>MTFMT|NM_139242|3'UTR
   1 TTAGGAAGAAGATGGATAAAAACCTATTACATATTTGTAATTTATTAAAAACCTTATTTACAAGGAATTATCTGGACTTT
  81 TTTTTTTTTTTTTTTTTTTGAGACAGAGTCTCACTCTGTCACCCAGGCTGGAATCCAGTGGCACTATCTCAGCTCACTGC
 161 AACCTCCGCCTCCCAGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCACACGCCACCACAC
 241 GCAGCTAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGTCAGGCTGGTCTCGAACTCCTGACCTTGTGAT
 321 CTGCCCACCTCAGCCTCCCAAAGTGCTATGATTACAGACGTGAGCCACCGTGCCTGGCCTGGAATTATCTGGACTTTCAA
 401 AGAAGATGGCATTATTATAAGAAGAGAAGATTATTGCCGAAAAGATGGATTGCCTCACTTTCCACTTTTTATGTAACAGT
 481 AGTTAAAAAACAGCTTTTTTTTTACTTGAATTACAAAAAAGTTTAAATAAAACTTGTATTTATGATACGAAACTCAAGGA
 561 GATTATCTTTCCTTAAGAACAAGGGCAACCCTAACTGGTGTATGTATGTACCTACATACATACTGAGAAGAGGTTTTTTG
 641 TTTTTATTTTTATTTTTTTGAGACGGAGTCTTGTTCTGTGGCCCAGGCTGGAGTGCAGTGGCGTGATGTCAGCTCACTGC
 721 AAGCTCCACCTCCCGGGTTCACACCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCGTCCGCCACCATGC
 801 CTGGCTAATTTTTTTTTTTGTATTTTTAGTAGAGATGGGGTTTCACTGTGTTAGCCAGGATGGTCTTGATCTCCTGACCT
 881 CGTGATCCACCCGCCTTGGCCTCCCAAAGTGCTGGGATTACAGCTGTGAGCCACCGTGCCTGGCCGAGAAGAGGTTTTTT
 961 TAAAAACAGTGCATCTATTTAATTTTTTAAAAATCGTGTCACCACTGACATTTTAGGAGTATTGAATCTGCATTTTTTAT
1041 TTCCTATAAGTAGTAAATCCAGCTCTTTACATTTCACTACCAGCTAGATTTAACCAAGTAGTAAACGTAGGTAATATTTA
1121 ATAATCTCTGCCACATTGATCTGTACTATAAATTAACATTTTACATCCAGATTTTATTTTTTTTTATTAATTTTTTTAGA
1201 GATGGGGTCTTGCTCTCTCACACAGTCTGGAGTCCAGTGGCGTGAAACACTGCTTACTGCATCTTCAACCTCCTGGGCTT
1281 AAGTGATCCTCCAGCCTCAGCCTCCCAAAGTGGGGCCACCACGCCTGGCTAATTTTCTTTCTTAGTTTTTAAAAAAAATT
1361 TTGTAGAGATAGGGGTCTCACTATGTTGCTTAGGCTGGTCTTGAACTCCTGGGCCCAAGCAATCCTCCTGCCTTGGCCTC
1441 TCAAAGTGCTGGGATTACAAGCATGAACCACTGCACCCGGCCCAGGTTTTCTTGAAGTAGGAACGTGCTAACATTTTTCA
1521 ACTTACTTGTGCAATAAAGGTTATTGAGCAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ccuguAAC--AAAGUCACGGGUUCa 5' ||| | | | ||||||| Target 5' tggtcTTGAACTCCTGGGCCCAAGc 3'	1396 - 1420	148.00	-12.30
2	miRNA 3' ccuguAACAAAGUCA-CGGGUUCa 5' ||| ||| || |||||:| Target 5' gagtcTTG-TTCTGTGGCCCAGGc 3'	666 - 688	145.00	-14.50
3	miRNA 3' ccuGUAACAAAGUCACGGGUUCa 5' || || | | |||||:| Target 5' aacCACTGCACCCG-GCCCAGGt 3'	1466 - 1487	131.00	-12.20

Mutant ID	Mutant Position	Mutant Source
1178547	100	ClinVar
1205642	100	ClinVar
COSN32053347	18	COSMIC
COSN26679042	23	COSMIC
COSN30477451	24	COSMIC
COSN20078325	61	COSMIC
COSN20401592	72	COSMIC
COSN19589963	299	COSMIC
COSN20268796	388	COSMIC
COSN28834444	652	COSMIC
COSN22817914	954	COSMIC
