ID	Duplex structure	Position	Score	MFE
1	miRNA 3' acaauuaCG-AUUAUACAUCCUc 5' || | | |||||||| Target 5' gtcctcgGCATCACATGTAGGAg 3'	245 - 267	151.00	-13.20
2	miRNA 3' acaauuacgAUUAUACAUCCuc 5' | :| |||:|| Target 5' atcgcagaaTTGTTTGTGGGca 3'	559 - 580	109.00	-6.50
3	miRNA 3' acaauuacgaUUAUACAUCcuc 5' |||||||:| Target 5' gttcaaaaaaAATATGTGGcct 3'	271 - 292	104.00	-6.52

Mutant ID	Mutant Position	Mutant Source
COSN30522068	3	COSMIC
COSN31599073	14	COSMIC
COSN30499090	22	COSMIC
COSN30508329	51	COSMIC
COSN508526	86	COSMIC
COSN30164176	140	COSMIC
COSN20074539	164	COSMIC
COSN9861769	165	COSMIC
COSN23998529	222	COSMIC
COSN1794677	226	COSMIC
COSN31603356	343	COSMIC
COSN31597320	402	COSMIC
COSN23522340	403	COSMIC
COSN7344859	447	COSMIC
COSN31576957	465	COSMIC
COSN6194531	478	COSMIC
COSN8607609	482	COSMIC
COSN24299075	510	COSMIC
COSN31480976	519	COSMIC
COSN31595460	563	COSMIC
COSN16506088	689	COSMIC
COSN23730625	1154	COSMIC
COSN30341303	1466	COSMIC
COSN9065887	1780	COSMIC
COSN20097213	2119	COSMIC
COSN23189943	2329	COSMIC
COSN21973508	2370	COSMIC
COSN22157454	2464	COSMIC
COSN17121747	2502	COSMIC
COSN22643093	2546	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs780069606	8	dbSNP
rs1301477508	9	dbSNP
rs1420352315	11	dbSNP
rs767332988	12	dbSNP
rs1397047227	17	dbSNP
rs1327406409	18	dbSNP
rs759368176	22	dbSNP
rs371348248	26	dbSNP
rs1328362802	32	dbSNP
rs576790834	36	dbSNP
rs1390239481	41	dbSNP
rs761947879	50	dbSNP
rs951739589	53	dbSNP
rs1340831078	61	dbSNP
rs1027166575	79	dbSNP
rs1260498093	96	dbSNP
rs758644671	104	dbSNP
rs995711654	110	dbSNP
rs1212331212	121	dbSNP
rs558904138	125	dbSNP
rs897327867	127	dbSNP
rs1215244564	143	dbSNP
rs1257338471	144	dbSNP
rs1335453273	156	dbSNP
rs1037714155	157	dbSNP
rs997954141	164	dbSNP
rs550709063	165	dbSNP
rs779079603	193	dbSNP
rs1242959055	196	dbSNP
rs1476432047	197	dbSNP
rs1008467746	198	dbSNP
rs1217299892	199	dbSNP
rs914887201	211	dbSNP
rs532277358	226	dbSNP
rs757710377	227	dbSNP
rs1386611720	232	dbSNP
rs571034597	236	dbSNP
rs1318531762	243	dbSNP
rs1270707695	251	dbSNP
rs1401689860	260	dbSNP
rs1277029960	267	dbSNP
rs891133745	271	dbSNP
rs1335318429	273	dbSNP
rs1049710648	274	dbSNP
rs1235090181	283	dbSNP
rs1338328354	283	dbSNP
rs927501139	285	dbSNP
rs932745514	288	dbSNP
rs1355342852	296	dbSNP
rs754136015	303	dbSNP
rs552540243	304	dbSNP
rs971543387	307	dbSNP
rs1262607565	311	dbSNP
rs1054465568	318	dbSNP
rs1190670691	319	dbSNP
rs917456922	325	dbSNP
rs1415451142	332	dbSNP
rs200075913	343	dbSNP
rs756507083	344	dbSNP
rs187090673	353	dbSNP
rs1386606132	354	dbSNP
rs1398596531	366	dbSNP
rs981776350	369	dbSNP
rs961445851	377	dbSNP
rs1355562588	379	dbSNP
rs949972541	382	dbSNP
rs1173269001	390	dbSNP
rs1477162253	401	dbSNP
rs1423510657	402	dbSNP
rs1192352837	403	dbSNP
rs142859776	405	dbSNP
rs767086243	406	dbSNP
rs991121941	408	dbSNP
rs530054999	410	dbSNP
rs951686572	411	dbSNP
rs1258541379	415	dbSNP
