>MRPS27|NM_015084|3'UTR
   1 TAGGGTCCCCCAGGGCCCCACCTGTCTCACAAGAACTTCACTCAACCCCGTGCCAGGACTCAGCAGTGGCCTGGACAACA
  81 GCCTCAGCTTCCTCTACCCATCTTCTTTTCTTAAAGCAGGCTATGTGCCCTACATGGCAAGGCACCATGACTGCCCATCG
 161 AGATGCCAAGAAGGGCTATGGAACTATGCAGGTGGCTAGTGGTCAGACTGAAGTCACCAGCTGAATACCTTAAGGAGGAC
 241 TCTTGAGGCTCATAATGGAGTTCCTGGGGCACAGGGATTAGTTATGAGCATTAAAGTTCCTAAGACCCAGTGACAGTACT
 321 GGGAGAAACCAAGGCTGAAGAGTCAGGTTGAAGCACAGGCTTTTGTTTTTTGTTGTTTTTGTTTTTTGAGACAGAGTCTC
 401 ATTCTGTCACCCAGGCTGGAGTGCAGTGGCGCAATCTTGGCTCACTGCAACCTCCGACTCCCAGGTTCAAGCAATTCTCC
 481 TGCCTCGGCCTCCTTTAGTAGGTGGGATTACAGGTGCATACCACCACACCTTTCTAATTTTTGCATTTTTAGTAGAGATG
 561 GGGTTTCACCATGTTGGTCAGGCTGGTCTCAACCTCCTGACCTCAAGTGATCTGCCCGCCTCAGCCTCCCAAAGTGCTGG
 641 GATGATAGGCGTGAGCCACCACACCCGGCCAAGCACAGGCTTTTGAATGGTCTCCCTCTCCCCAGCCCAGGTACATGAGG
 721 CCAAGGTGAACTGTGCATCCTGAGACCTTGTGTCCCTGAGTCTCCTTTCTGAGTGCAAGCTGCACTGTGAGCTGGCTGTG
 801 GGATACTCACACATTCCCACATTCTCCTTTCTGCCACATCTCGCCCTTCTGGACCTGCACTGGGAGAAATTCAGGACAGG
 881 AGTGAACTCAAGGCCATGAACTCACTGGATTTCCATTTTTAGGCACCCATAGGGATGTTTTTAGGATGTAAGTTTCTGAG
 961 GAGAAAGCTAGCTCTAGCATGAAGCTTTTTTGGATTGGCTTCTCCATCGTGTTGGGGTAACATTTTTTTTCCAATTTTTT
1041 TTTTCCCAAAACATCGTCTCAGCTCATTTATCAAGTAGGTAAAATGAGCCTTTTGTGTACACACAGAGGCACATGTGCAT
1121 GCACACACAACTTGTGAACACACATTTCTGTTAAAGAAGTTAGAAAATGAGAGATGGGTTGGGGCTTGAAGTGCATCAGA
1201 GGTATGAATGTTGTAAAACTGTCAGGAGATGTAAAATTCCTTTCTGAAGTGTCTCTTCTGTGAAAGGGTTCAGAGCAGAT
1281 TTTGCTTACTATGTAGTGTTGCCCTTAAGTACAGTGGTGTAATTTTATTCAAGATTGTGCTCTTCTATCAAAAGCCTCTG
1361 GAAATAAATGTTCCGGGATCATGTTAGTGTACTCTTTATCTTTGGGGAAAGGGAGGAGGGAGAGGGACTCATTATTGTTA
1441 CTATGATTTTGAGGAGTGTACTTTAAACCCTCCCCCATTAAACTATGGGATTTATTGTAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gaucACCCAUUU-----CUCCCUCUc 5' |||| ||| |||||||| Target 5' tcttTGGGGAAAGGGAGGAGGGAGAg 3'	1399 - 1424	161.00	-25.20
2	miRNA 3' gaucacccauuucuCCCUCUc 5' |||||| Target 5' ccagtgacagtactGGGAGAa 3'	307 - 327	120.00	-11.69
3	miRNA 3' gaucacccauuucuCCCUCUc 5' |||||| Target 5' tctggacctgcactGGGAGAa 3'	848 - 868	120.00	-10.51

Mutant ID	Mutant Position	Mutant Source
COSN16359962	27	COSMIC
COSN31612989	45	COSMIC
COSN31588630	49	COSMIC
COSN14177514	50	COSMIC
COSN30134495	53	COSMIC
COSN31610153	65	COSMIC
COSN30454878	85	COSMIC
COSN30129259	105	COSMIC
COSN30486757	105	COSMIC
COSN31590862	121	COSMIC
COSN31510357	141	COSMIC
COSN31578876	154	COSMIC
COSN31603723	184	COSMIC
COSN30427137	539	COSMIC
COSN7952142	592	COSMIC
COSN4949042	617	COSMIC
COSN31561842	731	COSMIC
COSN17181615	884	COSMIC
COSN30544090	985	COSMIC
COSN31567601	1041	COSMIC
COSN17694239	1043	COSMIC
COSN20464699	1120	COSMIC
