>FAM9C|NM_174901|3'UTR
   1 GCCACCACACGAGCAATTCACAAAGCTGCAGCAAGAGTTGGCACTTATTCAGATGTATCTTCAACCTCTGTTATTCTGGT
  81 GACTGACAAAAGAACTTGAACCTATGTTATATGATACATGCATAACTTGAGCTACACTAAACCACATGACAGTGTTTAGT
 161 TAATTCTTGTATAAATTAGTATATCTCTTCTATTATTAGTCTGTTTGTTAAATGCCAGACCACGTTTCTATGATCTGTTG
 241 AATGAACCCTAGACAGTTCTGTGAGAAAGCAGCAATTGCACAGTTACATACACAGTCAATTAAATTTTAACATTAAAGAT
 321 AATTTAGTTTTAGGTTTGGCCTCTGTGGATCTGTATCAGTTCCAAAATGTGGAAAGCACGGGCATGGAAAAGTACATTTT
 401 TCTCTAATAAAAGAAGACAAACCCTTA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gggUGGACG-AGUCAGGCUcg 5' |:|||: |||||:| | Target 5' tggATCTGTATCAGTTCCAaa 3'	346 - 366	101.00	-12.36
2	miRNA 3' ggGUGGACG--AGUCAGGCucg 5' | :|| : |:||||:| Target 5' ctCTTCTATTATTAGTCTGttt 3'	185 - 206	96.00	-11.52
3	miRNA 3' ggguGGACGAGUCAGG---CUCg 5' ||| ||||:| ||| Target 5' gaacCCTAGACAGTTCTGTGAGa 3'	244 - 266	92.00	-11.50

Mutant ID	Mutant Position	Mutant Source
rs762995508	9	dbSNP
rs148153694	10	dbSNP
rs1003205845	11	dbSNP
rs751451837	11	dbSNP
rs760534023	14	dbSNP
rs1317318839	16	dbSNP
rs1387158123	17	dbSNP
rs1391650428	21	dbSNP
rs775440350	40	dbSNP
rs771785770	44	dbSNP
rs759266746	51	dbSNP
rs190602980	52	dbSNP
rs1196924127	55	dbSNP
rs1042313797	58	dbSNP
rs945214845	59	dbSNP
rs766875592	70	dbSNP
rs753667930	71	dbSNP
rs1233058723	73	dbSNP
rs915097659	84	dbSNP
rs1348882323	90	dbSNP
rs1227995396	92	dbSNP
rs1310936840	96	dbSNP
rs754045711	97	dbSNP
rs765989061	103	dbSNP
rs1210308107	109	dbSNP
rs373476193	112	dbSNP
rs773921059	113	dbSNP
rs1328691936	115	dbSNP
rs112861168	116	dbSNP
rs1471432694	135	dbSNP
rs1157911806	143	dbSNP
rs147116056	150	dbSNP
rs1459171970	167	dbSNP
rs954725835	172	dbSNP
rs761231144	188	dbSNP
rs56835940	191	dbSNP
rs769064255	203	dbSNP
rs1336300877	210	dbSNP
rs1346773624	211	dbSNP
rs749623406	230	dbSNP
rs1289244101	247	dbSNP
rs1352496502	253	dbSNP
rs1230006908	257	dbSNP
rs1254020565	268	dbSNP
rs1344293312	272	dbSNP
rs1200938518	277	dbSNP
rs776037265	296	dbSNP
rs1418449178	297	dbSNP
rs1379703269	299	dbSNP
rs1176925404	310	dbSNP
rs963568013	319	dbSNP
rs1016393992	329	dbSNP
rs1244028774	337	dbSNP
rs1473368847	343	dbSNP
rs1197273300	346	dbSNP
rs1377405731	348	dbSNP
rs1467040131	356	dbSNP
rs1174861203	375	dbSNP
rs770128047	376	dbSNP
rs761998991	380	dbSNP
rs746159867	388	dbSNP
rs1429199870	395	dbSNP
rs1046064544	396	dbSNP
rs1344102174	406	dbSNP
rs1308641441	425	dbSNP
rs1372713966	431	dbSNP
rs945156477	432	dbSNP
rs781570912	438	dbSNP
rs1298981086	450	dbSNP
rs1330263233	454	dbSNP
rs147783530	464	dbSNP
rs1276564750	476	dbSNP
rs144283393	517	dbSNP
rs768882069	524	dbSNP
rs1274717645	534	dbSNP
rs760891814	556	dbSNP
rs1217048924	559	dbSNP
rs1207667842	562	dbSNP
rs1266178994	567	dbSNP
rs747216640	572	dbSNP
rs1003646551	573	dbSNP
rs1201389169	575	dbSNP
rs1388862519	586	dbSNP
rs1449388480	596	dbSNP
rs1353702342	598	dbSNP
rs556859923	607	dbSNP
rs1306438987	613	dbSNP
rs1247593124	632	dbSNP
rs1456616849	634	dbSNP
rs1293187955	646	dbSNP
rs1391660671	649	dbSNP
rs1387147335	660	dbSNP
rs906178700	672	dbSNP