rs1220221397	423	dbSNP
rs1285640019	426	dbSNP
rs954066392	437	dbSNP
rs1277448980	438	dbSNP
rs1027447208	439	dbSNP
rs1423757289	455	dbSNP
rs558616838	460	dbSNP
rs1365941978	467	dbSNP
rs1468237391	473	dbSNP
rs971790418	479	dbSNP
rs538906352	482	dbSNP
rs562578536	483	dbSNP
rs1447661458	494	dbSNP
rs901004074	494	dbSNP
rs1042262345	498	dbSNP
rs1015734286	512	dbSNP
rs1333747854	517	dbSNP
rs1333851819	531	dbSNP
rs1008914985	541	dbSNP
rs1053958701	542	dbSNP
rs1348938470	543	dbSNP
rs544278699	544	dbSNP
rs891342854	549	dbSNP
rs926305486	561	dbSNP
rs774184710	562	dbSNP
rs1196906568	569	dbSNP
rs1253341258	570	dbSNP
rs576972183	574	dbSNP
rs1044661461	583	dbSNP
rs182585056	600	dbSNP
rs1028985459	603	dbSNP
rs996842048	606	dbSNP
rs950320384	626	dbSNP
rs1173298238	632	dbSNP
rs1166226660	633	dbSNP
rs917509324	634	dbSNP
rs1423906502	643	dbSNP
rs1394327936	654	dbSNP
rs893120183	655	dbSNP
rs1360740122	656	dbSNP
rs1371909104	661	dbSNP
rs1443420257	666	dbSNP
rs1299220636	667	dbSNP
rs116007755	668	dbSNP
rs1228292619	672	dbSNP
rs940198529	676	dbSNP
rs573044687	679	dbSNP
rs1179600511	681	dbSNP
rs761535240	689	dbSNP
rs1472293024	693	dbSNP
rs1189081795	695	dbSNP
rs1266284465	706	dbSNP
rs934715880	707	dbSNP
rs903031462	712	dbSNP
rs1171972171	713	dbSNP
rs1176515936	713	dbSNP
rs909946241	713	dbSNP
rs1464850089	716	dbSNP
rs1421316488	718	dbSNP
rs762822640	721	dbSNP
rs1165323527	722	dbSNP
rs950018974	728	dbSNP
rs189026966	744	dbSNP
rs1367243052	747	dbSNP
rs769802549	752	dbSNP
rs1297822502	755	dbSNP
rs1339038885	762	dbSNP
rs1218593767	763	dbSNP
rs1274408689	766	dbSNP
rs185916563	769	dbSNP
rs1219914872	772	dbSNP
rs1222140749	774	dbSNP
rs1264477692	776	dbSNP
rs1485996782	788	dbSNP
rs1187690520	793	dbSNP
rs930320607	796	dbSNP
rs1323429005	808	dbSNP
rs1310742272	811	dbSNP
rs776531896	813	dbSNP
rs971821594	814	dbSNP
rs961797868	816	dbSNP
rs866159076	823	dbSNP
rs1016184913	824	dbSNP
rs987021213	839	dbSNP
rs1163826924	845	dbSNP
rs893648899	861	dbSNP
rs1454532272	863	dbSNP
rs1300062540	880	dbSNP
rs1358683532	887	dbSNP
rs181676446	889	dbSNP
rs1399524592	897	dbSNP
rs1032072865	903	dbSNP
rs1001988654	905	dbSNP
rs1312461105	916	dbSNP
rs776917212	916	dbSNP
rs955725008	919	dbSNP
rs949042008	922	dbSNP
rs1283499024	925	dbSNP
rs1028555576	933	dbSNP
rs1211060469	941	dbSNP
rs997039931	944	dbSNP
rs1259511998	953	dbSNP
rs557021934	960	dbSNP
rs1037710595	971	dbSNP
rs1181027927	978	dbSNP
rs1348629527	983	dbSNP
rs538732062	998	dbSNP
rs571404699	1005	dbSNP
rs1420710676	1006	dbSNP
rs1162143593	1010	dbSNP
rs1378774774	1010	dbSNP
rs940186942	1013	dbSNP
rs1313570911	1015	dbSNP
rs1361335516	1018	dbSNP
rs1446496807	1022	dbSNP
rs910067850	1049	dbSNP
rs984212186	1064	dbSNP
rs1242817374	1069	dbSNP
rs893149869	1070	dbSNP
rs1404207921	1071	dbSNP
rs1380558992	1073	dbSNP
rs1032948767	1074	dbSNP
rs1180071476	1078	dbSNP
rs759874721	1079	dbSNP
rs1352600210	1090	dbSNP
