>FAM180B|NM_001164379|3'UTR
   1 CCCTCCTCTTTTGTTCTTTCACCTGCCATTACCCCCTCCCATCTCCTCCTCAACCCCCCAGGCAGACCCATCTTGCGCAG
  81 GGGCTTCTGTCTGGCATCTGATTCTTTTCACCGTGTTCAGATCTCTGGGCTTGGCTTGCACCCTGGACACCCCCTCTCTG
 161 CTTACCCCGACCAGATCTTGTTTCCTAGATCTTGAGAGGCTAAGAACCCAGGCTCTGGGTCGCAAGGAGTGCGCAAGGAG
 241 TGGGCACAGAGCTAAGGGCACGACTTGCAGGCAGTGTGTGTGTGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
 321 TGGAGATCAGGGGTCAGGGTTGAGAAGTGTGTTCAAGAGATGCTGAAGGGAAGCTGCCCCAAGTAAGGCCTGGTCAGACC
 401 TTCCAACTCCTACCCTGGCAGTCTGTGACAGGTCCTGTGGAATTCACAGGAATCCTCTAGGTGCTGAGCATCCCCTTTTA
 481 GGCACAACCAAGGATTTGGGGTCTCTGAGCCTCCAAGTTCCCATCTGGGTTGGGAGAATCGACTTTTTGAGTTCTGTCAG
 561 TTGGAAGAGTGGAGGGAAGCAGGGGGAGGGAGGAACATTATCTCTTTTGGGGTAGGGAGGCAATATCTCAACAAGCGTCG
 641 GGTGAATACCTCAGAGGGGGGAGTAAGGCTGGGAGACCAAGGAGAGACAAGCGGAGGTGGGCTGGAGCAGGTGTGGCCCT
 721 GATTCTGTGTTGCTCTTCTCATAAAATGTTCTGTTTCGGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ucgUCCUCCCGACC-CGUCCGc 5' ||| ||||||| |||||: Target 5' cggAGGTGGGCTGGAGCAGGTg 3'	692 - 713	134.00	-33.80
2	miRNA 3' ucguccuCCCGACCCGUCCGc 5' ||| | || |||| Target 5' ctcttttGGGGTAGGGAGGCa 3'	602 - 622	122.00	-16.30
3	miRNA 3' ucguccucccgaccCGUCCGc 5' |||||| Target 5' taagggcacgacttGCAGGCa 3'	253 - 273	120.00	-14.70

Mutant ID	Mutant Position	Mutant Source
COSN7010122	49	COSMIC
COSN20065415	77	COSMIC
COSN20108216	287	COSMIC
COSN20108219	287	COSMIC
COSN30232339	287	COSMIC
COSN17951614	288	COSMIC
COSN18713974	290	COSMIC
COSN32056478	292	COSMIC
COSN20576698	458	COSMIC
COSN28374102	537	COSMIC
COSN18825616	759	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs750581813	1	dbSNP
rs758541290	3	dbSNP
rs1185358246	7	dbSNP
rs780097648	14	dbSNP
rs747530612	17	dbSNP
rs769089560	20	dbSNP
rs1462024629	21	dbSNP
rs190163835	22	dbSNP
rs1044996590	23	dbSNP
rs1193594500	25	dbSNP
rs1393723781	28	dbSNP
rs1407539629	31	dbSNP
rs1327174552	33	dbSNP
rs1370646449	34	dbSNP
rs983649565	36	dbSNP
rs1450531499	41	dbSNP
rs748591083	48	dbSNP
rs115468467	49	dbSNP
rs1360269825	54	dbSNP
rs939593251	55	dbSNP
rs906319887	56	dbSNP
rs190264387	58	dbSNP
rs916247462	59	dbSNP
rs1046789280	60	dbSNP
rs1399358091	77	dbSNP
rs569599780	78	dbSNP
rs1299932034	81	dbSNP
rs1434447374	82	dbSNP
rs1349369925	83	dbSNP
rs1165828001	84	dbSNP
rs577497965	86	dbSNP
rs1417821965	90	dbSNP
rs1228984857	92	dbSNP
rs1170364604	93	dbSNP
rs1040199	95	dbSNP
rs1322808938	97	dbSNP
rs1266037168	100	dbSNP
rs1204217280	109	dbSNP
rs750889226	110	dbSNP
rs963762220	112	dbSNP
