>AP3B1|NM_003664|3'UTR
   1 CCTGCTTACATCTGGACTTTAGAATCTGGCACACAACAAAAGTGCCTGGCATCCACTACTGCTGCCTTTCATTTATAATA
  81 ATAGCCCTTCCATCTGGCAGTGGGGGTAGAATACACTCTTGACATTCTTGTCTCCTGCTTTAGAATGCTAGTGTGTATCT
 161 ATCATGTATGCAATACTTTCCCCCTTTTTGCTTTGCTAACCAAAGAGCATATATTTTACTGTCAGTTGTCTCAACTCTTG
 241 AATCCATGTGGCGTTTTCTCTGTCCTGCTGCTTCTTTTGGCCTCCTCGTTTTCCTTCTCTTTTTCGACAATGGTAGACAT
 321 GAATGAGATATTTAAAGTTCATTGGAAATCTTCTTCCCTACAGCAGTAAGCAAAAATTAGCAAAGAGATAGTCTAAATGG
 401 CCTCTCAGCTTGGTATGTGAAAATGAGATCACATACTTTTTAAATCCAAATACAAAAGCATAGTCTCTGCAAGATTTTGT
 481 TCTTTGAATTTCTTGATATTGTAATTGATTATTGATAACTGTCATCATGAAATTATCTCTCAATAATAAGATAAATAAAC
 561 TAGCATATGAATCATAAAAAAAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ugGAAGAUCAAAAGUCUCAGcg 5' | |||:| ||:||| || Target 5' taCATCTGGACTTTAGAATCtg 3'	7 - 28	116.00	-9.80
2	miRNA 3' ugGAAGAUCAAAA------G--UCUCagcg 5' |||:| | ||| | |||| Target 5' ccCTTTTTGCTTTGCTAACCAAAGAGcata 3'	182 - 211	92.00	-8.00
3	miRNA 3' ugGAAGAUCAAAAGUCUCAGCg 5' | |||:| | :|:|| | Target 5' tcCATCTGGCAGTGGGGGTAGa 3'	89 - 110	92.00	-11.50

Mutant ID	Mutant Position	Mutant Source
1207984	41	ClinVar
906459	44	ClinVar
354219	70	ClinVar
354218	101	ClinVar
354217	107	ClinVar
354216	141	ClinVar
906458	191	ClinVar
354215	379	ClinVar
904843	380	ClinVar
904844	380	ClinVar
354214	447	ClinVar
904842	482	ClinVar
354213	507	ClinVar
354212	560	ClinVar
COSN31586346	12	COSMIC
COSN14179940	20	COSMIC
COSN26548293	26	COSMIC
COSN26554009	37	COSMIC
COSN17153502	41	COSMIC
COSN30455483	54	COSMIC
COSN31492258	57	COSMIC
COSN30457382	91	COSMIC
COSN14792393	107	COSMIC
COSN26565373	123	COSMIC
COSN31604053	132	COSMIC
COSN30132927	141	COSMIC
COSN30460943	180	COSMIC
COSN31504564	190	COSMIC
COSN31516201	287	COSMIC
COSN31595757	318	COSMIC
COSN31549929	399	COSMIC
COSN24777144	447	COSMIC
COSN31543978	560	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1021165592	1	dbSNP
rs755752427	2	dbSNP
rs1277325815	7	dbSNP
rs942517218	8	dbSNP
rs199521659	10	dbSNP
rs1390030764	14	dbSNP
rs1162592102	15	dbSNP
rs1398426452	19	dbSNP
rs1369968306	20	dbSNP
rs1009638675	24	dbSNP
rs200456538	27	dbSNP
rs780915786	28	dbSNP
rs375163910	29	dbSNP
rs763841787	36	dbSNP
rs1466601526	38	dbSNP
rs1423406222	39	dbSNP
rs112214336	41	dbSNP
rs182487478	44	dbSNP
rs1206790418	46	dbSNP
rs1268972846	47	dbSNP
rs765141824	49	dbSNP
rs760757738	51	dbSNP
rs1486440499	53	dbSNP
rs941977192	55	dbSNP
rs1213669190	59	dbSNP
rs1349978530	64	dbSNP
rs886060769	70	dbSNP
rs1286218825	78	dbSNP
