ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gaCCCUUCCUCUC-------------UUCUCUUc 5' ||||:||| || ||||||| Target 5' gtGGGAGGGACAGGTTATGGTATTTAAAGAGAAt 3'	1297 - 1330	151.00	-19.81
2	miRNA 3' gacccuUCCUCUC------UUC-UCUUc 5' || |||| ||| |||| Target 5' gactatAGAAGAGCCAATTAAGTAGAAa 3'	409 - 436	117.00	-6.41
3	miRNA 3' gacccUUCCUCUCUUCUCUUc 5' || |||:|||| ||| Target 5' tttttAATGAGGGAAG-GAAg 3'	70 - 89	116.00	-15.00

Mutant ID	Mutant Position	Mutant Source
COSN30156086	8	COSMIC
COSN31564369	11	COSMIC
COSN5915434	23	COSMIC
COSN31557742	40	COSMIC
COSN31504494	45	COSMIC
COSN31493443	49	COSMIC
COSN30105083	80	COSMIC
COSN30522734	80	COSMIC
COSN30105775	89	COSMIC
COSN30544035	108	COSMIC
COSN16178739	124	COSMIC
COSN30167678	124	COSMIC
COSN30160362	197	COSMIC
COSN26134868	228	COSMIC
COSN8686105	229	COSMIC
COSN17181783	326	COSMIC
COSN27928776	462	COSMIC
COSN28201462	477	COSMIC
COSN8282138	780	COSMIC
COSN31582692	842	COSMIC
COSN15601696	867	COSMIC
COSN27662122	1250	COSMIC
COSN31513715	1277	COSMIC
COSN22717314	1281	COSMIC
COSN8584328	1321	COSMIC
COSN31533945	1336	COSMIC
COSN28693624	1476	COSMIC
COSN31522049	1576	COSMIC
COSN31606590	1619	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1382714021	2	dbSNP
rs774173882	5	dbSNP
rs770711296	11	dbSNP
rs749283314	17	dbSNP
rs1212563421	20	dbSNP
rs1157035149	22	dbSNP
rs377284623	25	dbSNP
rs116909879	26	dbSNP
rs117523528	30	dbSNP
rs376467001	35	dbSNP
rs751825278	38	dbSNP
rs372859616	39	dbSNP
rs892122132	41	dbSNP
rs1480906132	44	dbSNP
rs758775727	45	dbSNP
rs1285260761	46	dbSNP
rs1373259068	50	dbSNP
rs1052129604	62	dbSNP
rs1003855934	64	dbSNP
rs781631720	66	dbSNP
rs1269468782	77	dbSNP
rs1329328055	80	dbSNP
rs1202602392	94	dbSNP
rs936515315	114	dbSNP
rs1044896191	124	dbSNP
rs947871378	126	dbSNP
rs1443877508	129	dbSNP
rs920460642	130	dbSNP
rs923667956	138	dbSNP
rs1389934659	142	dbSNP
rs1184329112	151	dbSNP
rs1414270327	164	dbSNP
rs1472988724	176	dbSNP
rs115437866	187	dbSNP
rs1400374899	189	dbSNP
rs545618532	194	dbSNP
rs1335295306	197	dbSNP
rs575292282	200	dbSNP
rs1408536381	202	dbSNP
rs1290798254	205	dbSNP
rs1170203211	212	dbSNP
rs1350541304	216	dbSNP
rs990449307	220	dbSNP
rs180993721	223	dbSNP
rs144253532	229	dbSNP
rs143829068	236	dbSNP
rs922883117	240	dbSNP
rs975520870	247	dbSNP
rs995619773	250	dbSNP
rs1200684411	262	dbSNP
rs964170824	275	dbSNP
rs545200740	280	dbSNP
rs1207187439	281	dbSNP
rs1252480359	285	dbSNP
rs1265896196	289	dbSNP
rs1010592278	291	dbSNP
rs961550679	306	dbSNP
rs956509980	315	dbSNP
rs552818310	319	dbSNP
rs1376080606	322	dbSNP
rs1031055353	328	dbSNP
rs534897497	333	dbSNP
rs1389914625	334	dbSNP
rs1428274387	339	dbSNP
rs1003228696	340	dbSNP
rs1310336474	341	dbSNP
rs1371744966	355	dbSNP
rs1403715184	361	dbSNP
rs906403329	362	dbSNP
rs570792500	365	dbSNP
rs1044995600	368	dbSNP
rs138416286	369	dbSNP
rs562593820	371	dbSNP
rs1217605882	372	dbSNP
rs1233513981	383	dbSNP
rs1315736594	386	dbSNP
rs1339750182	390	dbSNP
rs1284891829	401	dbSNP
rs1230378696	414	dbSNP