rs78369932	113	dbSNP
rs1255942046	114	dbSNP
rs1029920002	117	dbSNP
rs1262699989	124	dbSNP
rs1318294733	129	dbSNP
rs1280096901	130	dbSNP
rs955726952	134	dbSNP
rs1367017598	136	dbSNP
rs977621529	139	dbSNP
rs1197432975	141	dbSNP
rs568370353	142	dbSNP
rs935137591	146	dbSNP
rs1466506452	154	dbSNP
rs924677795	154	dbSNP
rs957466586	155	dbSNP
rs1050885978	159	dbSNP
rs1423892811	169	dbSNP
rs1191217298	170	dbSNP
rs891006582	185	dbSNP
rs1236018992	189	dbSNP
rs1197618079	194	dbSNP
rs1458095459	199	dbSNP
rs1179177499	200	dbSNP
rs990245192	211	dbSNP
rs1006752041	219	dbSNP
rs375632808	221	dbSNP
rs1221063953	223	dbSNP
rs1289751242	226	dbSNP
rs1385244649	229	dbSNP
rs1374723108	231	dbSNP
rs1401450368	233	dbSNP
rs1018183880	234	dbSNP
rs181919228	244	dbSNP
rs1402911939	246	dbSNP
rs994876180	249	dbSNP
rs1301419715	250	dbSNP
rs571206210	251	dbSNP
rs1360297007	262	dbSNP
rs948750541	263	dbSNP
rs1045385045	264	dbSNP
rs927934654	266	dbSNP
rs1224101396	267	dbSNP
rs1439857148	269	dbSNP
rs1179854121	271	dbSNP
rs1028124423	272	dbSNP
rs1212147763	273	dbSNP
rs1262706844	273	dbSNP
rs1157490316	274	dbSNP
rs1305168575	274	dbSNP
rs1310816741	274	dbSNP
rs1358084282	274	dbSNP
rs1379331772	274	dbSNP
rs1380339477	274	dbSNP
rs1395847072	274	dbSNP
rs1418350522	274	dbSNP
rs1485191300	274	dbSNP
rs1365234732	276	dbSNP
rs1419954832	276	dbSNP
rs1285147198	278	dbSNP
rs1162223424	280	dbSNP
rs1189987425	280	dbSNP
rs1423098459	280	dbSNP
rs1262595543	282	dbSNP
rs1314986019	282	dbSNP
rs1487243973	282	dbSNP
rs1355904250	283	dbSNP
rs146171408	284	dbSNP
rs1491526721	284	dbSNP
rs950833799	284	dbSNP
rs1340403655	285	dbSNP
rs1491301143	285	dbSNP
rs1171312320	286	dbSNP
rs1198197186	286	dbSNP
rs1255171520	286	dbSNP
rs1327462202	286	dbSNP
rs1376029767	286	dbSNP
rs1391062859	286	dbSNP
rs1433826554	286	dbSNP
rs1475520890	286	dbSNP
rs1476315193	286	dbSNP
rs1491556576	286	dbSNP
rs149775746	286	dbSNP
rs61895146	286	dbSNP
rs878985138	286	dbSNP
rs1408570233	287	dbSNP
rs55944090	287	dbSNP
rs5020951	288	dbSNP
rs1198110446	290	dbSNP
rs201828486	290	dbSNP
rs149663299	292	dbSNP
rs144968047	294	dbSNP
rs865995743	296	dbSNP
rs1331171728	297	dbSNP
rs979140747	298	dbSNP
rs923645148	300	dbSNP
rs1046902441	302	dbSNP
rs935101971	304	dbSNP
rs1050833039	306	dbSNP
rs750031466	308	dbSNP
rs1365908258	310	dbSNP
rs1396955529	310	dbSNP
rs1421183128	312	dbSNP
rs1177019102	314	dbSNP
rs58699057	321	dbSNP
rs1439271025	322	dbSNP
rs1491040466	322	dbSNP
rs1491248813	322	dbSNP