rs1329847042	86	dbSNP
rs918624052	92	dbSNP
rs766029582	101	dbSNP
rs1469676030	102	dbSNP
rs1199071824	103	dbSNP
rs929044217	105	dbSNP
rs11552314	107	dbSNP
rs1159865656	116	dbSNP
rs1414822950	118	dbSNP
rs540703378	120	dbSNP
rs1332981670	123	dbSNP
rs570942210	130	dbSNP
rs1311668066	135	dbSNP
rs753283084	141	dbSNP
rs992209236	145	dbSNP
rs1324423823	147	dbSNP
rs1214978590	151	dbSNP
rs1335436050	157	dbSNP
rs1440106437	161	dbSNP
rs1281402252	166	dbSNP
rs959070738	167	dbSNP
rs1329947807	170	dbSNP
rs926831596	172	dbSNP
rs1287028640	179	dbSNP
rs190285646	182	dbSNP
rs369987939	183	dbSNP
rs1327396462	184	dbSNP
rs1210257683	185	dbSNP
rs6864605	191	dbSNP
rs1021123097	218	dbSNP
rs1348945440	229	dbSNP
rs1009753859	232	dbSNP
rs1164467388	239	dbSNP
rs1251829155	240	dbSNP
rs1474614632	246	dbSNP
rs544830395	248	dbSNP
rs970215199	251	dbSNP
rs868442378	252	dbSNP
rs867801817	253	dbSNP
rs1396023532	262	dbSNP
rs1408365912	264	dbSNP
rs1449453109	273	dbSNP
rs1405454504	279	dbSNP
rs899824806	281	dbSNP
rs1010683230	283	dbSNP
rs893452770	285	dbSNP
rs1038816649	287	dbSNP
rs575976353	288	dbSNP
rs1467281732	302	dbSNP
rs773135696	305	dbSNP
rs769645790	306	dbSNP
rs1265111406	316	dbSNP
rs1274932745	337	dbSNP
rs559226132	342	dbSNP
rs887724674	354	dbSNP
rs1309003047	355	dbSNP
rs901056728	356	dbSNP
rs1227553036	357	dbSNP
rs1040995881	361	dbSNP
rs1371655771	363	dbSNP
rs1304904590	366	dbSNP
rs115124715	379	dbSNP
rs911081557	380	dbSNP
rs1048945561	381	dbSNP
rs1056222654	385	dbSNP
rs937789738	386	dbSNP
rs1311202859	398	dbSNP
rs1404463183	401	dbSNP
rs1463262881	403	dbSNP
rs187770688	404	dbSNP
rs1804790	412	dbSNP
rs1294813663	413	dbSNP
rs554959862	415	dbSNP
rs931449825	417	dbSNP
rs926304522	418	dbSNP
rs1167116461	434	dbSNP
rs918581877	436	dbSNP
rs972670538	437	dbSNP
rs1230391887	440	dbSNP
rs960041888	441	dbSNP
rs886060768	447	dbSNP
rs1281768704	449	dbSNP
rs759104986	458	dbSNP
rs753338653	459	dbSNP
rs1445608580	460	dbSNP
rs928864823	466	dbSNP
rs1266818201	467	dbSNP
rs552733544	479	dbSNP
rs538570213	482	dbSNP
rs1172016011	485	dbSNP
rs970615539	499	dbSNP
rs1466640659	500	dbSNP
rs1288190526	505	dbSNP
rs865863660	507	dbSNP
rs1481772970	515	dbSNP
rs1436998194	519	dbSNP
rs1321043722	529	dbSNP
rs1011067836	532	dbSNP
rs1438175120	540	dbSNP
rs914176898	550	dbSNP
rs1204179254	552	dbSNP
rs957771030	557	dbSNP
rs1031175064	560	dbSNP
rs886060767	560	dbSNP
rs988271636	562	dbSNP
rs999162849	565	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.