rs1363019479	673	dbSNP
rs1227551302	679	dbSNP
rs1297748134	681	dbSNP
rs754916480	690	dbSNP
rs1042054546	695	dbSNP
rs1264508485	698	dbSNP
rs771857653	699	dbSNP
rs1488564498	708	dbSNP
rs1009501328	709	dbSNP
rs1464880287	710	dbSNP
rs1189735975	711	dbSNP
rs893695829	713	dbSNP
rs1392522518	714	dbSNP
rs745803799	720	dbSNP
rs753611800	725	dbSNP
rs1054032384	728	dbSNP
rs774817201	736	dbSNP
rs943214260	738	dbSNP
rs1459631745	761	dbSNP
rs1166896909	765	dbSNP
rs910661891	767	dbSNP
rs1426670864	770	dbSNP
rs1434039204	785	dbSNP
rs1051845296	786	dbSNP
rs1363919630	797	dbSNP
rs183128283	819	dbSNP
rs1385975341	824	dbSNP
rs1187045546	855	dbSNP
rs1422287679	863	dbSNP
rs933348482	886	dbSNP
rs1264293349	890	dbSNP
rs1311382779	899	dbSNP
rs1322008176	903	dbSNP
rs1234724449	904	dbSNP
rs919271745	907	dbSNP
rs1328938314	908	dbSNP
rs1209693393	926	dbSNP
rs778881482	935	dbSNP
rs1482522647	940	dbSNP
rs1181418901	944	dbSNP
rs756700614	951	dbSNP
rs750008159	978	dbSNP
rs1488236543	981	dbSNP
rs748869267	982	dbSNP
rs1284551862	987	dbSNP
rs972003670	1013	dbSNP
rs1456520180	1023	dbSNP
rs1159542969	1024	dbSNP
rs963599698	1035	dbSNP
rs1225404396	1041	dbSNP
rs909462844	1043	dbSNP
rs767087331	1047	dbSNP
rs191030302	1051	dbSNP
rs958886940	1052	dbSNP
rs1286091397	1053	dbSNP
rs751061675	1069	dbSNP
rs1349429459	1078	dbSNP
rs1242081175	1102	dbSNP
rs1286769956	1110	dbSNP
rs185793447	1117	dbSNP
rs1209998611	1119	dbSNP
rs1257063339	1124	dbSNP
rs1486708431	1126	dbSNP
rs1180031689	1129	dbSNP
rs1251368079	1145	dbSNP
rs1182704477	1148	dbSNP
rs1327905786	1148	dbSNP
rs1033868968	1168	dbSNP
rs1431407538	1173	dbSNP
rs1399224459	1189	dbSNP
rs1359619061	1211	dbSNP
rs5934063	1219	dbSNP
rs1003310734	1222	dbSNP
rs763427628	1239	dbSNP
rs1304836829	1242	dbSNP
rs1410036177	1243	dbSNP
rs1405507292	1245	dbSNP
rs1391469408	1264	dbSNP
rs1218962213	1286	dbSNP
rs869227564	1297	dbSNP
rs1302604611	1306	dbSNP
rs970438492	1322	dbSNP
rs538412391	1323	dbSNP
rs1483532566	1325	dbSNP
rs869132265	1331	dbSNP
rs869073103	1332	dbSNP
rs777183120	1337	dbSNP
rs1375049534	1342	dbSNP
rs770218139	1346	dbSNP
rs1190351004	1380	dbSNP
rs1477675731	1383	dbSNP
rs1455527467	1389	dbSNP
rs913635738	1415	dbSNP
rs113820865	1420	dbSNP
rs5979792	1421	dbSNP
rs1330505862	1451	dbSNP
rs149918802	1468	dbSNP
rs893769422	1474	dbSNP
rs1373906447	1481	dbSNP
rs1266055531	1483	dbSNP
rs1207616016	1489	dbSNP
rs1343003126	1493	dbSNP
rs747083307	1500	dbSNP
rs777768982	1512	dbSNP
rs1032252869	1522	dbSNP
rs1186632562	1523	dbSNP
rs1220638246	1523	dbSNP
rs1366506824	1523	dbSNP
rs1007835149	1524	dbSNP
rs1475466247	1526	dbSNP
rs888937141	1527	dbSNP
rs1411268517	1543	dbSNP
rs1284972914	1545	dbSNP
rs1052010414	1553	dbSNP
rs1165992997	1559	dbSNP
rs1397100589	1562	dbSNP
rs933414049	1566	dbSNP
rs897874336	1576	dbSNP
rs1366478562	1578	dbSNP
rs374082072	1583	dbSNP
rs1330509124	1584	dbSNP
rs1355981962	1593	dbSNP
rs1229075915	1595	dbSNP
rs1275243001	1600	dbSNP
rs1322946753	1619	dbSNP
rs1385198279	1627	dbSNP
rs1206530837	1629	dbSNP
rs1398764571	1635	dbSNP