rs3029432	323	dbSNP
rs942561315	324	dbSNP
rs1201510612	325	dbSNP
rs1278614542	325	dbSNP
rs1405031973	328	dbSNP
rs1294714652	329	dbSNP
rs553897661	330	dbSNP
rs1237551858	333	dbSNP
rs1039582463	334	dbSNP
rs1375636799	336	dbSNP
rs576919525	338	dbSNP
rs995221467	341	dbSNP
rs1309506462	352	dbSNP
rs1444168598	353	dbSNP
rs1371166407	354	dbSNP
rs1338482201	358	dbSNP
rs1005231020	369	dbSNP
rs1223141519	371	dbSNP
rs1396478558	376	dbSNP
rs1049068202	379	dbSNP
rs1377360489	384	dbSNP
rs1156875963	390	dbSNP
rs1419145569	402	dbSNP
rs1381195462	413	dbSNP
rs185671635	421	dbSNP
rs1355553219	422	dbSNP
rs1004968456	425	dbSNP
rs755385757	437	dbSNP
rs1030320125	438	dbSNP
rs891407998	440	dbSNP
rs999007718	448	dbSNP
rs1291354472	455	dbSNP
rs1352299021	470	dbSNP
rs1031813523	473	dbSNP
rs1490556521	476	dbSNP
rs1354012426	483	dbSNP
rs1035126460	486	dbSNP
rs1224838003	488	dbSNP
rs1233844706	490	dbSNP
rs112897173	497	dbSNP
rs569963671	498	dbSNP
rs1480630344	499	dbSNP
rs1178250377	502	dbSNP
rs1410683589	503	dbSNP
rs1296234239	507	dbSNP
rs1012436488	511	dbSNP
rs1399548663	518	dbSNP
rs1443194070	519	dbSNP
rs1320545789	526	dbSNP
rs1023088644	528	dbSNP
rs1163260606	533	dbSNP
rs1384237503	534	dbSNP
rs190548237	541	dbSNP
rs544195926	552	dbSNP
rs535798165	555	dbSNP
rs968332919	557	dbSNP
rs1193575516	559	dbSNP
rs979472678	568	dbSNP
rs923621365	575	dbSNP
rs373959666	581	dbSNP
rs140366535	584	dbSNP
rs529662476	586	dbSNP
rs1032263499	587	dbSNP
rs912340411	588	dbSNP
rs1038085614	595	dbSNP
rs374178389	603	dbSNP
rs1362751591	605	dbSNP
rs1271959631	608	dbSNP
rs1434606664	619	dbSNP
rs1039529600	624	dbSNP
rs932296968	625	dbSNP
rs150041758	626	dbSNP
rs1398546138	628	dbSNP
rs1170610006	632	dbSNP
rs1478397211	635	dbSNP
rs1419652126	637	dbSNP
rs931238726	640	dbSNP
rs879150424	641	dbSNP
rs890806027	644	dbSNP
rs999073272	656	dbSNP
rs1255840310	658	dbSNP
rs537039219	658	dbSNP
rs532223600	659	dbSNP
rs1235135160	662	dbSNP
rs1307953145	668	dbSNP
rs1460326030	669	dbSNP
rs1217587649	671	dbSNP
rs1011785943	674	dbSNP
rs552273111	676	dbSNP
rs1023456124	679	dbSNP
rs1183425551	690	dbSNP
rs1443305578	692	dbSNP
rs1244125836	694	dbSNP
rs1444906461	697	dbSNP
rs1331052957	709	dbSNP
rs753675502	716	dbSNP
rs1462965722	719	dbSNP
rs970189349	720	dbSNP
rs1174568123	721	dbSNP
rs981949804	743	dbSNP
rs1423786371	744	dbSNP
rs1035665979	747	dbSNP
rs950728849	748	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.

- 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.