COSN8749420	1058	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1173356817	2	dbSNP
rs765532671	3	dbSNP
rs1431066309	5	dbSNP
rs374370833	11	dbSNP
rs886558021	13	dbSNP
rs1047806508	14	dbSNP
rs775056172	18	dbSNP
rs771725066	24	dbSNP
rs745563259	31	dbSNP
rs773906080	32	dbSNP
rs1275473169	33	dbSNP
rs577476593	37	dbSNP
rs770398802	40	dbSNP
rs559032718	41	dbSNP
rs1159362504	42	dbSNP
rs777603471	47	dbSNP
rs755906213	50	dbSNP
rs142950216	51	dbSNP
rs1217358610	56	dbSNP
rs943246021	57	dbSNP
rs186819833	62	dbSNP
rs1318776287	65	dbSNP
rs878903632	76	dbSNP
rs1265492016	77	dbSNP
rs987742398	82	dbSNP
rs77916904	96	dbSNP
rs966565604	98	dbSNP
rs71136309	99	dbSNP
rs1157750360	100	dbSNP
rs1171293152	100	dbSNP
rs1202042160	100	dbSNP
rs1269972389	100	dbSNP
rs1409590046	100	dbSNP
rs1477999574	100	dbSNP
rs1487550738	100	dbSNP
rs1491509627	100	dbSNP
rs398027674	100	dbSNP
rs758544219	100	dbSNP
rs866953579	100	dbSNP
rs1171484107	101	dbSNP
rs1344595658	101	dbSNP
rs1375688879	101	dbSNP
rs1434269358	101	dbSNP
rs1224400313	107	dbSNP
rs1285309285	122	dbSNP
rs183933238	124	dbSNP
rs1351798543	125	dbSNP
rs1021144671	126	dbSNP
rs989230468	127	dbSNP
rs1292995040	130	dbSNP
rs1451360220	132	dbSNP
rs1197447468	133	dbSNP
rs1235099925	135	dbSNP
rs1316303987	145	dbSNP
rs957712438	151	dbSNP
rs1377898684	156	dbSNP
rs1022684495	166	dbSNP
rs1033283961	166	dbSNP
rs1001743972	167	dbSNP
rs1389804169	168	dbSNP
rs1403374707	172	dbSNP
rs553880992	175	dbSNP
rs1335303941	180	dbSNP
rs1024553073	186	dbSNP
rs1013098922	192	dbSNP
rs1374708093	194	dbSNP
rs1248491376	209	dbSNP
rs565851717	212	dbSNP
rs552214398	215	dbSNP
rs886591568	219	dbSNP
rs761886409	222	dbSNP
rs1208436803	227	dbSNP
rs1035329807	229	dbSNP
rs776492692	230	dbSNP
rs1345126953	231	dbSNP
rs532408550	235	dbSNP
rs1407569282	240	dbSNP
rs1039015627	241	dbSNP
rs1471565529	246	dbSNP
rs568126075	268	dbSNP
rs1465067178	269	dbSNP
rs1329184426	278	dbSNP
rs1398260945	279	dbSNP
rs1043187101	287	dbSNP
rs2414866	288	dbSNP
rs1340110463	289	dbSNP
rs1242824192	290	dbSNP
rs62015300	293	dbSNP
rs766525648	296	dbSNP
rs763151119	297	dbSNP
rs771948745	301	dbSNP
rs570724028	302	dbSNP
rs191345701	303	dbSNP
rs188166671	304	dbSNP
rs183239178	310	dbSNP
rs1254788251	316	dbSNP
rs1440357517	319	dbSNP
rs1223768699	325	dbSNP
rs929189760	327	dbSNP
rs919205187	328	dbSNP
rs1272338989	332	dbSNP
rs1477359188	333	dbSNP
rs548249262	338	dbSNP
rs1231179052	348	dbSNP
rs1319558236	349	dbSNP