rs1234298931	1092	dbSNP
rs552693598	1095	dbSNP
rs999345468	1096	dbSNP
rs1209309591	1102	dbSNP
rs1233432181	1108	dbSNP
rs772182677	1109	dbSNP
rs1046227341	1111	dbSNP
rs527903328	1118	dbSNP
rs787174	1119	dbSNP
rs965361638	1127	dbSNP
rs201238279	1128	dbSNP
rs1354445975	1136	dbSNP
rs141682011	1140	dbSNP
rs776939245	1150	dbSNP
rs1020845732	1151	dbSNP
rs920277032	1152	dbSNP
rs1035991200	1171	dbSNP
rs76821106	1176	dbSNP
rs1353258593	1179	dbSNP
rs1329742901	1183	dbSNP
rs957889044	1196	dbSNP
rs1441208673	1211	dbSNP
rs1276300839	1213	dbSNP
rs1342227829	1216	dbSNP
rs1218203945	1217	dbSNP
rs1273616070	1218	dbSNP
rs911684374	1241	dbSNP
rs987606851	1246	dbSNP
rs1302477247	1248	dbSNP
rs1196451401	1252	dbSNP
rs1388861741	1254	dbSNP
rs1237373492	1258	dbSNP
rs1032630384	1259	dbSNP
rs1194477719	1272	dbSNP
rs1366161416	1281	dbSNP
rs1248713198	1291	dbSNP
rs1190741044	1298	dbSNP
rs757361629	1299	dbSNP
rs1002041083	1303	dbSNP
rs921401479	1305	dbSNP
rs369303419	1308	dbSNP
rs975654241	1310	dbSNP
rs904910547	1313	dbSNP
rs1160090934	1322	dbSNP
rs957577267	1329	dbSNP
rs1417543305	1331	dbSNP
rs1325113957	1332	dbSNP
rs1013235920	1334	dbSNP
rs1435058446	1335	dbSNP
rs562540385	1337	dbSNP
rs749664519	1344	dbSNP
rs1270279220	1351	dbSNP
rs1342247982	1358	dbSNP
rs897510065	1366	dbSNP
rs1037275250	1368	dbSNP
rs1176577036	1375	dbSNP
rs1335198410	1376	dbSNP
rs940298332	1382	dbSNP
rs1265212938	1391	dbSNP
rs1190497527	1394	dbSNP
rs1032979636	1402	dbSNP
rs544241476	1405	dbSNP
rs1265520990	1406	dbSNP
rs1198167887	1408	dbSNP
rs1242800027	1413	dbSNP
rs919915963	1416	dbSNP
rs967782489	1419	dbSNP
rs1423633661	1420	dbSNP
rs532431049	1423	dbSNP
rs1256774625	1429	dbSNP
rs1165379492	1434	dbSNP
rs565236949	1441	dbSNP
rs147814870	1443	dbSNP
rs894327927	1447	dbSNP
rs572968700	1448	dbSNP
rs1342933746	1449	dbSNP
rs1299553503	1452	dbSNP
rs1277480437	1457	dbSNP
rs1238483056	1467	dbSNP
rs1397554831	1473	dbSNP
rs1246638973	1474	dbSNP
rs1055613296	1478	dbSNP
rs1354451998	1485	dbSNP
rs913920105	1491	dbSNP
rs3731956	1493	dbSNP
rs1467405960	1494	dbSNP
rs542918972	1524	dbSNP
rs1263032142	1525	dbSNP
rs375392801	1527	dbSNP
rs899048689	1528	dbSNP
rs958155511	1529	dbSNP
rs1190006661	1536	dbSNP
rs1478142886	1537	dbSNP
rs925232881	1541	dbSNP
rs1158752286	1544	dbSNP
rs1425653539	1546	dbSNP
rs1417304632	1549	dbSNP
rs1036278364	1554	dbSNP
rs969230030	1561	dbSNP
rs1487979531	1575	dbSNP
rs140560332	1576	dbSNP
rs556985114	1585	dbSNP
rs771449122	1595	dbSNP
rs961727003	1608	dbSNP
rs1051533744	1609	dbSNP
rs1310250386	1610	dbSNP
rs1356145416	1610	dbSNP
rs1015041181	1614	dbSNP
rs538643145	1618	dbSNP
rs1005885977	1631	dbSNP
rs1202676802	1635	dbSNP
rs547981265	1645	dbSNP
rs761028876	1654	dbSNP
rs1276815043	1656	dbSNP
rs1216281317	1662	dbSNP
rs1179718927	1668	dbSNP
rs1048638739	1669	dbSNP
rs1325296468	1674	dbSNP
rs996946340	1682	dbSNP
rs552811210	1684	dbSNP
rs1467172106	1690	dbSNP
rs1041095690	1695	dbSNP