COSN27627793	1431	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1445518902	4	dbSNP
rs1360746397	9	dbSNP
rs377574757	10	dbSNP
rs771804261	13	dbSNP
rs1265899854	15	dbSNP
rs747835918	16	dbSNP
rs778503131	20	dbSNP
rs1299150156	21	dbSNP
rs558107345	24	dbSNP
rs182626416	28	dbSNP
rs776454105	30	dbSNP
rs372769656	34	dbSNP
rs1342676138	35	dbSNP
rs961848042	38	dbSNP
rs1392092616	39	dbSNP
rs369855570	49	dbSNP
rs750230896	50	dbSNP
rs780985970	51	dbSNP
rs1190800520	56	dbSNP
rs977020025	78	dbSNP
rs1005671104	86	dbSNP
rs1198826440	92	dbSNP
rs1021539259	100	dbSNP
rs986476896	101	dbSNP
rs970138396	103	dbSNP
rs1159633688	105	dbSNP
rs1022992342	116	dbSNP
rs1014221938	119	dbSNP
rs548545760	121	dbSNP
rs536863553	134	dbSNP
rs569318409	136	dbSNP
rs1387259516	137	dbSNP
rs1300581017	141	dbSNP
rs551280322	147	dbSNP
rs962088374	151	dbSNP
rs1286487609	157	dbSNP
rs191523104	159	dbSNP
rs1015052796	160	dbSNP
rs1293282386	162	dbSNP
rs1488549097	163	dbSNP
rs1223621888	165	dbSNP
rs1006224462	168	dbSNP
rs887804039	169	dbSNP
rs1291756475	171	dbSNP
rs1045310333	172	dbSNP
rs1438032607	175	dbSNP
rs1165763886	176	dbSNP
rs1012882540	178	dbSNP
rs904429398	181	dbSNP
rs1388412786	185	dbSNP
rs1448930428	214	dbSNP
rs1309661198	225	dbSNP
rs1345631557	235	dbSNP
rs1237477231	240	dbSNP
rs763687059	240	dbSNP
rs1316783736	245	dbSNP
rs1042936120	247	dbSNP
rs1455787522	251	dbSNP
rs1321954553	252	dbSNP
rs1431746685	260	dbSNP
rs896750607	263	dbSNP
rs746949454	264	dbSNP
rs1481884845	266	dbSNP
rs574134776	274	dbSNP
rs1177192307	295	dbSNP
rs1185655034	296	dbSNP
rs1051484775	302	dbSNP
rs1041485492	306	dbSNP
rs1480171683	309	dbSNP
rs1162706025	316	dbSNP
rs1427782801	321	dbSNP
rs1467090750	325	dbSNP
rs779918131	329	dbSNP
rs1332013726	345	dbSNP
rs1399257258	357	dbSNP
rs932990990	359	dbSNP
rs547009956	367	dbSNP
rs1475941869	372	dbSNP
rs947035118	372	dbSNP
rs973404377	375	dbSNP
rs1309924443	378	dbSNP
rs188823529	380	dbSNP
rs985832551	386	dbSNP
rs1258060943	389	dbSNP
rs183867422	391	dbSNP
rs1205904293	392	dbSNP
rs112660977	393	dbSNP
rs984281980	398	dbSNP
rs529912272	405	dbSNP
rs1023021852	414	dbSNP
rs992831547	426	dbSNP
rs562513090	430	dbSNP
rs772211158	431	dbSNP
rs1015000424	433	dbSNP
rs1006340639	434	dbSNP
rs952178856	441	dbSNP
rs1359569015	444	dbSNP
rs765287456	449	dbSNP
rs999260423	455	dbSNP
rs904465063	456	dbSNP
rs1021541100	463	dbSNP
rs1316539564	463	dbSNP
rs544125755	464	dbSNP
rs1056749990	470	dbSNP
rs888928167	474	dbSNP
rs192100834	477	dbSNP
rs1469341528	486	dbSNP
rs111927288	487	dbSNP
rs1192980766	490	dbSNP
rs539839520	492	dbSNP
rs572703533	496	dbSNP
rs902711865	498	dbSNP