rs989207959	357	dbSNP
rs530149858	359	dbSNP
rs957745085	360	dbSNP
rs973741730	365	dbSNP
rs141657757	369	dbSNP
rs1359335730	370	dbSNP
rs1294742309	372	dbSNP
rs980439574	377	dbSNP
rs114841970	388	dbSNP
rs532635290	391	dbSNP
rs1395795445	407	dbSNP
rs991222877	409	dbSNP
rs544577358	415	dbSNP
rs1460143080	426	dbSNP
rs1035318385	431	dbSNP
rs16948459	432	dbSNP
rs886621538	439	dbSNP
rs1171467597	445	dbSNP
rs1487721134	446	dbSNP
rs1191254627	469	dbSNP
rs1270716667	472	dbSNP
rs1026461672	485	dbSNP
rs1480743379	491	dbSNP
rs11635570	497	dbSNP
rs1377190685	498	dbSNP
rs1464600199	499	dbSNP
rs1417513048	503	dbSNP
rs1021800700	504	dbSNP
rs1296756764	515	dbSNP
rs1012258652	521	dbSNP
rs1387898989	523	dbSNP
rs1301157875	532	dbSNP
rs899280502	538	dbSNP
rs1252222469	539	dbSNP
rs192921877	548	dbSNP
rs553817852	549	dbSNP
rs891254784	553	dbSNP
rs1251667113	556	dbSNP
rs1293728493	559	dbSNP
rs1047082403	568	dbSNP
rs929932797	569	dbSNP
rs919943794	570	dbSNP
rs1265182141	573	dbSNP
rs1420729046	575	dbSNP
rs188475186	578	dbSNP
rs1305378251	580	dbSNP
rs1052129083	582	dbSNP
rs796075728	587	dbSNP
rs945288295	588	dbSNP
rs1157048299	589	dbSNP
rs1367903950	590	dbSNP
rs1372367787	594	dbSNP
rs915739702	615	dbSNP
rs1389223785	635	dbSNP
rs913727013	644	dbSNP
rs959766326	647	dbSNP
rs1375484602	661	dbSNP
rs574477349	663	dbSNP
rs777496365	665	dbSNP
rs928413816	665	dbSNP
rs773370665	667	dbSNP
rs377199628	672	dbSNP
rs1243799219	673	dbSNP
rs1299074802	686	dbSNP
rs966992275	695	dbSNP
rs936501249	702	dbSNP
rs926415157	703	dbSNP
rs28488304	713	dbSNP
rs538036086	714	dbSNP
rs1177066721	717	dbSNP
rs1387307077	721	dbSNP
rs570590193	730	dbSNP
rs558408692	732	dbSNP
rs950959851	734	dbSNP
rs1026495421	737	dbSNP
rs1018442180	740	dbSNP
rs1398995150	741	dbSNP
rs995041342	746	dbSNP
rs963518611	751	dbSNP
rs1441430938	756	dbSNP
rs1227334676	758	dbSNP
rs1310345866	759	dbSNP
rs1251035611	761	dbSNP
rs1176361958	764	dbSNP
rs1219224127	770	dbSNP
rs1479472838	773	dbSNP
rs199801306	776	dbSNP
rs371615102	776	dbSNP
rs1017729264	777	dbSNP
rs1047156839	780	dbSNP
rs149468965	783	dbSNP
rs1483720380	786	dbSNP
rs566497543	787	dbSNP
rs1051729230	788	dbSNP
rs1430653933	789	dbSNP
rs12440520	790	dbSNP
rs920614110	791	dbSNP
rs530093992	798	dbSNP
rs1464466441	799	dbSNP
rs892417531	799	dbSNP
rs1391110798	802	dbSNP
rs569323101	809	dbSNP
rs1277261706	820	dbSNP
rs1363882478	820	dbSNP
rs1400375747	820	dbSNP
rs1315074060	822	dbSNP
rs936533801	824	dbSNP