rs1312997803	1698	dbSNP
rs1401483398	1710	dbSNP
rs944159042	1711	dbSNP
rs1397487720	1712	dbSNP
rs921433896	1719	dbSNP
rs975517267	1720	dbSNP
rs372340656	1724	dbSNP
rs1444875387	1729	dbSNP
rs957529807	1739	dbSNP
rs534751983	1740	dbSNP
rs1254751459	1742	dbSNP
rs1344938548	1757	dbSNP
rs1335891679	1759	dbSNP
rs980705917	1760	dbSNP
rs926248629	1762	dbSNP
rs1456137083	1765	dbSNP
rs1177592556	1770	dbSNP
rs1267695650	1771	dbSNP
rs1434384636	1783	dbSNP
rs969195091	1784	dbSNP
rs368706787	1792	dbSNP
rs764200862	1792	dbSNP
rs753306305	1799	dbSNP
rs1172495655	1807	dbSNP
rs1397817159	1808	dbSNP
rs1464939975	1816	dbSNP
rs1330926476	1817	dbSNP
rs967435180	1821	dbSNP
rs565655360	1822	dbSNP
rs1475132380	1832	dbSNP
rs1014686069	1839	dbSNP
rs1014360205	1842	dbSNP
rs549905750	1845	dbSNP
rs1316443471	1848	dbSNP
rs1189700729	1871	dbSNP
rs1006272738	1880	dbSNP
rs754600525	1884	dbSNP
rs1265607000	1888	dbSNP
rs548811698	1890	dbSNP
rs1207513501	1903	dbSNP
rs751057941	1908	dbSNP
rs1477892129	1909	dbSNP
rs1195708863	1910	dbSNP
rs951764802	1914	dbSNP
rs1477363997	1922	dbSNP
rs766060066	1923	dbSNP
rs1027176153	1924	dbSNP
rs1350616115	1933	dbSNP
rs1459667116	1949	dbSNP
rs1014870647	1952	dbSNP
rs1390078379	1953	dbSNP
rs544607145	1960	dbSNP
rs1459334060	1961	dbSNP
rs1280634723	1966	dbSNP
rs1005178122	1975	dbSNP
rs1218335843	1977	dbSNP
rs890144543	1979	dbSNP
rs762475749	1980	dbSNP
rs1008402427	1987	dbSNP
rs1488326769	1989	dbSNP
rs1218231911	1990	dbSNP
rs1357663407	2000	dbSNP
rs1487923461	2009	dbSNP
rs144150306	2010	dbSNP
rs368288826	2014	dbSNP
rs1421886363	2015	dbSNP
rs1338380930	2026	dbSNP
rs900292863	2027	dbSNP
rs569219566	2053	dbSNP
rs77195936	2054	dbSNP
rs116547682	2055	dbSNP
rs565346192	2062	dbSNP
rs926111954	2063	dbSNP
rs1430674798	2065	dbSNP
rs1303986478	2066	dbSNP
rs1044993826	2067	dbSNP
rs1394717894	2070	dbSNP
rs947993780	2075	dbSNP
rs1409375056	2076	dbSNP
rs977717041	2082	dbSNP
rs374352729	2084	dbSNP
rs946268853	2085	dbSNP
rs546763092	2086	dbSNP
rs1210700636	2089	dbSNP
rs1239177385	2095	dbSNP
rs1482146214	2097	dbSNP
rs1181081826	2106	dbSNP
rs188551902	2107	dbSNP
rs1242693099	2110	dbSNP
rs1165112599	2111	dbSNP
rs1456420935	2112	dbSNP
rs1384869353	2113	dbSNP
rs1179427531	2115	dbSNP
rs62167034	2117	dbSNP
rs1441933789	2118	dbSNP
rs917845154	2123	dbSNP
rs1177414326	2134	dbSNP
rs1336487805	2134	dbSNP
rs1378531012	2134	dbSNP
rs1400237735	2134	dbSNP
rs61418485	2134	dbSNP
rs796916353	2134	dbSNP
rs528612503	2139	dbSNP
rs992369366	2148	dbSNP
rs940549684	2153	dbSNP
rs1375477109	2156	dbSNP
rs547411303	2157	dbSNP
rs1219365702	2158	dbSNP
rs1280575812	2171	dbSNP
rs1178391966	2173	dbSNP
rs1452738964	2174	dbSNP
rs1258495342	2181	dbSNP
rs958687908	2182	dbSNP
rs1034457426	2187	dbSNP
rs371527529	2192	dbSNP
rs907594772	2193	dbSNP
rs149967294	2197	dbSNP
rs963219347	2198	dbSNP
rs1015145861	2203	dbSNP
rs1191856254	2211	dbSNP
rs1427784264	2213	dbSNP