rs891214382	416	dbSNP
rs1049746415	417	dbSNP
rs1208056515	421	dbSNP
rs1265357327	423	dbSNP
rs753289025	426	dbSNP
rs1453443304	430	dbSNP
rs1199827912	440	dbSNP
rs996882037	442	dbSNP
rs1170880066	445	dbSNP
rs1391263202	445	dbSNP
rs1457830784	447	dbSNP
rs1162044438	455	dbSNP
rs1053724423	457	dbSNP
rs1319425354	457	dbSNP
rs141433582	457	dbSNP
rs898981524	463	dbSNP
rs537195054	467	dbSNP
rs1298049958	473	dbSNP
rs941414982	474	dbSNP
rs1242482538	475	dbSNP
rs1042620413	476	dbSNP
rs1210539634	476	dbSNP
rs1267202518	476	dbSNP
rs370842131	476	dbSNP
rs796690726	476	dbSNP
rs1463720789	478	dbSNP
rs1190815861	479	dbSNP
rs1401096501	486	dbSNP
rs1330832121	487	dbSNP
rs908645070	494	dbSNP
rs1047469306	497	dbSNP
rs879249151	510	dbSNP
rs934017740	520	dbSNP
rs570120160	528	dbSNP
rs1464259667	531	dbSNP
rs1423635957	539	dbSNP
rs949123955	540	dbSNP
rs1431722700	543	dbSNP
rs917698458	547	dbSNP
rs1477917196	549	dbSNP
rs922636575	555	dbSNP
rs189042723	556	dbSNP
rs1376386924	557	dbSNP
rs990439408	562	dbSNP
rs1184558834	563	dbSNP
rs1458488691	595	dbSNP
rs1438946799	596	dbSNP
rs13891	604	dbSNP
rs1378148934	605	dbSNP
rs4040	613	dbSNP
rs1314724096	615	dbSNP
rs1340996316	622	dbSNP
rs1197529069	623	dbSNP
rs1245533821	635	dbSNP
rs1287790507	636	dbSNP
rs1327244366	640	dbSNP
rs1210788359	642	dbSNP
rs1269061782	648	dbSNP
rs1483106662	649	dbSNP
rs1199101079	652	dbSNP
rs920160093	652	dbSNP
rs1424891327	655	dbSNP
rs1182179657	664	dbSNP
rs530284712	665	dbSNP
rs566399617	668	dbSNP
rs1264646473	670	dbSNP
rs915395625	677	dbSNP
rs1227186436	682	dbSNP
rs1008849700	689	dbSNP
rs1409129451	692	dbSNP
rs746562160	695	dbSNP
rs955475215	698	dbSNP
rs989675523	700	dbSNP
rs1348681552	703	dbSNP
rs548141092	706	dbSNP
rs1230328899	707	dbSNP
rs1028852860	736	dbSNP
rs1311842735	743	dbSNP
rs956634476	748	dbSNP
rs1404320715	759	dbSNP
rs996829959	765	dbSNP
rs1258130657	769	dbSNP
rs1483808688	770	dbSNP
rs755401807	774	dbSNP
rs1250279752	781	dbSNP
rs893117931	783	dbSNP
rs1182271514	791	dbSNP
rs982151352	793	dbSNP
rs970416866	795	dbSNP
rs1023330973	805	dbSNP
rs1054472865	810	dbSNP
rs1330681113	812	dbSNP
rs185733905	816	dbSNP
rs753421082	818	dbSNP
rs11558183	822	dbSNP
rs1444672585	823	dbSNP
rs1306053943	827	dbSNP
rs1372336553	828	dbSNP
rs1408508175	832	dbSNP
rs1012158461	834	dbSNP
rs1298805733	843	dbSNP
rs1367080161	846	dbSNP
rs902430437	846	dbSNP
rs1303746966	863	dbSNP
rs779456875	863	dbSNP
rs1348992055	864	dbSNP
rs1228173413	896	dbSNP
rs1335138201	908	dbSNP
rs1042222039	931	dbSNP
rs1344949417	934	dbSNP
rs1205896601	953	dbSNP
rs949278777	955	dbSNP
rs563970485	956	dbSNP
rs1192549216	970	dbSNP
rs1054826156	971	dbSNP
rs1448603369	972	dbSNP
rs899096123	990	dbSNP
rs766032076	1002	dbSNP
rs1391847303	1003	dbSNP
rs1016083534	1007	dbSNP
rs1430326851	1016	dbSNP
rs193013565	1021	dbSNP
rs1349353185	1027	dbSNP
rs187539489	1034	dbSNP
rs1295469358	1037	dbSNP
rs530529358	1039	dbSNP
rs1047138504	1052	dbSNP
rs1177420090	1055	dbSNP
rs1437316158	1057	dbSNP
rs781303271	1063	dbSNP
rs563010829	1064	dbSNP