rs926445949	827	dbSNP
rs1225226567	831	dbSNP
rs1374966521	835	dbSNP
rs550828233	836	dbSNP
rs532715418	837	dbSNP
rs1209755737	839	dbSNP
rs111305656	840	dbSNP
rs1194867709	841	dbSNP
rs973665704	847	dbSNP
rs982437910	848	dbSNP
rs1425317277	852	dbSNP
rs951115054	853	dbSNP
rs919531008	854	dbSNP
rs973637071	855	dbSNP
rs1346598719	864	dbSNP
rs1419867308	867	dbSNP
rs1297391246	871	dbSNP
rs914234696	874	dbSNP
rs1188301354	876	dbSNP
rs540894148	879	dbSNP
rs1254845396	881	dbSNP
rs1017761726	882	dbSNP
rs964309466	886	dbSNP
rs1218109806	889	dbSNP
rs986622452	892	dbSNP
rs943628618	893	dbSNP
rs954782666	897	dbSNP
rs766605793	898	dbSNP
rs1018913711	900	dbSNP
rs1315571944	902	dbSNP
rs1295465902	903	dbSNP
rs1009610316	907	dbSNP
rs1188964482	909	dbSNP
rs1355003163	910	dbSNP
rs955487254	920	dbSNP
rs1025826418	921	dbSNP
rs1358453236	924	dbSNP
rs150377487	935	dbSNP
rs1032250549	936	dbSNP
rs758823062	946	dbSNP
rs905054162	949	dbSNP
rs1044839240	954	dbSNP
rs750545100	971	dbSNP
rs560143110	972	dbSNP
rs541841888	983	dbSNP
rs1308782207	988	dbSNP
rs574392366	989	dbSNP
rs1474691157	995	dbSNP
rs141305164	996	dbSNP
rs1194706628	998	dbSNP
rs1451557148	998	dbSNP
rs929684795	1003	dbSNP
rs1239517984	1006	dbSNP
rs895159769	1007	dbSNP
rs1177698555	1009	dbSNP
rs1447131212	1010	dbSNP
rs1378106498	1016	dbSNP
rs1260423551	1017	dbSNP
rs369734044	1021	dbSNP
rs72744620	1024	dbSNP
rs1403570116	1039	dbSNP
rs1412746489	1039	dbSNP
rs576941321	1065	dbSNP
rs938602530	1068	dbSNP
rs907009786	1069	dbSNP
rs1447602291	1070	dbSNP
rs1330680852	1071	dbSNP
rs973668248	1075	dbSNP
rs1450407460	1080	dbSNP
rs183355881	1085	dbSNP
rs1285198865	1088	dbSNP
rs1041566363	1094	dbSNP
rs1356065091	1094	dbSNP
rs1260548134	1101	dbSNP
rs1319134288	1103	dbSNP
rs762080296	1106	dbSNP
rs914330106	1107	dbSNP
rs1234239838	1109	dbSNP
rs776000797	1110	dbSNP
rs776687467	1123	dbSNP
rs989819124	1125	dbSNP
rs1172811315	1142	dbSNP
rs942337728	1145	dbSNP
rs1170088709	1153	dbSNP
rs1291605572	1157	dbSNP
rs1416429937	1157	dbSNP
rs1335089237	1158	dbSNP
rs1340317833	1159	dbSNP
rs72744618	1165	dbSNP
rs1280431100	1177	dbSNP
rs1341706981	1182	dbSNP
rs987018334	1185	dbSNP
rs1255646936	1186	dbSNP
rs955644762	1186	dbSNP
rs1200731797	1189	dbSNP
rs955042504	1190	dbSNP
rs1030440104	1191	dbSNP
rs1025816700	1196	dbSNP
rs1195592218	1198	dbSNP
rs972922991	1198	dbSNP
rs1380510298	1199	dbSNP
rs1263569882	1200	dbSNP
rs988619945	1212	dbSNP
rs956720057	1226	dbSNP