rs1004802357	2219	dbSNP
rs1413296531	2223	dbSNP
rs1240339845	2229	dbSNP
rs1176099322	2234	dbSNP
rs1355404428	2235	dbSNP
rs951702296	2236	dbSNP
rs1353573673	2251	dbSNP
rs890334473	2265	dbSNP
rs575567398	2269	dbSNP
rs1436491743	2276	dbSNP
rs773346029	2281	dbSNP
rs1276138157	2284	dbSNP
rs1030238723	2288	dbSNP
rs563599569	2290	dbSNP
rs995840141	2291	dbSNP
rs974383209	2296	dbSNP
rs772525411	2299	dbSNP
rs1331640894	2304	dbSNP
rs528468284	2305	dbSNP
rs1019836632	2311	dbSNP
rs544988576	2312	dbSNP
rs1053499006	2313	dbSNP
rs1477109179	2315	dbSNP
rs764993189	2318	dbSNP
rs185031389	2319	dbSNP
rs1478974339	2321	dbSNP
rs1042239247	2322	dbSNP
rs946328435	2324	dbSNP
rs917524522	2325	dbSNP
rs564374801	2328	dbSNP
rs1347582784	2329	dbSNP
rs552963435	2332	dbSNP
rs903850518	2343	dbSNP
rs1045050948	2345	dbSNP
rs1379907025	2348	dbSNP
rs139030565	2353	dbSNP
rs573721192	2356	dbSNP
rs192234571	2357	dbSNP
rs1216688324	2360	dbSNP
rs536452315	2361	dbSNP
rs189644742	2362	dbSNP
rs1264443582	2370	dbSNP
rs1223022707	2372	dbSNP
rs1191896582	2379	dbSNP
rs1372846519	2384	dbSNP
rs530918729	2386	dbSNP
rs1276549058	2387	dbSNP
rs1158725881	2389	dbSNP
rs1362333225	2390	dbSNP
rs1398093269	2393	dbSNP
rs940501454	2396	dbSNP
rs907730349	2405	dbSNP
rs550877647	2406	dbSNP
rs1030689705	2407	dbSNP
rs1357559340	2408	dbSNP
rs996038024	2409	dbSNP
rs1245289757	2410	dbSNP
rs538980897	2410	dbSNP
rs112925688	2418	dbSNP
rs1358904094	2422	dbSNP
rs192340597	2433	dbSNP
rs1415419364	2435	dbSNP
rs542464897	2438	dbSNP
rs1171183246	2441	dbSNP
rs902227337	2442	dbSNP
rs1424942556	2443	dbSNP
rs1190069906	2444	dbSNP
rs1193804155	2448	dbSNP
rs1478488834	2449	dbSNP
rs1443659516	2451	dbSNP
rs187764976	2453	dbSNP
rs1417363401	2456	dbSNP
rs1214547219	2458	dbSNP
rs1442636297	2460	dbSNP
rs561440802	2461	dbSNP
rs549172789	2465	dbSNP
rs1380795834	2482	dbSNP
rs1226600610	2483	dbSNP
rs1322780667	2483	dbSNP
rs1057401825	2484	dbSNP
rs1220572344	2485	dbSNP
rs1237051444	2486	dbSNP
rs930433916	2505	dbSNP
rs1338452415	2508	dbSNP
rs937553111	2509	dbSNP
rs1449119838	2515	dbSNP
rs927279541	2517	dbSNP
rs1361101583	2519	dbSNP
rs1239690879	2522	dbSNP
rs1332665056	2523	dbSNP
rs1037668742	2524	dbSNP
rs530742485	2531	dbSNP
rs1478980441	2536	dbSNP
rs1405040850	2540	dbSNP
rs1466006102	2541	dbSNP
rs1401690386	2544	dbSNP
rs1402743961	2546	dbSNP
rs942032249	2547	dbSNP
rs1306433703	2548	dbSNP
rs1332135873	2549	dbSNP
rs1236045098	2552	dbSNP
rs1281976458	2553	dbSNP
rs370170325	2557	dbSNP
rs1466735668	2563	dbSNP
rs907990091	2564	dbSNP
rs1259525808	2568	dbSNP
rs575119166	2570	dbSNP
rs545304390	2571	dbSNP
rs1194689126	2574	dbSNP
rs141622290	2578	dbSNP
rs182783239	2579	dbSNP
rs1460670913	2585	dbSNP
rs1428581168	2587	dbSNP
rs921693094	2594	dbSNP
rs762316770	2615	dbSNP
rs771659810	2615	dbSNP
rs974350581	2615	dbSNP
rs965701063	2617	dbSNP
rs192159207	2628	dbSNP
rs1031975853	2629	dbSNP
rs957082273	2635	dbSNP