rs527718844	501	dbSNP
rs554664934	503	dbSNP
rs933052039	510	dbSNP
rs1425587565	511	dbSNP
rs1419457173	516	dbSNP
rs1413762181	521	dbSNP
rs1041435567	525	dbSNP
rs947108678	529	dbSNP
rs1297000872	534	dbSNP
rs1337831780	536	dbSNP
rs58705052	548	dbSNP
rs779226631	551	dbSNP
rs1036050395	563	dbSNP
rs1367342498	571	dbSNP
rs1050481695	577	dbSNP
rs1183883520	578	dbSNP
rs11557160	580	dbSNP
rs186475423	582	dbSNP
rs1354632320	585	dbSNP
rs1253683182	601	dbSNP
rs910147853	610	dbSNP
rs984314380	617	dbSNP
rs557572766	618	dbSNP
rs1223663737	625	dbSNP
rs923179905	627	dbSNP
rs757582601	628	dbSNP
rs916043390	635	dbSNP
rs992947642	644	dbSNP
rs1384791942	649	dbSNP
rs140796602	650	dbSNP
rs1032156203	651	dbSNP
rs561925517	657	dbSNP
rs984638794	666	dbSNP
rs1323651667	667	dbSNP
rs1349751932	671	dbSNP
rs1434985951	672	dbSNP
rs1377267590	677	dbSNP
rs1299917633	679	dbSNP
rs547265217	682	dbSNP
rs969097258	687	dbSNP
rs1378175817	690	dbSNP
rs528492949	700	dbSNP
rs1307427826	701	dbSNP
rs1358738126	704	dbSNP
rs1228900926	705	dbSNP
rs1462593417	706	dbSNP
rs567521581	707	dbSNP
rs991218724	709	dbSNP
rs1239753656	710	dbSNP
rs146465993	714	dbSNP
rs778187785	715	dbSNP
rs1167318275	716	dbSNP
rs1378029020	719	dbSNP
rs756503021	724	dbSNP
rs548509511	726	dbSNP
rs1163292181	729	dbSNP
rs1412495247	740	dbSNP
rs1404071732	748	dbSNP
rs1334017444	760	dbSNP
rs999761913	770	dbSNP
rs1386323096	781	dbSNP
rs1446418101	783	dbSNP
rs180748336	784	dbSNP
rs1022381319	787	dbSNP
rs1283647264	789	dbSNP
rs997758286	797	dbSNP
rs1011038855	798	dbSNP
rs1231367658	800	dbSNP
rs562739163	801	dbSNP
rs1318521472	802	dbSNP
rs753182621	803	dbSNP
rs1443758238	805	dbSNP
rs1178400253	810	dbSNP
rs1187875767	812	dbSNP
rs1480699287	816	dbSNP
rs1005903937	825	dbSNP
rs1172194189	836	dbSNP
rs887401805	838	dbSNP
rs189944939	842	dbSNP
rs757858128	843	dbSNP
rs1232216280	845	dbSNP
rs532320029	846	dbSNP
rs1404856889	849	dbSNP
rs1203016099	855	dbSNP
rs1361505149	864	dbSNP
rs949005467	871	dbSNP
rs564839376	872	dbSNP
rs1040079125	879	dbSNP
rs540103206	883	dbSNP
rs916159681	884	dbSNP
rs907794577	894	dbSNP
rs535383972	901	dbSNP
rs1320104291	902	dbSNP
rs1277393031	906	dbSNP
rs867498695	914	dbSNP
rs1484491553	917	dbSNP
rs749969349	928	dbSNP
rs572818472	932	dbSNP
rs1477765353	934	dbSNP
rs1191734238	944	dbSNP
rs775250314	945	dbSNP
rs554244903	954	dbSNP
rs1466938404	962	dbSNP
rs960976786	971	dbSNP
rs1373806466	972	dbSNP
rs764770125	974	dbSNP
rs1034955538	978	dbSNP
rs1360035648	982	dbSNP
rs1302881285	992	dbSNP
rs1293428387	1004	dbSNP
rs914542548	1009	dbSNP
rs1366328151	1012	dbSNP
rs542740233	1019	dbSNP
rs1274046860	1021	dbSNP
