNP
rs1394557071	587	dbSNP
rs567773377	588	dbSNP
rs1025384256	608	dbSNP
rs1233384056	610	dbSNP
rs1289585655	613	dbSNP
rs1043225083	625	dbSNP
rs189330031	638	dbSNP
rs1387032106	640	dbSNP
rs140743566	643	dbSNP
rs574117039	644	dbSNP
rs542846978	645	dbSNP
rs934737223	647	dbSNP
rs1422952222	650	dbSNP
rs1261999109	652	dbSNP
rs886045593	654	dbSNP
rs1053170457	658	dbSNP
rs375732273	662	dbSNP
rs1453909644	671	dbSNP
rs895798339	673	dbSNP
rs1358171699	681	dbSNP
rs1034441714	695	dbSNP
rs959614964	703	dbSNP
rs1174311706	704	dbSNP
rs1263513457	710	dbSNP
rs1242872120	711	dbSNP
rs1063282	719	dbSNP
rs991480699	721	dbSNP
rs1321272782	725	dbSNP
rs1298621755	727	dbSNP
rs1437323064	741	dbSNP
rs918088729	742	dbSNP
rs971337061	745	dbSNP
rs1320451193	746	dbSNP
rs1014697782	747	dbSNP
rs978157865	753	dbSNP
rs1393323580	754	dbSNP
rs1046279739	772	dbSNP
rs1373240299	774	dbSNP
rs924045643	775	dbSNP
rs905125278	782	dbSNP
rs1447099006	792	dbSNP
rs1389065737	799	dbSNP
rs936757075	802	dbSNP
rs1386148921	803	dbSNP
rs1265184609	808	dbSNP
rs546840059	811	dbSNP
rs1321211218	815	dbSNP
rs182319107	818	dbSNP
rs1230956693	825	dbSNP
rs1340127172	830	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.