>ZNF446|NM_017908|3'UTR
   1 GCAGCCAGACAGCACAGTCCCTCGGGGCCTCGGTGTTCTCGGGGCCTGGATACAGCCTCTGGGGCACCAGCAGAAGACTC
  81 TGGAGGCAGCAGGGGATGCCAGAGTGAACAAGGGGTCCCAAGCCAGTTCCCTGCCCCTGGTCTGGTCTCCCCCAAAAGAC
 161 CTGGGTGCAAGGAAAAGGAGCTGCTCTCTCTCTTCTTGCCCCTGCCTCCTAGAGGGAGGTCTGGGTTCCCTTCTATGGCT
 241 GACCAGTGCCTGTGGGGTGACTGCCAAGCACCAGGCTCCCTCCCTCCCTGTGACATGGCCTGGGCTGACAACACTCCCTC
 321 TCCTGGGACCTCCTTGCCTCAGGTGGGTGTTCAAAAACTGTGCCTTCCCACTCGTCTGTGCAGAGGCTGGGCCTGAGGTC
 401 TCAGTGTGGAGAGCAGCAGAAGACCCAGGAAAGCACAGTTGGCTTCCGTTTCTCCTGCTCCCTGTGTGTGTTAGAATTTT
 481 AACATAAATTCCACTTTCATAATATGGAAAAAAAAAAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gaCAAGAGAAGGAAACCGGAac 5' |||| || || |||:|| Target 5' caGTTCCCTGCCCCTGGTCTgg 3'	124 - 145	132.00	-15.60
2	miRNA 3' gacaAGAGAAGGA-A----ACCGGAac 5' || || ||| | |||||| Target 5' tcccTCCCTCCCTGTGACATGGCCTgg 3'	277 - 303	132.00	-11.90
3	miRNA 3' gaCAAGAGAAGGAAACCGGaac 5' |||| ||| || ||||: Target 5' ggGTTCCCTT-CTATGGCTgac 3'	223 - 243	115.00	-12.52

Mutant ID	Mutant Position	Mutant Source
COSN30616461	16	COSMIC
COSN30447031	22	COSMIC
COSN13840716	24	COSMIC
COSN13840719	25	COSMIC
COSN30482881	26	COSMIC
COSN16662433	43	COSMIC
COSN31503516	43	COSMIC
COSN30744676	48	COSMIC
COSN30494408	56	COSMIC
COSN30502094	61	COSMIC
COSN30157180	68	COSMIC
COSN22874361	72	COSMIC
COSN30494396	82	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs912016304	2	dbSNP
rs1471033003	3	dbSNP
rs1176467417	5	dbSNP
rs374472449	9	dbSNP
rs1231955659	11	dbSNP
rs760735773	12	dbSNP
rs765210220	17	dbSNP
rs752576309	20	dbSNP
rs1405340828	21	dbSNP
rs201374214	24	dbSNP
rs929429692	25	dbSNP
rs777508907	27	dbSNP
rs200530035	28	dbSNP
rs756908072	32	dbSNP
rs780745517	33	dbSNP
rs1209407193	37	dbSNP
rs745376408	40	dbSNP
rs536773451	41	dbSNP
rs779722627	42	dbSNP
rs749745248	44	dbSNP
rs1418250604	45	dbSNP
rs372929896	46	dbSNP
rs1439422293	48	dbSNP
rs1449734083	53	dbSNP
rs756661430	55	dbSNP
rs895043781	58	dbSNP
rs1372271851	65	dbSNP
rs1012522739	68	dbSNP
rs1024754860	72	dbSNP
rs906330063	75	dbSNP
rs140945018	76	dbSNP
rs1013825435	78	dbSNP
rs1014590871	83	dbSNP
rs1473231169	92	dbSNP
rs762271308	94	dbSNP
rs902239010	95	dbSNP
rs1460375178	98	dbSNP
rs1253249405	113	dbSNP
rs1205056663	120	dbSNP
rs3752112	128	dbSNP
rs1368815238	129	dbSNP
rs1031979545	135	dbSNP
rs1388882760	137	dbSNP