rs1022538056	1022	dbSNP
rs1218391800	1028	dbSNP
rs36017651	1031	dbSNP
rs1286088574	1032	dbSNP
rs1487711233	1043	dbSNP
rs185625826	1044	dbSNP
rs1011489926	1045	dbSNP
rs1434270145	1045	dbSNP
rs181562310	1053	dbSNP
rs953315658	1069	dbSNP
rs1198539632	1070	dbSNP
rs1393693004	1072	dbSNP
rs1441753475	1081	dbSNP
rs1030239492	1088	dbSNP
rs1159539552	1093	dbSNP
rs1359973759	1105	dbSNP
rs1410492295	1106	dbSNP
rs1295373153	1108	dbSNP
rs1392729022	1113	dbSNP
rs555682125	1119	dbSNP
rs6831	1120	dbSNP
rs537290431	1121	dbSNP
rs1241858299	1123	dbSNP
rs901614679	1124	dbSNP
rs1040021578	1129	dbSNP
rs1014679357	1134	dbSNP
rs1489070220	1139	dbSNP
rs1006347744	1146	dbSNP
rs1487413599	1156	dbSNP
rs774997311	1159	dbSNP
rs1179656728	1161	dbSNP
rs1240112513	1170	dbSNP
rs887518213	1171	dbSNP
rs1417577200	1183	dbSNP
rs1286471761	1195	dbSNP
rs776201027	1200	dbSNP
rs571826687	1202	dbSNP
rs1049045039	1231	dbSNP
rs765097515	1241	dbSNP
rs1303131244	1243	dbSNP
rs553721558	1247	dbSNP
rs546390340	1250	dbSNP
rs1392015454	1251	dbSNP
rs1385438074	1260	dbSNP
rs930453715	1267	dbSNP
rs916444860	1275	dbSNP
rs1389353111	1276	dbSNP
rs1387674206	1280	dbSNP
rs1321856540	1284	dbSNP
rs1244693308	1288	dbSNP
rs1271746380	1293	dbSNP
rs1320640564	1296	dbSNP
rs991073326	1298	dbSNP
rs939427682	1301	dbSNP
rs1479760186	1309	dbSNP
rs1183863242	1313	dbSNP
rs928060092	1314	dbSNP
rs978055746	1325	dbSNP
rs1162886715	1335	dbSNP
rs1011848352	1336	dbSNP
rs966722480	1343	dbSNP
rs894760524	1347	dbSNP
rs1353749618	1354	dbSNP
rs1460132722	1357	dbSNP
rs528265022	1358	dbSNP
rs1057498008	1359	dbSNP
rs915475909	1368	dbSNP
rs989778418	1370	dbSNP
rs1413566026	1372	dbSNP
rs1290925844	1375	dbSNP
rs954457813	1380	dbSNP
rs938883924	1386	dbSNP
rs1156270578	1387	dbSNP
rs1219823784	1388	dbSNP
rs534981293	1389	dbSNP
rs1306183575	1398	dbSNP
rs142879714	1398	dbSNP
rs189966083	1399	dbSNP
rs1198148140	1400	dbSNP
rs1256744603	1402	dbSNP
rs1483057303	1412	dbSNP
rs1041815268	1419	dbSNP
rs1431226055	1421	dbSNP
rs1263505557	1422	dbSNP
rs1185836433	1427	dbSNP
rs1205519203	1427	dbSNP
rs1464579828	1429	dbSNP
rs1265469189	1430	dbSNP
rs1478744742	1432	dbSNP
rs1194364970	1435	dbSNP
rs1418521657	1440	dbSNP
rs1266514581	1443	dbSNP
rs549094133	1444	dbSNP
rs1177980485	1453	dbSNP
rs1324434665	1458	dbSNP
rs1433744218	1475	dbSNP
rs1283194940	1482	dbSNP
rs537593858	1485	dbSNP
rs986154867	1486	dbSNP
rs1401124873	1488	dbSNP
rs1270200754	1497	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.

- mBio, 2013

UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.

- 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.