- Nature, 2009

MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets-Ago-miRNA and Ago-mRNA binding sites-that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.

- Cell, 2013

The induction of pluripotency or trans-differentiation of one cell type to another can be accomplished with cell-lineage-specific transcription factors. Here, we report that repression of a single RNA binding polypyrimidine-tract-binding (PTB) protein, which occurs during normal brain development via the action of miR-124, is sufficient to induce trans-differentiation of fibroblasts into functional neurons. Besides its traditional role in regulated splicing, we show that PTB has a previously undocumented function in the regulation of microRNA functions, suppressing or enhancing microRNA targeting by competitive binding on target mRNA or altering local RNA secondary structure. A key event during neuronal induction is the relief of PTB-mediated blockage of microRNA action on multiple components of the REST complex, thereby derepressing a large array of neuronal genes, including miR-124 and multiple neuronal-specific transcription factors, in nonneuronal cells. This converts a negative feedback loop to a positive one to elicit cellular reprogramming to the neuronal lineage.

- 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.

- Nucleic acids research, 2016

MicroRNAs (miRs) have emerged as key biological effectors in human health and disease. These small noncoding RNAs are incorporated into Argonaute (Ago) proteins, where they direct post-transcriptional gene silencing via base-pairing with target transcripts. Although miRs have become intriguing biological entities and attractive therapeutic targets, the translational impacts of miR research remain limited by a paucity of empirical miR targeting data, particularly in human primary tissues. Here, to improve our understanding of the diverse roles miRs play in cardiovascular function and disease, we applied high-throughput methods to globally profile miR:target interactions in human heart tissues. We deciphered Ago2:RNA interactions using crosslinking immunoprecipitation coupled with high-throughput sequencing (HITS-CLIP) to generate the first transcriptome-wide map of miR targeting events in human myocardium, detecting 4000 cardiac Ago2 binding sites across >2200 target transcripts. Our initial exploration of this interactome revealed an abundance of miR target sites in gene coding regions, including several sites pointing to new miR-29 functions in regulating cardiomyocyte calcium, growth and metabolism. Also, we uncovered several clinically-relevant interactions involving common genetic variants that alter miR targeting events in cardiomyopathy-associated genes. Overall, these data provide a critical resource for bolstering translational miR research in heart, and likely beyond.