rs1332236403	1637	dbSNP
rs1447509772	1638	dbSNP
rs942027774	1639	dbSNP
rs1235222702	1642	dbSNP
rs1472283231	1643	dbSNP
rs869298271	1647	dbSNP
rs1465308767	1648	dbSNP
rs1421848245	1680	dbSNP
rs1419507279	1686	dbSNP
rs1455985897	1687	dbSNP
rs1158799501	1688	dbSNP
rs909481335	1693	dbSNP
rs749287352	1713	dbSNP
rs1402936613	1729	dbSNP
rs766843043	1730	dbSNP
rs1339981845	1733	dbSNP
rs1448793446	1742	dbSNP
rs1295366456	1744	dbSNP
rs758887935	1747	dbSNP
rs937563982	1758	dbSNP
rs779969249	1767	dbSNP
rs1267245913	1781	dbSNP
rs1377608476	1788	dbSNP
rs1351374463	1805	dbSNP
rs1196094359	1816	dbSNP
rs1276366755	1829	dbSNP
rs1439004445	1853	dbSNP
rs1210904273	1854	dbSNP
rs750940575	1862	dbSNP
rs1186891434	1865	dbSNP
rs1471400973	1874	dbSNP
rs928833483	1880	dbSNP
rs1364713418	1897	dbSNP
rs1471340042	1898	dbSNP
rs981575840	1900	dbSNP
rs755844120	1902	dbSNP
rs750239331	1913	dbSNP
rs765809660	1924	dbSNP
rs1435428143	1958	dbSNP
rs970470992	1970	dbSNP
rs1020717033	1995	dbSNP
rs1409417293	2002	dbSNP
rs780856542	2028	dbSNP
rs1287537041	2061	dbSNP
rs1336158856	2072	dbSNP
rs1240857336	2076	dbSNP
rs987839843	2084	dbSNP
rs957715255	2095	dbSNP
rs1032698714	2106	dbSNP
rs1007494831	2129	dbSNP
rs1344176573	2176	dbSNP
rs1272958332	2178	dbSNP
rs1241123880	2197	dbSNP
rs1337549240	2201	dbSNP
rs1203957366	2222	dbSNP
rs1310080489	2226	dbSNP
rs1446323691	2227	dbSNP
rs888996393	2237	dbSNP
rs1439936410	2244	dbSNP
rs1197123776	2255	dbSNP
rs1377623029	2261	dbSNP
rs1030166735	2264	dbSNP
rs1455077751	2288	dbSNP
rs1175661325	2296	dbSNP
rs997301803	2310	dbSNP
rs1339082034	2329	dbSNP
rs1429143725	2342	dbSNP
rs553441218	2346	dbSNP
rs181716091	2350	dbSNP
rs897948169	2356	dbSNP
rs1392920444	2360	dbSNP
rs1036389716	2372	dbSNP
rs1370230837	2377	dbSNP
rs1234903474	2389	dbSNP
rs9887220	2391	dbSNP
rs369487131	2392	dbSNP
rs776723570	2396	dbSNP
rs1171288585	2409	dbSNP
rs146754113	2429	dbSNP
rs1380306994	2432	dbSNP
rs942058540	2436	dbSNP
rs887801260	2438	dbSNP
rs762558130	2444	dbSNP
rs1196092150	2445	dbSNP
rs1246672342	2448	dbSNP
rs1437410740	2452	dbSNP
rs1056169834	2454	dbSNP
rs1210422019	2456	dbSNP
rs1441581651	2489	dbSNP
rs1171140013	2499	dbSNP
rs1276258957	2508	dbSNP
rs1456570973	2509	dbSNP
rs1206749863	2519	dbSNP
rs937617491	2547	dbSNP
rs1393415335	2558	dbSNP
rs1259873701	2572	dbSNP
rs1310066717	2577	dbSNP
rs764093276	2584	dbSNP
rs928842451	2589	dbSNP
rs1374919899	2594	dbSNP
rs1295658271	2621	dbSNP
rs1317380439	2628	dbSNP
rs1242127866	2634	dbSNP
rs1272106302	2648	dbSNP
rs1335947181	2665	dbSNP
rs1215880247	2667	dbSNP
rs753198428	2672	dbSNP
rs981648001	2676	dbSNP
rs1464835048	2682	dbSNP
rs191898203	2689	dbSNP
rs1187243564	2700	dbSNP
rs1263918089	2711	dbSNP
rs1422324829	2748	dbSNP
rs1187143887	2750	dbSNP
rs1461774577	2756	dbSNP
rs1340185777	2761	dbSNP
rs946191703	2776	dbSNP
rs1402949691	2779	dbSNP
rs1452946035	2783	dbSNP
rs913682051	2806	dbSNP
rs1361791065	2809	dbSNP
rs759943181	2810	dbSNP
rs1363495953	2816	dbSNP
rs1157494671	2820	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.