rs1356556093	138	dbSNP
rs953692945	139	dbSNP
rs144592094	140	dbSNP
rs1230856472	160	dbSNP
rs575148786	161	dbSNP
rs987679405	169	dbSNP
rs966310447	184	dbSNP
rs976637181	185	dbSNP
rs1325237804	187	dbSNP
rs1406187173	188	dbSNP
rs1393936078	189	dbSNP
rs912068748	191	dbSNP
rs543880636	193	dbSNP
rs1163046687	194	dbSNP
rs577510541	200	dbSNP
rs977516912	203	dbSNP
rs926036155	204	dbSNP
rs936022913	226	dbSNP
rs1248846625	230	dbSNP
rs1319364682	230	dbSNP
rs1222703248	236	dbSNP
rs1468647694	240	dbSNP
rs1055784969	241	dbSNP
rs984901439	244	dbSNP
rs895088680	248	dbSNP
rs1330666979	251	dbSNP
rs938005908	254	dbSNP
rs1219357854	261	dbSNP
rs1223179397	266	dbSNP
rs751681599	267	dbSNP
rs755202983	273	dbSNP
rs1324193289	276	dbSNP
rs979583176	283	dbSNP
rs1042587494	285	dbSNP
rs1158410719	288	dbSNP
rs1211430983	289	dbSNP
rs560583240	297	dbSNP
rs147643704	299	dbSNP
rs1454155951	304	dbSNP
rs1251501641	306	dbSNP
rs546334844	309	dbSNP
rs1194619344	312	dbSNP
rs906382729	316	dbSNP
rs1000987270	317	dbSNP
rs1004642912	318	dbSNP
rs1474259311	319	dbSNP
rs1314607469	323	dbSNP
rs1164774296	326	dbSNP
rs1280721783	328	dbSNP
rs1350978484	331	dbSNP
rs1219713369	342	dbSNP
rs1459843039	348	dbSNP
rs199772469	356	dbSNP
rs528684332	363	dbSNP
rs1437571383	371	dbSNP
rs534901003	374	dbSNP
rs77197580	375	dbSNP
rs1360954842	377	dbSNP
rs531272668	378	dbSNP
rs752816925	379	dbSNP
rs1177488131	381	dbSNP
rs1434609912	383	dbSNP
rs1393692980	387	dbSNP
rs1278429638	392	dbSNP
rs756098590	396	dbSNP
rs987731780	404	dbSNP
rs1019180149	406	dbSNP
rs188578028	407	dbSNP
rs562268177	410	dbSNP
rs1262073541	415	dbSNP
rs1185557129	420	dbSNP
rs1484634356	424	dbSNP
rs1226124504	429	dbSNP
rs142310880	440	dbSNP
rs926058426	443	dbSNP
rs376381316	448	dbSNP
rs1230262468	449	dbSNP
rs1322280720	450	dbSNP
rs1307860613	455	dbSNP
rs7245854	461	dbSNP
rs553514015	463	dbSNP
rs556772985	463	dbSNP
rs985397769	463	dbSNP
rs566624703	464	dbSNP
rs146145193	471	dbSNP
rs917931153	473	dbSNP
rs950018735	474	dbSNP
rs1046309782	475	dbSNP
rs114711961	477	dbSNP
rs1181364886	478	dbSNP
rs1426322692	484	dbSNP
rs940559009	490	dbSNP
rs1414562548	491	dbSNP
rs1415355558	493	dbSNP
rs1036192718	494	dbSNP
rs778560919	498	dbSNP
rs1485309233	499	dbSNP
rs1207198805	502	dbSNP
rs898951227	504	dbSNP
rs1157513792	505	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.