rs1326374478	1230	dbSNP
rs1371466811	1239	dbSNP
rs577079143	1241	dbSNP
rs910700113	1242	dbSNP
rs1012348048	1244	dbSNP
rs895098422	1247	dbSNP
rs905086834	1249	dbSNP
rs1169351950	1250	dbSNP
rs1332489231	1256	dbSNP
rs1475518545	1261	dbSNP
rs1034990101	1265	dbSNP
rs1294037336	1268	dbSNP
rs1023968388	1270	dbSNP
rs1233342313	1280	dbSNP
rs1273671129	1288	dbSNP
rs190753004	1291	dbSNP
rs1218288790	1299	dbSNP
rs1041513225	1303	dbSNP
rs775515300	1313	dbSNP
rs896293884	1314	dbSNP
rs892988917	1319	dbSNP
rs1054574301	1322	dbSNP
rs114847210	1323	dbSNP
rs1452857780	1325	dbSNP
rs1197819159	1328	dbSNP
rs1340296414	1335	dbSNP
rs373879412	1336	dbSNP
rs10431803	1341	dbSNP
rs569183625	1343	dbSNP
rs1287412766	1344	dbSNP
rs551022218	1346	dbSNP
rs1387804802	1349	dbSNP
rs28729192	1350	dbSNP
rs942335529	1351	dbSNP
rs972995185	1353	dbSNP
rs376949022	1358	dbSNP
rs1236633449	1359	dbSNP
rs910845574	1359	dbSNP
rs963178260	1359	dbSNP
rs986769538	1361	dbSNP
rs991276238	1363	dbSNP
rs933533126	1365	dbSNP
rs1209136968	1370	dbSNP
rs1266830960	1371	dbSNP
rs923406514	1373	dbSNP
rs988262396	1374	dbSNP
rs1239021968	1376	dbSNP
rs1440071930	1380	dbSNP
rs956750731	1381	dbSNP
rs571828899	1384	dbSNP
rs1458900429	1399	dbSNP
rs971275464	1400	dbSNP
rs979438778	1405	dbSNP
rs1331362962	1406	dbSNP
rs969360323	1410	dbSNP
rs1375723645	1412	dbSNP
rs145919286	1415	dbSNP
rs1314662043	1419	dbSNP
rs1322082125	1422	dbSNP
rs1165654702	1424	dbSNP
rs892926660	1427	dbSNP
rs1054330534	1430	dbSNP
rs775459547	1430	dbSNP
rs1238814537	1434	dbSNP
rs1480446848	1435	dbSNP
rs528741096	1442	dbSNP
rs1424755481	1443	dbSNP
rs1454195828	1446	dbSNP
rs960588810	1446	dbSNP
rs1025858384	1449	dbSNP
rs186190644	1452	dbSNP
rs898282136	1462	dbSNP
rs1438643578	1470	dbSNP
rs1038122712	1471	dbSNP
rs1272480938	1472	dbSNP
rs76791673	1478	dbSNP
rs142153649	1479	dbSNP
rs1350226528	1483	dbSNP
rs1379699586	1484	dbSNP
rs747434934	1499	dbSNP
rs562367036	1504	dbSNP
rs371517118	1505	dbSNP
rs889437901	1508	dbSNP
rs1050713792	1511	dbSNP
rs1219119367	1512	dbSNP
rs544263668	1522	dbSNP
rs923467781	1533	dbSNP
rs576877489	1534	dbSNP
rs1053000371	1537	dbSNP
rs935495696	1540	dbSNP
rs16948457	1549	dbSNP

- Cell, 2010

RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.

- Nature methods, 2011

Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.

- Nature, 2013

Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.

- 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.