rs764199162	1069	dbSNP
rs557266130	1072	dbSNP
rs1289851393	1084	dbSNP
rs147057705	1085	dbSNP
rs1223167685	1088	dbSNP
rs1273364011	1092	dbSNP
rs141611264	1101	dbSNP
rs1464152381	1103	dbSNP
rs1186355613	1105	dbSNP
rs34188718	1110	dbSNP
rs1249632585	1112	dbSNP
rs559107656	1115	dbSNP
rs986972582	1121	dbSNP
rs772626017	1126	dbSNP
rs1403614051	1131	dbSNP
rs1206679230	1134	dbSNP
rs1028512588	1136	dbSNP
rs1347899059	1141	dbSNP
rs1456906594	1145	dbSNP
rs990015180	1148	dbSNP
rs957450078	1152	dbSNP
rs1237999694	1163	dbSNP
rs1431959542	1167	dbSNP
rs1284081202	1175	dbSNP
rs935520649	1178	dbSNP
rs17593836	1184	dbSNP
rs577063794	1191	dbSNP
rs577079347	1192	dbSNP
rs1021320780	1193	dbSNP
rs558684817	1197	dbSNP
rs1447327841	1209	dbSNP
rs1023278741	1212	dbSNP
rs1320612867	1224	dbSNP
rs774483588	1225	dbSNP
rs537413773	1226	dbSNP
rs963253173	1230	dbSNP
rs1418621089	1234	dbSNP
rs1157352970	1237	dbSNP
rs1427164891	1245	dbSNP
rs1415317617	1247	dbSNP
rs1016192696	1251	dbSNP
rs1157151807	1252	dbSNP
rs1182005124	1253	dbSNP
rs768571944	1254	dbSNP
rs1401580770	1262	dbSNP
rs1235396631	1265	dbSNP
rs1357856825	1267	dbSNP
rs576627939	1274	dbSNP
rs1314077884	1275	dbSNP
rs749102762	1277	dbSNP
rs1285091815	1278	dbSNP
rs367798159	1281	dbSNP
rs184291664	1282	dbSNP
rs1361570261	1293	dbSNP
rs1290672670	1294	dbSNP
rs566315602	1297	dbSNP
rs1227810917	1306	dbSNP
rs998266350	1307	dbSNP
rs901277361	1309	dbSNP
rs746009105	1327	dbSNP
rs1211475549	1335	dbSNP
rs138601568	1338	dbSNP
rs1251018623	1343	dbSNP
rs1037990937	1345	dbSNP
rs939709146	1351	dbSNP
rs1039654454	1353	dbSNP
rs942705423	1358	dbSNP
rs908772399	1374	dbSNP
rs1470632978	1393	dbSNP
rs1272180504	1400	dbSNP
rs1172254629	1410	dbSNP
rs1400889116	1414	dbSNP
rs1416542431	1415	dbSNP
rs987433251	1416	dbSNP
rs934272684	1421	dbSNP
rs1407395677	1429	dbSNP
rs921397897	1432	dbSNP
rs150128153	1433	dbSNP
rs1435265603	1434	dbSNP
rs1296799413	1450	dbSNP
rs1272765498	1453	dbSNP
rs957438724	1460	dbSNP
rs1054032911	1468	dbSNP
rs76478883	1476	dbSNP
rs977436910	1477	dbSNP
rs967806773	1478	dbSNP
rs924119546	1480	dbSNP
rs1411127151	1502	dbSNP
rs866906322	1510	dbSNP
rs1198367806	1511	dbSNP
rs1172333297	1513	dbSNP
rs1245236849	1525	dbSNP
rs1455808189	1529	dbSNP
rs1477971069	1531	dbSNP
rs1428373912	1550	dbSNP
rs754374036	1550	dbSNP
rs1047013832	1559	dbSNP
rs1396559905	1560	dbSNP
rs1404263406	1562	dbSNP
rs1321129119	1569	dbSNP
rs551901458	1570	dbSNP
rs1013894274	1577	dbSNP
rs1296578336	1580	dbSNP
rs1362818443	1583	dbSNP
rs916334404	1595	dbSNP
rs1191314000	1600	dbSNP
rs1340109730	1600	dbSNP
rs1209326524	1605	dbSNP
rs1489382734	1605	dbSNP
rs1469985553	1609	dbSNP
rs1247227303	1622	dbSNP
rs747072971	1626	dbSNP
rs1247760695	1633	dbSNP
rs1448093711	1635	dbSNP
rs777685274	1637	dbSNP
rs747159903	1640	dbSNP
rs963029009	1659	dbSNP
rs1160960878	1660	dbSNP
rs1472138950	1660	dbSNP
rs1396107677	1662	dbSNP
rs908907760	1673	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, 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.